9GY4: 60S ribosomal subunit

60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map). Determined by electron microscopy at 3.0 Å resolution. Released 14 May 2025.

Method
Electron microscopy
Resolution
3.0 Å
Organism
Homo sapiens
Chains
55
Atoms
169,625
Mol. weight
3177.89 kDa
Ligands
MG, ZN
Released
14 May 2025

Explore 9GY4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GY4 contains 585 α-helices and 418 β-strands across 50 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain a: 9 helices, 18 β-strands

ElementResiduesLengthSheet
α-helix4-52
α-helix9-124
α-helix29-324
α-helix34-385
β-strand40-5011133
β-strand57-648133
β-strand71-777133
β-strand791134
β-strand831107
β-strand87-915133
β-strand101-1033133
α-helix1081
β-strand112-1143133
β-strand1161135
β-strand1261135
β-strand134-1407133
β-strand145-1495133
β-strand155-1595133
β-strand163-1664133
β-strand1691134
β-strand1711108
α-helix174-1763
α-helix178-1792
α-helix182-1909
β-strand224-2252136
α-helix229-2302
β-strand237-2382136
Chain B: 24 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix2-65
α-helix81
β-strand9118
α-helix16-183
α-helix31-4515
α-helix53-575
α-helix65-728
α-helix98-1047
α-helix112-1209
α-helix121-1255
α-helix126-16742
α-helix175-1817
α-helix182-1854
α-helix186-19914
α-helix202-21514
α-helix225-2328
β-strand237119
α-helix238-2425
α-helix337-3404
β-strand342119
α-helix347-37024
α-helix377-3826
α-helix388-3914
α-helix395-41319
α-helix415-42511
α-helix427-46640
α-helix469-49325
β-strand499118
Chain C: 7 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix119-19173
α-helix193-1953
β-strand197-202621
α-helix209-22517
β-strand228122
α-helix231-2388
α-helix242-25413
β-strand260-261222
β-strand269-270222
α-helix273-28614
β-strand288-290323
α-helix291-30111
Chain D: 2 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand3-10821
β-strand18-24721
β-strand28125
α-helix29-3911
β-strand48-50321
β-strand56121
β-strand62125
α-helix63-697
β-strand73-77521
Chain E: 35 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix31-4111
β-strand48-49223
β-strand55-57323
α-helix59-7214
β-strand77-78230
α-helix79-868
α-helix90-956
α-helix97-1037
β-strand107-110430
β-strand113-116430
α-helix117-13418
β-strand136-138331
α-helix139-1468
α-helix150-1589
β-strand161132
β-strand165132
β-strand168-169231
β-strand176-178331
α-helix180-19415
β-strand201-202233
α-helix203-2108
α-helix214-22714
β-strand233-235333
β-strand238134
β-strand243-245333
α-helix247-26418
β-strand266-268335
α-helix269-2746
α-helix280-2878
β-strand293-295335
β-strand299-302435
α-helix303-31816
β-strand322-324336
α-helix335-34612
α-helix347-3493
β-strand356136
β-strand362-364336
α-helix366-3749
α-helix377-3859
β-strand394-396337
α-helix486-4883
α-helix495-52127
β-strand525138
α-helix538-55821
α-helix563-57311
α-helix574-5785
α-helix579-59214
α-helix600-6023
α-helix605-61410
α-helix617-62913
α-helix636-64813
α-helix658-67821
α-helix682-69817
α-helix706-7083
α-helix709-7157
α-helix722-74423
α-helix756-78429
Chain F: 113 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix18-2811
α-helix42-443
α-helix64-718
α-helix77-9317
α-helix96-994
α-helix106-1138
α-helix119-13618
α-helix137-1437
α-helix144-15512
α-helix160-17314
α-helix178-1858
α-helix187-19812
α-helix203-2064
α-helix214-23825
α-helix241-2455
α-helix248-2547
α-helix258-2614
α-helix262-2654
α-helix270-28516
α-helix291-2933
α-helix294-3018
α-helix312-32615
α-helix330-3334
α-helix336-3405
α-helix341-35010
α-helix363-3686
α-helix372-3754
α-helix378-39417
α-helix396-4005
α-helix402-42221
α-helix427-4337
α-helix434-4385
α-helix439-4479
α-helix449-4524
α-helix456-47318
α-helix477-50226
α-helix509-52315
α-helix584-60825
α-helix611-62313
α-helix627-6315
α-helix658-6614
α-helix662-6665
α-helix667-6715
α-helix679-69113
α-helix695-70410
α-helix705-7095
α-helix712-7209
α-helix733-7364
α-helix739-75820
α-helix764-77815
β-strand781140
β-strand786140
α-helix790-80920
α-helix817-83317
α-helix841-85515
α-helix865-88420
α-helix888-8903
α-helix894-90815
α-helix914-93118
α-helix938-9458
α-helix951-9566
α-helix964-9663
α-helix967-9726
α-helix994-9952
α-helix996-101217
α-helix1020-103920
α-helix1045-105612
α-helix1061-10644
α-helix1065-10673
α-helix1070-108314
α-helix1087-109711
α-helix1103-11108
α-helix1123-11308
α-helix1136-11449
α-helix1147-11515
α-helix1155-11584
α-helix1161-11655
α-helix1166-117510
α-helix1183-119917
α-helix1215-123319
α-helix1242-126019
α-helix1268-127710
α-helix1281-129010
α-helix1293-12975
α-helix1301-13066
α-helix1307-13115
α-helix1312-132918
α-helix1338-13403
α-helix1343-13475
α-helix1348-13514
α-helix1355-13584
α-helix1377-138610
α-helix1388-13914
α-helix1395-140814
α-helix1409-14113
α-helix1412-14187
α-helix1421-14255
α-helix1436-145318
α-helix14571
α-helix1464-14652
α-helix1471-149020
α-helix1493-150614
α-helix1508-151912
β-strand1525141
α-helix1527-15293
α-helix1537-15393
β-strand1540141
α-helix1559-157416
α-helix1576-158510
α-helix1588-159710
α-helix1598-16025
α-helix1603-161513
β-strand1624142
β-strand1627-1629342
β-strand1634-1639642
β-strand1646-1651642
α-helix1660-16612
β-strand1662-1664342
α-helix1677-168812
α-helix1694-170916
α-helix1713-17153
β-strand1732-1733243
β-strand1740-1741243
α-helix1743-175311
β-strand1757144
β-strand1764144
Chain La: 7 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix3-53
α-helix7-115
α-helix42-487
β-strand72-74345
α-helix78-814
α-helix84-929
β-strand97-98296
β-strand100-102346
α-helix103-1064
β-strand110-112345
β-strand123-126446
β-strand128-129245
α-helix131-1399
β-strand143-146446
Chain Lb: 7 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix12-187
α-helix22-254
α-helix37-4812
α-helix49-535
α-helix54-7421
α-helix92-1009
α-helix106-11712

42 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
28S rRNA5RNA5070Homo sapiens
5S rRNA7RNA121Homo sapiens
5.8S rRNA8RNA157Homo sapiens
CDK5 regulatory subunit-associated protein 3Bprotein506Homo sapiensQ96JB5 (AlphaFold model)
DDRGK domain-containing protein 1Cprotein314Homo sapiensQ96HY6 (AlphaFold model)
Ubiquitin-fold modifier 1Dprotein85Homo sapiensP61960 (AlphaFold model)
E3 UFM1-protein ligase 1Eprotein794Homo sapiensO94874 (AlphaFold model)
E3 ubiquitin-protein ligase listerinFprotein1766Homo sapiensO94822
tRNAGRNA76Homo sapiens
60S ribosomal protein L3LBprotein403Homo sapiensP39023
60S ribosomal protein L4LCprotein427Homo sapiensP36578
60S ribosomal protein L5LDprotein297Homo sapiensP46777

43 more molecules are not listed.

Sequence of entity 1 (5), FASTA
>9GY4_1 28S rRNA (chains 5)
CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAG
AAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGA
AUCCCCGCCCCGCGGCGGGGCGCGGGACAUGUGGCGUACGGAAGACCCGCUCCCCGGCGC
CGCUCGUGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCG
GUAGCGGCCCCCGGCGCGCCGGGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCA
GCCCAAAGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAA
CAAGUACCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAA
CCGUUAAGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGC
GGGUCCGGCCGUGUCGGCGGCCCGGCGGAUCUUUCCCGCCCCCCGUUCCUCCCGACCCCU
CCACCCGCCCUCCCUUCCCCCGCCGCCCCUCCUCCUCCUCCCCGGAGGGGGCGGGCUCCG
GCGGGUGCGGGGGUGGGCGGGCGGGGCCGGGGGUGGGGUCGGCGGGGGACCGUCCCCCGA
CCGGCGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCGCGACCGGCUCCG
GGACGGCUGGGAAGGCCCGGCGGGGAAGGUGGCUCGGGGGGCCCCGUCCGUCCGUCCGUC
CGUCCUCCUCCUCCCCCGUCUCCGCCCCCCGGCCCCGCGUCCUCCCUCGGGAGGGCGCGC
GGGUCGGGGCGGCGGCGGCGGCGGCGGUGGCGGCGGCGGCGGCGGCGGCGGGACCGAAAC
CCCCCCCGAGUGUUACAGCCCCCCCGGCAGCAGCACUCGCCGAAUCCCGGGGCCGAGGGA
GCGAGACCCGUCGCCGCGCUCUCCCCCCUCCCGGCGCCCACCCCCGCGGGGAAUCCCCCG
CGAGGGGGGUCUCCCCCGCGGGGGCGCGCCGGCGUCUCCUCGUGGGGGGGCCGGGCCACC
CCUCCCACGGCGCGACCGCUCUCCCACCCCUCCUCCCCGCGCCCCCGCCCCGGCGACGGG
GGGGGUGCCGCGCGCGGGUCGGGGGGCGGGGCGGACUGUCCCCAGUGCGCCCCGGGCGGG
UCGCGCCGUCGGGCCCGGGGGAGGUUCUCUCGGGGCCACGCGCGCGUCCCCCGAAGAGGG
GGACGGCGGAGCGAGCGCACGGGGUCGGCGGCGACGUCGGCUACCCACCCGACCCGUCUU
GAAACACGGACCAAGGAGUCUAACACGUGCGCGAGUCGGGGGCUCGCACGAAAGCCGCCG
UGGCGCAAUGAAGGUGAAGGCCGGCGCGCUCGCCGGCCGAGGUGGGAUCCCGAGGCCUCU
CCAGUCCGCCGAGGGCGCACCACCGGCCCGUCUCGCCCGCCGCGCCGGGGAGGUGGAGCA
CGAGCGCACGUGUUAGGACCCGAAAGAUGGUGAACUAUGCCUGGGCAGGGCGAAGCCAGA
GGAAACUCUGGUGGAGGUCCGUAGCGGUCCUGACGUGCAAAUCGGUCGUCCGACCUGGGU
AUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCCUCCGAAGUUUCCCUCAG
GAUAGCUGGCGCUCUCGCAGACCCGACGCACCCCCGCCACGCAGUUUUAUCCGGUAAAGC
GAAUGAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUCUCAAACUUUAAAUGGGU
AAGAAGCCCGGCUCGCUGGCGUGGAGCCGGGCGUGGAAUGCGAGUGCCUAGUGGGCCACU
UUUGGUAAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAGGCGCCCGAUGC
CGACGCUCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAU
GGAAGUCGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGA
AAAUGGAUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGCCGGCAGUCGAGAGUGGA
CGGGAGCGGCGGCGGCGGCGCGCGCGCGCGCGCGUGUGGUGUGCGUCGGAGGGCGGCGGC
GGCGGCGGCGGCGGGGGUGUGGGGUCCUUCCCCCGCCCCCCCCCCCACGCCUCCUCCCCU
CCUCCCGCCCACGCCCCGCUCCCCGCCCCCGGAGCCCCGCGGACGCUACGCCGCGACGAG
UAGGAGGGCCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGCCGC
AGGUGCAGAUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAGUGG
AGAAGGGUUCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGGCGA
GCGCCGUUCCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCGGCCGAUCGAAAGGGAGUC
GGGUUCAGAUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGCGGU
AACGCGACCGAUCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUUGUG
AAGGGCAGGGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAAGCG
UCGCGGUUCCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGAGGG
UGUAAAUCUCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGCCUC
UGGCAUGUUGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGGGAU
AAGGAUUGGCUCUAAGGGCUGGGUCGGUCGGGCUGGGGCGCGAAGCGGGGCUGGGCGCGC
GCCGCGGCUGGACGAGGCGCCGCCGCCCCCCCCACGCCCGGGGCACCCCCCUCGCGGCCC
UCCCCCGCCCCACCCCGCGCGCGCCGCUCGCUCCCUCCCCGCCCCGCGCCCUCUCUCUCU
CUCUCUCCCCCGCUCCCCGUCCUCCCCCCUCCCCGGGGGAGCGCCGCGUGGGGGCGGCGG
CGGGGGGAGAAGGGUCGGGGCGGCAGGGGCCGGCGGCGGCCCGCCGCGGGGCCCCGGCGG
CGGGGGCACGGUCCCCCGCGAGGGGGGCCCGGGCACCCGGGGGGCCGGCGGCGGCGGCGA
CUCUGGACGCGAGCCGGGCCCUUCCCGUGGAUCGCCCCAGCUGCGGCGGGCGUCGCGGCC
GCCCCCGGGGAGCCCGGCGGGCGCCGGCGCGCCCCCCCCCCCACCCCACGUCUCGUCGCG
CGCGCGUCCGCUGGGGGCGGGGAGCGGUCGGGCGGCGGCGGUCGGCGGGCGGCGGGGCGG
GGCGGUUCGUCCCCCCGCCCUACCCCCCCGGCCCCGUCCGCCCCCCGUUCCCCCCUCCUC
CUCGGCGCGCGGCGGCGGCGGCGGCAGGCGGCGGAGGGGCCGCGGGCCGGUCCCCCCCGC
CGGGUCCGCCCCCGGGGCCGCGGUUCCGCGCGGCGCCUCGCCUCGGCCGGCGCCUAGCAG
CCGACUUAGAACUGGUGCGGACCAGGGGAAUCCGACUGUUUAAUUAAAACAAAGCAUCGC
GAAGGCCCGCGGCGGGUGUUGACGCGAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAG
UGAAGAAAUUCAAUGAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAG
CCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUGAACGAGAUUCCCACUGU
CCCUACCUACUAUCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAUCAGCGGGG
AAAGAAGACCCUGUUGAGCUUGACUCUAGUCUGGCACGGUGAAGAGACAUGAGAGGUGUA
GAAUAAGUGGGAGGCCCCCGGCGCCCCCCCGGUGUCCCCGCGAGGGGCCCGGGGCGGGGU
CCGCCGGCCCUGCGGGCCGCCGGUGAAAUACCACUACUCUGAUCGUUUUUUCACUGACCC
GGUGAGGCGGGGGGGCGAGCCCCGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGGCCGC
GCGCCGGCCGGGCGCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACUGGGGCG
GUACACCUGUCAAACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCU
CCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAAUACAGACCG
UGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGGUGUCAGAAA
AGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUG
AUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGU
UCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUAC
CCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGGUU
CAGACAUUUGGUGUAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGG
AUUAUGACUGAACGCCUCUAAGUCAGAAUCCCGCCCAGGCGGAACGAUACGGCAGCGCCG
CGGAGCCUCGGUUGGCCUCGGAUAGCCGGUCCCCCGCCUGUCCCCGCCGGCGGGCCGCCC
CCCCCCUCCACGCGCCCCGCGCGCGCGGGAGGGCGCGUGCCCCGCCGCGCGCCGGGACCG
GGGUCCGGUGCGGAGUGCCCUUCGUCCUGGGAAACGGGGCGCGGCUGGAAAGGCGGCCGC
CCCCUCGCCCGUCACGCACCGCACGUUCGUGGGGAACCUGGCGCUAAACCAUUCGUAGAC
GACCUGCUUCUGGGUCGGGG
Sequence of entity 2 (7), FASTA
>9GY4_2 5S rRNA (chains 7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
U
Sequence of entity 3 (8), FASTA
>9GY4_3 5.8S rRNA (chains 8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCUU
Sequence of entity 4 (B), FASTA
>9GY4_4 CDK5 regulatory subunit-associated protein 3 (chains B)
MEDHQHVPIDIQTSKLLDWLVDRRHCSLKWQSLVLTIREKINAAIQDMPESEEIAQLLSG
SYIHYFHCLRILDLLKGTEASTKNIFGRYSSQRMKDWQEIIALYEKDNTYLVELSSLLVR
NVNYEIPSLKKQIAKCQQLQQEYSRKEEECQAGAAEMREQFYHSCKQYGITGENVRGELL
ALVKDLPSQLAEIGAAAQQSLGEAIDVYQASVGFVCESPTEQVLPMLRFVQKRGNSTVYE
WRTGTEPSVVERPHLEELPEQVAEDAIDWGDFGVEAVSEGTDSGISAEAAGIDWGIFPES
DSKDPGGDGIDWGDDAVALQITVLEAGTQAPEGVARGPDALTLLEYTETRNQFLDELMEL
EIFLAQRAVELSEEADVLSVSQFQLAPAILQGQTKEKMVTMVSVLEDLIGKLTSLQLQHL
FMILASPRYVDRVTEFLQQKLKQSQLLALKKELMVQKQQEALEEQAALEPKLDLLLEKTK
ELQKLIEADISKRYSGRPVNLMGTSL
Sequence of entity 5 (C), FASTA
>9GY4_5 DDRGK domain-containing protein 1 (chains C)
MVAPVWYLVAAALLVGFILFLTRSRGRAASAGQEPLHNEELAGAGRVAQPGPLEPEEPRA
GGRPRRRRDLGSRLQAQRRAQRVAWAEADENEEEAVILAQEEEGVEKPAETHLSGKIGAK
KLRKLEEKQARKAQREAEEAEREERKRLESQREAEWKKEEERLRLEEEQKEEEERKAREE
QAQREHEEYLKLKEAFVVEEEGVGETMTEEQSQSFLTEFINYIKQSKVVLLEDLASQVGL
RTQDTINRIQDLLAEGTITGVIDDRGKFIYITPEELAAVANFIRQRGRVSIAELAQASNS
LIAWGRESPAQAPA
Sequence of entity 6 (D), FASTA
>9GY4_6 Ubiquitin-fold modifier 1 (chains D)
MSKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPA
QTAGNVFLKHGSELRIIPRDRVGSC
Sequence of entity 7 (E), FASTA
>9GY4_7 E3 UFM1-protein ligase 1 (chains E)
MADAWEEIRRLAADFQRAQFAEATQRLSERNCIEIVNKLIAQKQLEVVHTLDGKEYITPA
QISKEMRDELHVRGGRVNIVDLQQVINVDLIHIENRIGDIIKSEKHVQLVLGQLIDENYL
DRLAEEVNDKLQESGQVTISELCKTYDLPGNFLTQALTQRLGRIISGHIDLDNRGVIFTE
AFVARHKARIRGLFSAITRPTAVNSLISKYGFQEQLLYSVLEELVNSGRLRGTVVGGRQD
KAVFVPDIYSRTQSTWVDSFFRQNGYLEFDALSRLGIPDAVSYIKKRYKTTQLLFLKAAC
VGQGLVDQVEASVEEAISSGTWVDIAPLLPTSLSVEDAAILLQQVMRAFSKQASTVVFSD
TVVVSEKFINDCTELFRELMHQKAEKEMKNNPVHLITEEDLKQISTLESVSTSKKDKKDE
RRRKATEGSGSMRGGGGGNAREYKIKKVKKKGRKDDDSDDESQSSHTGKKKPEISFMFQD
EIEDFLRKHIQDAPEEFISELAEYLIKPLNKTYLEVVRSVFMSSTTSASGTGRKRTIKDL
QEEVSNLYNNIRLFEKGMKFFADDTQAALTKHLLKSVCTDITNLIFNFLASDLMMAVDDP
AAITSEIRKKILSKLSEETKVALTKLHNSLNEKSIEDFISCLDSAAEACDIMVKRGDKKR
ERQILFQHRQALAEQLKVTEDPALILHLTSVLLFQFSTHSMLHAPGRCVPQIIAFLNSKI
PEDQHALLVKYQGLVVKQLVSQSKKTGQGDYPLNNELDKEQEDVASTTRKELQELSSSIK
DLVLKSRKSSVTEE
Sequence of entity 8 (F), FASTA
>9GY4_8 E3 ubiquitin-protein ligase listerin (chains F)
MGGKNKQRTKGNLRPSNSGRAAELLAKEQGTVPGFIGFGTSQSDLGYVPAIQGAEEIDSL
VDSDFRMVLRKLSKKDVTTKLKAMQEFGTMCTERDTETVKGVLPYWPRIFCKISLDHDRR
VREATQQAFEKLILKVKKQLAPYLKSLMGYWLMAQCDTYTPAAFAAKDAFEAAFPPSKQP
EAIAFCKDEITSVLQDHLIKETPDTLSDPQTVPEEEREAKFYRVVTCSLLALKRLLCLLP
DNELDSLEEKFKSLLSQNKFWKYGKHSVPQIRSAYFELVSALCQRIPQLMKEEASKVSPS
VLLSIDDSDPIVCPALWEAVLYTLTTIEDCWLHVNAKKSVFPKLSTVIREGGRGLATVIY
PYLLPFISKLPQSITNPKLDFFKNFLTSLVAGLSTERTKTSSLESSAVISAFFECLRFIM
QQNLGEEEIEQMLVNDQLIPFIDAVLKDPGLQHGQLFNHLAETLSSWEAKADTEKDEKTA
HNLENVLIHFWERLSEICVAKISEPEADVESVLGVSNLLQVLQKPKSSLKSSKKKNGKVR
FADEILESNKENEKCVSSEGEKIEGWELTTEPSLTHNSSGLLSPLRKKPLEDLVCKLADI
SINYVNERKSEQHLRFLSTLLDSFSSSRVFKMLLGDEKQSIVQAKPLEIAKLVQKNPAVQ
FLYQKLIGWLNEDQRKDFGFLVDILYSALRCCDNDMERKKVLDDLTKVDLKWNSLLKIIE
KACPSSDKHALVTPWLKGDILGEKLVNLADCLCNEDLESRVSSESHFSERWTLLSLVLSQ
HVKNDYLIGDVYVERIIVRLHETLFKTKKLSEAESSDSSVSFICDVAYNYFSSAKGCLLM
PSSEDLLLTLFQLCAQSKEKTHLPDFLICKLKNTWLSGVNLLVHQTDSSYKESTFLHLSA
LWLKNQVQASSLDINSLQVLLSAVDDLLNTLLESEDSYLMGVYIGSVMPNDSEWEKMRQS
LPMQWLHRPLLEGRLSLNYECFKTDFKEQDIKTLPSHLCTSALLSKMVLIALRKETVLEN
NELEKIIAELLYSLQWCEELDNPPIFLIGFCEILQKMNITYDNLRVLGNTSGLLQLLFNR
SREHGTLWSLIIAKLILSRSISSDEVKPHYKRKESFFPLTEGNLHTIQSLCPFLSKEEKK
EFSAQCIPALLGWTKKDLCSTNGGFGHLAIFNSCLQTKSIDDGELLHGILKIIISWKKEH
EDIFLFSCNLSEASPEVLGVNIEIIRFLSLFLKYCSSPLAESEWDFIMCSMLAWLETTSE
NQALYSIPLVQLFACVSCDLACDLSAFFDSTTLDTIGNLPVNLISEWKEFFSQGIHSLLL
PILVTVTGENKDVSETSFQNAMLKPMCETLTYISKEQLLSHKLPARLVADQKTNLPEYLQ
TLLNTLAPLLLFRARPVQIAVYHMLYKLMPELPQYDQDNLKSYGDEEEEPALSPPAALMS
LLSIQEDLLENVLGCIPVGQIVTIKPLSEDFCYVLGYLLTWKLILTFFKAASSQLRALYS
MYLRKTKSLNKLLYHLFRLMPENPTYAETAVEVPNKDPKTFFTEELQLSIRETTMLPYHI
PHLACSVYHMTLKDLPAMVRLWWNSSEKRVFNIVDRFTSKYVSSVLSFQEISSVQTSTQL
FNGMTVKARATTREVMATYTIEDIVIELIIQLPSNYPLGSIIVESGKRVGVAVQQWRNWM
LQLSTYLTHQNGSIMEGLALWKNNVDKRFEGVEDCMICFSVIHGFNYSLPKKACRTCKKK
FHSACLYKWFTSSNKSTCPLCRETFF
Sequence of entity 9 (G), FASTA
>9GY4_9 tRNA (chains G)
GGGCGUGUGGCGUAGUCGGUAGCGCGCUCCCUUAGCAUGGGAGAGGUCUCCGGUUCGAUU
CCGGACUCGUCCGCCA
Sequence of entity 10 (LB), FASTA
>9GY4_10 60S ribosomal protein L3 (chains LB)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
Sequence of entity 11 (LC), FASTA
>9GY4_11 60S ribosomal protein L4 (chains LC)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKL
APGGHVGRFCIWTESAFRKLDELYGTWRKAASLKSNYNLPMHKMINTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVDKAAAAAAA
LQAKSDEKAAVAGKKPVVGKKGKKAAVGVKKQKKPLVGKKAAATKKPAPEKKPAEKKPTT
EEKKPAA
Sequence of entity 12 (LD), FASTA
>9GY4_12 60S ribosomal protein L5 (chains LD)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMY
KKAHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg219
ZNZinc ionZn5

Primary citation

UFMylation orchestrates spatiotemporal coordination of RQC at the ER. Penchev, I., Gumbin, S., Scavone, F. et al. Sci Adv (2025) 11:eadv0435-eadv0435. DOI 10.1126/sciadv.adv0435 · PubMed

Other PDB entries of the same protein (UniProt Q96JB5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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