6FRK: Ribosomal protein eL28

Structure of a prehandover mammalian ribosomal SRP and SRP receptor targeting complex. Determined by electron microscopy at 3.7 Å resolution. Released 28 Mar 2018.

Method
Electron microscopy
Resolution
3.7 Å
Organisms
Canis lupus familiaris, Oryctolagus cuniculus, Saccharomyces cerevisiae
Chains
58
Atoms
159,957
Mol. weight
2504.83 kDa
Ligands
MG, ZN, GTP, GNP
Released
28 Mar 2018

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

Secondary structure: helices and β-sheets

6FRK contains 376 α-helices and 369 β-strands across 53 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 3: 4 helices, 6 β-strands

ElementResiduesLengthSheet
α-helix3-108
β-strand17-2048
β-strand23-2648
α-helix32-343
β-strand49-5359
β-strand60-6569
β-strand77-7829
β-strand81-8229
α-helix88-9710
α-helix106-11813
Chain 4: 5 helices, 3 β-strands
ElementResiduesLengthSheet
β-strand12-17618
α-helix42-509
β-strand60-65618
β-strand70-73418
α-helix75-773
α-helix78-847
α-helix109-1135
α-helix129-1324
Chain 6: 9 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix10-2213
β-strand26-31625
α-helix37-4610
β-strand51-54425
α-helix58-603
α-helix63-675
α-helix74-763
β-strand86-91625
α-helix97-1037
β-strand121126
α-helix136-1394
β-strand145-147327
β-strand152-154327
β-strand161126
α-helix165-1673
α-helix170-1778
β-strand191-194425
Chain a: 4 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix42-487
β-strand73-74233
α-helix75-773
α-helix84-885
β-strand100-102334
β-strand110-112333
β-strand122-126534
β-strand128-129233
α-helix131-14010
β-strand142-146534
Chain A: 9 helices, 22 β-strands
ElementResiduesLengthSheet
α-helix34-374
β-strand44-47435
β-strand50136
β-strand57136
β-strand58-59237
β-strand60-62335
β-strand73135
β-strand76-77237
α-helix781
β-strand79138
β-strand83139
α-helix861
β-strand87135
α-helix881
β-strand90140
β-strand101-103340
β-strand112-114340
β-strand116141
β-strand126141
β-strand134-140740
α-helix142-1443
β-strand145-149540
β-strand155-159540
β-strand163-166440
β-strand169138
α-helix182-1898
α-helix198-2003
α-helix201-2033
β-strand224-225242
α-helix229-2302
β-strand237-238242
Chain b: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix12-165
α-helix22-243
α-helix26-272
α-helix37-4812
α-helix54-7522
Chain B: 14 helices, 19 β-strands
ElementResiduesLengthSheet
α-helix14-163
α-helix27-293
α-helix32-343
β-strand43143
β-strand45-591544
β-strand71-801044
α-helix82-832
β-strand84-951245
β-strand98-106945
α-helix113-1164
α-helix133-1364
α-helix140-1423
α-helix148-1558
β-strand159-165745
β-strand180-184545
β-strand185143
β-strand204-205245
α-helix207-2104
β-strand217-222644
α-helix223-2242
β-strand225-229546
α-helix231-2344
α-helix238-2414
β-strand270-273446
β-strand276-282744
α-helix2831
β-strand284-287444
β-strand320147
β-strand324147
β-strand330-335644
β-strand344-349644
β-strand365-368444
α-helix382-3854
Chain c: 3 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix14-2411
β-strand26-29448
α-helix34-407
β-strand45-49548
α-helix54-6512
β-strand70-74548
β-strand94-98548

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Canis lupus familiaris RNA, 7SL, cytoplasmic 1 (RN7SL1), SRP RNA1RNA299Canis lupus familiaris
tRNA2RNA76Oryctolagus cuniculus
Ribosomal protein eL283protein125Oryctolagus cuniculus
Ribosomal protein L124protein163Oryctolagus cuniculus
28S ribosomal RNA5RNA3658Oryctolagus cuniculus
60S acidic ribosomal protein P06protein202Oryctolagus cuniculus
5S ribosomal RNA7RNA120Oryctolagus cuniculus
5.8S ribosomal RNA8RNA156Oryctolagus cuniculus
Ribosomal protein L8Aprotein244Oryctolagus cuniculus
Ribosomal protein uL3Bprotein394Oryctolagus cuniculus
Ribosomal protein uL4Cprotein367Oryctolagus cuniculus
Ribosomal protein uL18Dprotein292Oryctolagus cuniculus

46 more molecules are not listed.

Sequence of entity 1 (1), FASTA
>6FRK_1 Canis lupus familiaris RNA, 7SL, cytoplasmic 1 (RN7SL1), SRP RNA (chains 1)
GCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUGAGGCAGGAGGAU
CGCUUGAGCCCAGGAGUUCUGGGCUGCAGUGCGCUAUGCCGAUCGGGUGUCCGCACUAAG
UUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGG
UGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGUAGUGGGA
UCGCGCCUGUGAAUAGCCACUGCACUCCAGCCUGGGCAACAUAGCGAGACCCCGUCUCU
Sequence of entity 2 (2), FASTA
>6FRK_2 tRNA (chains 2)
GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUAACACGCGAAAGGUCCCCGGUUCGAAA
CCGGGCGGAAACACCA
Sequence of entity 3 (3), FASTA
>6FRK_3 Ribosomal protein eL28 (chains 3)
SAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHHKTVGVEPAADGKGVV
VVIKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKNKYRPDLRMAAIRRASAILRSQ
KPVMV
Sequence of entity 4 (4), FASTA
>6FRK_4 Ribosomal protein L12 (chains 4)
MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITV
KLTIQNRQAQIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRS
LARELSGTIKEILGTAQSVGCNVDGRHPHDIIDDINSGAVECP
Sequence of entity 5 (5), FASTA
>6FRK_5 28S ribosomal RNA (chains 5)
CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAG
AAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGA
AUCCCCGCCCCGCGGCGGGGCGCGGGACAUGUGGCGUACGGAAGACCCGCUCCCCGGCGC
CGCUCGUGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCG
GUAGCGGCCCCCGGCGCGCCGGGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCA
GCCCAAAGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAA
CAAGUACCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAA
CCGUUAAGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGC
GGGUCCGGCCGUGUCGGCGGCCCGGCGGAUCUUUCCCGCGCGGGGGACCGUCCCCCGACC
GGCGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCGCGACCGGCUCCGGG
ACGGCUGGGAAGGCCCGGCGGGGAAGGUGGCUCGGCCGAGUGUUACAGCCCCCCCGGCAG
CAGCACUCGCCGAAUCCCGGGGCCGAGGGAGCGAGACCCGUCGCCGCGCUCUCCCCCCUC
CCGGCGCCGCCGGGGGGGGCCGGGCCACCCCUCCCACGGCGCGACCGCUCGGGGCGGACU
GUCCCCAGUGCGCCCCGGGCGGGUCGCGCCGUCGGGCCCGGGGGAGGGGCCACGCGCGCG
UCCCCCGAAGAGGGGGACGGCGGAGCGAGCGCACGGGGUCGGCGGCGACGUCGGCUACCC
ACCCGACCCGUCUUGAAACACGGACCAAGGAGUCUAACACGUGCGCGAGUCGGGGGCUCG
CACGAAAGCCGCCGUGGCGCAAUGAAGGUGAAGGCCGGCGCGCUCGCCGGCCGAGGUGGG
AUCCCGAGGCCUCUCCAGUCCGCCGAGGGCGCACCACCGGCCCGUCUCGCCCGCCGCGCC
GGGGAGGUGGAGCACGAGCGCACGUGUUAGGACCCGAAAGAUGGUGAACUAUGCCUGGGC
AGGGCGAAGCCAGAGGAAACUCUGGUGGAGGUCCGUAGCGGUCCUGACGUGCAAAUCGGU
CGUCCGACCUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCCUCC
GAAGUUUCCCUCAGGAUAGCUGGCGCUCUCGCACACGCAGUUUUAUCCGGUAAAGCGAAU
GAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUCUCAAACUUUAAAUGGGUAAGA
AGCCCGGCUCGCUGGCGUGAGCCGGGCGUGGAAUGGAGUGCCUAGUGGGCCACUUUUGGU
AAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAGGCGCCCGAUGCCGACGC
UCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAUGGAAGU
CGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGAAAAUGG
AUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGCCGGCAGUCGAGAGUGGACGGGAG
CGGCGGGGGCGGCGCGCGCGCGCGCCCGCCCCCGGAGCCCCGCGGACGCUACGCCGCGAC
GAGUAGGAGGGCCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGC
CGCAGGUGCAGAUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAG
UGGAGAAGGGUUCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGG
CGAGCGCCGUUCCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCGGCCGAUCGAAAGGGA
GUCGGGUUCAGAUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGC
GGUAACGCGACCGAUCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUU
GUGAAGGGCAGGGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAA
GCGUCGCGGUUCCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGA
GGGUGUAAAUCUCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGC
CUCUGGCAUGUUGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGG
GAUAAGGAUUGGCUCUAAGGGCUGGGUCGGUCGUCGGCCGGCGCCUAGCAGCCGACUUAG
AACUGGUGCGGACCAGGGGAAUCCGACUGUUUAAUUAAAACAAAGCAUCGCGAAGGCCCG
CGGCGGGUGUUGACGCGAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAU
UCAAUGAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCC
UCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUGAACGAGAUUCCCACUGUCCCUACCUA
CUAUCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAUCAGCGGGGAAAGAAGAC
CCUGUUGAGCUUGACUCUAGUCUGGCACGGUGAAGAGACAUGUUUUUUCACUGACCCGGU
GAGGCGGGGGGGCGAGCCCCGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGGCCGCGCG
CCGGCCGGGCGCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACUGGGGCGGUA
CACCUGUCAAACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCC
GUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAAUACAGACCGUGA
AAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGGUGUCAGAAAAGU
UACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUC
CUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGUUCA
CCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCU
ACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGGUUCAG
ACAUUUGGUGUAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGGAUU
AUGACUGAACGCCUCUAAGUCAGAAUCCCGCCCAGGCGGAACGAUACGGCAGCGCCGCGG
AGCCUCGGUUGGCCUCGGAUAGCCGGUCCCCCGCGGGGUCCGGUGCGGAGUGCCCUUCGU
CCUGGGAAACGGGGCGCGGCCGGAGAGGCGGCCGCCCCCUCGCCCGUCACGCACGCCGUU
CGUGGGGAACCUGGCGCUAAACCAUUCGUAGACGACCUGCUUCUGGGUCGGGGUUUCGUA
CGUAGCAGAGCAGCUCGCUGCGAUCUAUUGAAAGUCAGCCCUCGACACAAGGGUUUGU
Sequence of entity 6 (6), FASTA
>6FRK_6 60S acidic ribosomal protein P0 (chains 6)
DRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNTMMRKA
IRGHLENNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLRANKVPAAARAGAIAPCEVTVP
AQNTGLGPEKTSFFQALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFS
FGLVIQQVFDNGSIYNPEVLDI
Sequence of entity 7 (7), FASTA
>6FRK_7 5S ribosomal RNA (chains 7)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU
Sequence of entity 8 (8), FASTA
>6FRK_8 5.8S ribosomal RNA (chains 8)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU
Sequence of entity 9 (A), FASTA
>6FRK_9 Ribosomal protein L8 (chains A)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGR
Sequence of entity 10 (B), FASTA
>6FRK_10 Ribosomal protein uL3 (chains B)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDSSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMIVVGIVGYVETPRGLRTFKTIFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDAAGAAALAADFSSMKAYCQVIRVIAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKD
Sequence of entity 11 (C), FASTA
>6FRK_11 Ribosomal protein uL4 (chains C)
ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQ
TSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKR
YAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVESYKKTKEAVLLLKKLKAWNDIK
KVYASQRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRNIPGITLLNVSKLNILKLA
PGGHVGRFCIWTESAFRKLDELYGTWRKAATLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKIRMDKAAAAAAAL
KAKSGEK
Sequence of entity 12 (D), FASTA
>6FRK_12 Ribosomal protein uL18 (chains D)
FVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDIIC
QIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQ
VEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPG
YDSESKEFNAEVHRKHILGQNVADYMRYLIEEDEDAYKKQFSQYIKNNVTPDMMEEMYKK
AHAAIRENPVYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERA

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg133
ZNZinc ionZn3
GTPGuanosine-5'-triphosphateC10 H16 N5 O14 P31
GNPPhosphoaminophosphonic acid-guanylate esterC10 H17 N6 O13 P32

Primary citation

Structure of a prehandover mammalian ribosomal SRP·SRP receptor targeting complex. Kobayashi, K., Jomaa, A., Lee, J.H. et al. Science (2018) 360:323-327. DOI 10.1126/science.aar7924 · PubMed

Other PDB entries of the same protein (UniProt J9PAS6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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