6YLF: Rix1-Rea1 pre-60S particle - Rea1, body 3

Rix1-Rea1 pre-60S particle - Rea1, body 3 (rigid body refinement, composite structure of Rea1 ring and tail). Determined by electron microscopy at 4.2 Å resolution. Released 29 Jul 2020.

Method
Electron microscopy
Resolution
4.2 Å
Organism
Saccharomyces cerevisiae
Chains
2
Atoms
18,362
Mol. weight
617.06 kDa
Released
29 Jul 2020

Explore 6YLF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YLF contains 182 α-helices and 77 β-strands across 2 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 AP1: 181 helices, 70 β-strands

ElementResiduesLengthSheet
β-strand611
β-strand912
α-helix11-2313
α-helix42-5413
α-helix61-644
α-helix69-7810
α-helix85-9612
α-helix103-12119
α-helix130-14516
α-helix156-16813
α-helix175-18612
α-helix192-20110
α-helix224-23512
β-strand25112
β-strand25511
α-helix257-2593
β-strand264-26523
β-strand272-27323
α-helix294-30613
β-strand312-31544
α-helix321-33212
β-strand340-34125
β-strand35416
β-strand35717
β-strand36617
β-strand36916
α-helix371-3744
α-helix375-3795
β-strand381-38555
α-helix387-3893
α-helix392-40110
β-strand40818
β-strand41618
β-strand423-42755
α-helix447-4526
α-helix4541
β-strand455-45844
α-helix465-4717
α-helix481-50020
α-helix508-5114
α-helix513-52816
α-helix539-55113
α-helix562-5665
α-helix632-64413
α-helix656-66611
β-strand675-67739
α-helix816-8216
β-strand826110
β-strand827-82939
α-helix837-8437
β-strand854111
β-strand865111
β-strand873110
α-helix910-9156
α-helix927-93812
α-helix955-96410
α-helix976-98611
α-helix988-9914
α-helix998-10047
α-helix1062-107110
β-strand1079112
β-strand1081-1082213
α-helix1089-109911
α-helix1103-11064
β-strand1108114
α-helix1136-11405
β-strand1148115
β-strand1149114
α-helix1161-11677
β-strand1173-1175316
β-strand1180-1182316
β-strand1191115
β-strand1193-1194213
β-strand1215112
β-strand1218113
α-helix1225-12328
α-helix1237-12404
α-helix1244-12463
α-helix1261-127616
α-helix1285-129713
α-helix1306-131712
α-helix1346-135914
β-strand1364-1366317
α-helix1376-13849
β-strand1393-1394217
α-helix1479-14846
β-strand1491-1492217
α-helix1499-15046
α-helix1505-15084
β-strand1536-1538317
α-helix1539-15413
α-helix1545-15473
α-helix1552-15554
β-strand1559-1561317
α-helix1563-15653
α-helix1572-15787
α-helix1585-159814
α-helix1607-162216
α-helix1632-16409
α-helix1642-16454
α-helix1653-166715
α-helix1726-17349
β-strand1744118
α-helix1753-176311
β-strand1773119
α-helix1779-17813
α-helix1801-18055
β-strand1811-1812220
β-strand1815119
α-helix1824-18307
β-strand1838-1839221
β-strand1846-1847221
β-strand1854-1855220
α-helix1873-18764
β-strand1881118
α-helix1889-189911
α-helix1907-192418
α-helix1940-194910
α-helix1976-198611
β-strand2005-2008422
β-strand2011-2014422
α-helix2034-204613
β-strand2050-2053423
α-helix2061-207010
β-strand2075-2080624
α-helix2085-20884
β-strand2090-2094525
α-helix2099-212224
α-helix2127-214216
α-helix2150-215910
α-helix2167-218317
α-helix2184-21885
β-strand2193-2196425
α-helix2198-22058
β-strand2208-2214724
α-helix2222-22276
β-strand2235126
β-strand2250126
β-strand2261-2262223
α-helix2271-22733
β-strand2278-2281423
α-helix2285-22873
α-helix2291-22955
α-helix2328-23303
α-helix2338-235114
α-helix2372-238211
α-helix2391-240414
α-helix2408-24147
α-helix2416-242510
α-helix2447-24504
α-helix2455-24584
α-helix2461-248727
α-helix2496-25049
α-helix2523-253311
α-helix2543-255917
α-helix2567-25715
α-helix2573-258513
α-helix2597-26059
α-helix2614-26174
α-helix2628-264821
α-helix2653-26553
α-helix2658-267518
α-helix2679-270022
α-helix2711-272111
α-helix2727-27337
α-helix2741-27444
α-helix2758-27614
α-helix2780-279011
α-helix2797-27993
α-helix2803-281614
α-helix2818-28214
α-helix2825-284420
α-helix2854-286411
α-helix2867-28726
α-helix2873-28775
α-helix2878-28858
α-helix2891-290414
α-helix2916-294530
α-helix2953-29542
α-helix2955-29595
α-helix2971-29733
α-helix2982-299514
α-helix2998-300912
α-helix3015-303521
α-helix3044-306522
α-helix3066-30683
α-helix3083-30864
α-helix3088-310316
α-helix3113-31164
α-helix3118-31258
α-helix3130-31323
α-helix3133-315422
α-helix3175-31795
α-helix3203-32097
α-helix3212-32176
α-helix3226-324217
α-helix3257-327115
α-helix3288-330821
α-helix3316-332914
α-helix3337-335721
α-helix3365-338824
α-helix3393-33964
α-helix3398-34014
α-helix3402-341211
α-helix3429-344012
β-strand3443127
α-helix3444-34463
α-helix3448-346417
α-helix3472-348211
α-helix3483-34853
α-helix3486-351126
α-helix3518-354326
β-strand3546127
α-helix3548-35536
α-helix3582-35865
α-helix3602-361615
α-helix3624-363916
α-helix3653-367321
α-helix3691-36955
α-helix3711-372616
α-helix3738-375518
α-helix3757-378024
α-helix3793-380412
α-helix3806-382318
α-helix3831-384919
α-helix3856-387924
α-helix3885-389612
α-helix3914-393522
α-helix3949-396315
α-helix3965-398117
α-helix3992-39965
α-helix3997-39993
α-helix4003-403937
α-helix4626-463914
α-helix4641-465515
β-strand4703-4707528
β-strand4708-4709229
α-helix4720-473617
β-strand4742-4743228
β-strand4745-4748429
β-strand4752-4756529
α-helix4764-47729
α-helix4783-479917
β-strand4806-4813828
α-helix4821-483111
β-strand4835-4841728
β-strand4855-4860630
α-helix4861-48633
β-strand4865-4873930
β-strand4885128
α-helix4891-490616
Chain xP1: 1 helix, 7 β-strands
ElementResiduesLengthSheet
β-strand34-36330
β-strand50130
α-helix61-688
β-strand77-80431
β-strand81132
β-strand90132
β-strand117-119330
β-strand120-123431

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
MidasinAP1protein4910Saccharomyces cerevisiaeQ12019
Ribosome assembly protein 4xP1protein515Saccharomyces cerevisiaeP25382 (AlphaFold model)
Sequence of entity 1 (AP1), FASTA
>6YLF_1 Midasin (chains AP1)
MSQDRILLDLDVVNQRLILFNSAFPSDAIEAPFHFSNKESTSENLDNLAGTILHSRSITG
HVFLYKHIFLEIVARWIKDSKKKDYVLVIEKLASIITIFPVAMPLIEDYLDKENDHFITI
LQNPSTQKDSDMFKILLAYYRLLYHNKEVFARFIQPDILYQLVDLLTKEQENQVVIFLAL
KVLSLYLDMGEKTLNDMLDTYIKSRDSLLGHFEGDSGIDYSFLELNEAKRCANFSKLPSV
PECFTIEKKSSYFIIEPQDLSTKVASICGVIVPKVHTIHDKVFYPLTFVPTHKTVSSLRQ
LGRKIQNSTPIMLIGKAGSGKTFLINELSKYMGCHDSIVKIHLGEQTDAKLLIGTYTSGD
KPGTFEWRAGVLATAVKEGRWVLIEDIDKAPTDVLSILLSLLEKRELTIPSRGETVKAAN
GFQLISTVRINEDHQKDSSNKIYNLNMIGMRIWNVIELEEPSEEDLTHILAQKFPILTNL
IPKLIDSYKNVKSIYMNTKFISLNKGAHTRVVSVRDLIKLCERLDILFKNNGINKPDQLI
QSSVYDSIFSEAADCFAGAIGEFKALEPIIQAIGESLDIASSRISLFLTQHVPTLENLDD
SIKIGRAVLLKEKLNIQKKSMNSTLFAFTNHSLRLMEQISVCIQMTEPVLLVGETGTGKT
TVVQQLAKMLAKKLTVINVSQQTETGDLLGGYKPVNSKTVAVPIQENFETLFNATFSLKK
NEKFHKMLHRCFNKNQWKNVVKLWNEAYKMAQSILKITNTENENENAKKKKRRLNTHEKK
LLLDKWADFNDSVKKFEAQSSSIENSFVFNFVEGSLVKTIRAGEWLLLDEVNLATADTLE
SISDLLTEPDSRSILLSEKGDAEPIKAHPDFRIFACMNPATDVGKRDLPMGIRSRFTEIY
VHSPERDITDLLSIIDKYIGKYSVSDEWVGNDIAELYLEAKKLSDNNTIVDGSNQKPHFS
IRTLTRTLLYVTDIIHIYGLRRSLYDGFCMSFLTLLDQKSEAILKPVIEKFTLGRLKNVK
SIMSQTPPSPGPDYVQFKHYWMKKGPNTIQEQAHYIITPFVEKNMMNLVRATSGKRFPVL
IQGPTSSGKTSMIKYLADITGHKFVRINNHEHTDLQEYLGTYVTDDTGKLSFKEGVLVEA
LRKGYWIVLDELNLAPTDVLEALNRLLDDNRELFIPETQEVVHPHPDFLLFATQNPPGIY
GGRKILSRAFRNRFLELHFDDIPQDELEIILRERCQIAPSYAKKIVEVYRQLSIERSASR
LFEQKNSFATLRDLFRWALRDAVGYEQLAASGYMLLAERCRTPQEKVTVKKTLEKVMKVK
LDMDQYYASLEDKSLEAIGSVTWTKGMRRLSVLVSSCLKNKEPVLLVGETGCGKTTICQL
LAQFMGRELITLNAHQNTETGDILGAQRPVRNRSEIQYKLIKSLKTALNIANDQDVDLKE
LLQLYSKSDNKNIAEDVQLEIQKLRDSLNVLFEWSDGPLIQAMRTGNFFLLDEISLADDS
VLERLNSVLEPERSLLLAEQGSSDSLVTASENFQFFATMNPGGDYGKKELSPALRNRFTE
IWVPSMEDFNDVNMIVSSRLLEDLKDLANPIVKFSEWFGKKLGGGNATSGVISLRDILAW
VEFINKVFPKIQNKSTALIQGASMVFIDALGTNNTAYLAENENDLKSLRTECIIQLLKLC
GDDLELQQIETNEIIVTQDELQVGMFKIPRFPDAQSSSFNLTAPTTASNLVRVVRAMQVH
KPILLEGSPGVGKTSLITALANITGNKLTRINLSEQTDLVDLFGADAPGERSGEFLWHDA
PFLRAMKKGEWVLLDEMNLASQSVLEGLNACLDHRGEAYIPELDISFSCHPNFLVFAAQN
PQYQGGGRKGLPKSFVNRFSVVFIDMLTSDDLLLIAKHLYPSIEPDIIAKMIKLMSTLED
QVCKRKLWGNSGSPWEFNLRDTLRWLKLLNQYSICEDVDVFDFVDIIVKQRFRTISDKNK
AQLLIEDIFGKFSTKENFFKLTEDYVQINNEVALRNPHYRYPITQNLFPLECNVAVYESV
LKAINNNWPLVLVGPSNSGKTETIRFLASILGPRVDVFSMNSDIDSMDILGGYEQVDLTR
QISYITEELTNIVREIISMNMKLSPNATAIMEGLNLLKYLLNNIVTPEKFQDFRNRFNRF
FSHLEGHPLLKTMSMNIEKMTEIITKEASVKFEWFDGMLVKAVEKGHWLILDNANLCSPS
VLDRLNSLLEIDGSLLINECSQEDGQPRVLKPHPNFRLFLTMDPKYGELSRAMRNRGVEI
YIDELHSRSTAFDRLTLGFELGENIDFVSIDDGIKKIKLNEPDMSIPLKHYVPSYLSRPC
IFAQVHDILLLSDEEPIEESLAAVIPISHLGEVGKWANNVLNCTEYSEKKIAERLYVFIT
FLTDMGVLEKINNLYKPANLKFQKALGLHDKQLTEETVSLTLNEYVLPTVSKYSDKIKSP
ESLYLLSSLRLLLNSLNALKLINEKSTHGKIDELTYIELSAAAFNGRHLKNIPRIPIFCI
LYNILTVMSENLKTESLFCGSNQYQYYWDLLVIVIAALETAVTKDEARLRVYKELIDSWI
ASVKSKSDIEITPFLNINLEFTDVLQLSRGHSITLLWDIFRKNYPTTSNSWLAFEKLINL
SEKFDKVRLLQFSESYNSIKDLMDVFRLLNDDVLNNKLSEFNLLLSKLEDGINELELISN
KFLNKRKHYFADEFDNLIRYTFSVDTAELIKELAPASSLATQKLTKLITNKYNYPPIFDV
LWTEKNAKLTSFTSTIFSSQFLEDVVRKSNNLKSFSGNQIKQSISDAELLLSSTIKCSPN
LLKSQMEYYKNMLLSWLRKVIDIHVGGDCLKLTLKELCSLIEEKTASETRVTFAEYIFPA
LDLAESSKSLEELGEAWITFGTGLLLLFVPDSPYDPAIHDYVLYDLFLKTKTFSQNLMKS
WRNVRKVISGDEEIFTEKLINTISDDDAPQSPRVYRTGMSIDSLFDEWMAFLSSTMSSRQ
IKELVSSYKCNSDQSDRRLEMLQQNSAHFLNRLESGYSKFADLNDILAGYIYSINFGFDL
LKLQKSKDRASFQISPLWSMDPINISCAENVLSAYHELSRFFKKGDMEDTSIEKVLMYFL
TLFKFHKRDTNLLEIFEAALYTLYSRWSVRRFRQEQEENEKSNMFKFNDNSDDYEADFRK
LFPDYEDTALVTNEKDISSPENLDDIYFKLADTYISVFDKDHDANFSSELKSGAIITTIL
SEDLKNTRIEELKSGSLSAVINTLDAETQSFKNTEVFGNIDFYHDFSIPEFQKAGDIIET
VLKSVLKLLKQWPEHATLKELYRVSQEFLNYPIKTPLARQLQKIEQIYTYLAEWEKYASS
EVSLNNTVKLITDLIVSWRKLELRTWKGLFNSEDAKTRKSIGKWWFYLYESIVISNFVSE
KKETAPNATLLVSSLNLFFSKSTLGEFNARLDLVKAFYKHIQLIGLRSSKIAGLLHNTIK
FYYQFKPLIDERITNGKKSLEKEIDDIILLASWKDVNVDALKQSSRKSHNNLYKIVRKYR
DLLNGDAKTIIEAGLLYSNENKLKLPTLKQHFYEDPNLEASKNLVKEISTWSMRAAPLRN
IDTVASNMDSYLEKISSQEFPNFADLASDFYAEAERLRKETPNVYTKENKKRLAYLKTQK
SKLLGDALKELRRIGLKVNFREDIQKVQSSTTTILANIAPFNNEYLNSSDAFFFKILDLL
PKLRSAASNPSDDIPVAAIERGMALAQSLMFSLITVRHPLSEFTNDYCKINGMMLDLEHF
TCLKGDIVHSSLKANVDNVRLFEKWLPSLLDYAAQTLSVISKYSATSEQQKILLDAKSTL
SSFFVHFNSSRIFDSSFIESYSRFELFINELLKKLENAKETGNAFVFDIIIEWIKANKGG
PIKKEQKRGPSVEDVEQAFRRTFTSIILSFQKVIGDGIESISETDDNWLSASFKKVMVNV
KLLRSSVVSKNIETALSLLKDFDFTTTESIYVKSVISFTLPVITRYYNAMTVVLERSRIY
YTNTSRGMYILSTILHSLAKNGFCSPQPPSEEVDDKNLQEGTGLGDGEGAQNNNKDVEQD
EDLTEDAQNENKEQQDKDERDDENEDDAVEMEGDMAGELEDLSNGEENDDEDTDSEEEEL
DEEIDDLNEDDPNAIDDKMWDDKASDNSKEKDTDQNLDGKNQEEDVQAAENDEQQRDNKE
GGDEDPNAPEDGDEEIENDENAEEENDVGEQEDEVKDEEGEDLEANVPEIETLDLPEDMN
LDSEHEESDEDVDMSDGMPDDLNKEEVGNEDEEVKQESGIESDNENDEPGPEEDAGETET
ALDEEEGAEEDVDMTNDEGKEDEENGPEEQAMSDEEELKQDAAMEENKEKGGEQNTEGLD
GVEEKADTEDIDQEAAVQQDSGSKGAGADATDTQEQDDVGGSGTTQNTYEEDQEDVTKNN
EESREEATAALKQLGDSMKEYHRRRQDIKEAQTNGEEDENLEKNNERPDEFEHVEGANTE
TDTQALGSATQDQLQTIDEDMAIDDDREEQEVDQKELVEDADDEKMDIDEEEMLSDIDAH
DANNDVDSKKSGFIGKRKSEEDFENELSNEHFSADQEDDSEIQSLIENIEDNPPDASASL
TPERSLEESRELWHKSEISTADLVSRLGEQLRLILEPTLATKLKGDYKTGKRLNMKRIIP
YIASQFRKDKIWLRRTKPSKRQYQIMIALDDSKSMSESKCVKLAFDSLCLVSKTLTQLEA
GGLSIVKFGENIKEVHSFDQQFSNESGARAFQWFGFQETKTDVKKLVAESTKIFERARAM
VHNDQWQLEIVISDGICEDHETIQKLVRRARENKIMLVFVIIDGITSNESILDMSQVNYI
PDQYGNPQLKITKYLDTFPFEFYVVVHDISELPEMLSLILRQYFTDLASS
Sequence of entity 2 (xP1), FASTA
>6YLF_2 Ribosome assembly protein 4 (chains xP1)
MSTLIPPPSKKQKKEAQLPREVAIIPKDLPNVSIKFQALDTGDNVGGALRVPGAISEKQL
EELLNQLNGTSDDPVPYTFSCTIQGKKASDPVKTIDITDNLYSSLIKPGYNSTEDQITLL
YTPRAVFKVKPVTRSSSAIAGHGSTILCSAFAPHTSSRMVTGAGDNTARIWDCDTQTPMH
TLKGHYNWVLCVSWSPDGEVIATGSMDNTIRLWDPKSGQCLGDALRGHSKWITSLSWEPI
HLVKPGSKPRLASSSKDGTIKIWDTVSRVCQYTMSGHTNSVSCVKWGGQGLLYSGSHDRT
VRVWDINSQGRCINILKSHAHWVNHLSLSTDYALRIGAFDHTGKKPSTPEEAQKKALENY
EKICKKNGNSEEMMVTASDDYTMFLWNPLKSTKPIARMTGHQKLVNHVAFSPDGRYIVSA
SFDNSIKLWDGRDGKFISTFRGHVASVYQVAWSSDCRLLVSCSKDTTLKVWDVRTRKLSV
DLPGHKDEVYTVDWSVDGKRVCSGGKDKMVRLWTH

Primary citation

Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis. Kater, L., Mitterer, V., Thoms, M. et al. Mol Cell (2020) 79:615-628.e5. DOI 10.1016/j.molcel.2020.06.032 · PubMed

Other PDB entries of the same protein (UniProt Q12019), best resolution first:

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