4V7I: Ribosome-SecY complex

Ribosome-SecY complex. Determined by electron microscopy at 9.6 Å resolution. Released 9 Jul 2014.

Method
Electron microscopy
Resolution
9.6 Å
Organisms
Escherichia coli, Methanocaldococcus jannaschii, Escherichia coli K-12
Chains
56
Atoms
148,250
Mol. weight
2233.34 kDa
Released
9 Jul 2014

Explore 4V7I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V7I contains 219 α-helices and 305 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 A0: 1 helix, 0 β-strands

ElementResiduesLengthSheet
α-helix9-157
Chain A1: 0 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand7-8217
β-strand10-12318
β-strand22-23217
β-strand37-39319
β-strand44-46319
β-strand48-50318
Chain A2: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix12-143
α-helix18-203
Chain A3: 5 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix7-104
β-strand14-15230
β-strand21-24430
α-helix37-415
β-strand46-48330
α-helix49-502
α-helix54-563
α-helix58-603
Chain A4: 1 helix, 2 β-strands
ElementResiduesLengthSheet
β-strand14133
β-strand27133
α-helix31-333
Chain A5: 8 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix6-127
β-strand20-21214
α-helix23-308
α-helix31-333
β-strand41-47714
β-strand66115
β-strand68115
β-strand75-78416
α-helix86-916
α-helix101-1044
β-strand113-116416
α-helix120-1234
α-helix154-1596
β-strand163-164214
β-strand170-177814
α-helix182-19817
β-strand212-216514
β-strand221-224414
Chain A6: 7 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand23120
α-helix30-323
β-strand33121
β-strand42122
β-strand48122
β-strand62121
β-strand80120
β-strand91-94423
β-strand100-103423
β-strand116-117224
β-strand127-128224
α-helix134-1352
β-strand140-142324
α-helix161-1622
β-strand163-165325
β-strand172-174325
β-strand180-182325
β-strand190-191224
α-helix193-1942
α-helix207-2115
α-helix241-2433
α-helix262-2643
β-strand266-268325
Chain AA: 15 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix5-84
β-strand1418
α-helix23-4018
β-strand4419
α-helix59-635
β-strand6919
α-helix76-9116
α-helix101-12828
α-helix137-16428
α-helix169-18719
α-helix192-20110
α-helix207-22418
β-strand237110
β-strand250110
α-helix263-28422
β-strand293111
β-strand301111
α-helix302-3065
α-helix320-34324
β-strand357112
β-strand359112
α-helix377-3837
α-helix392-40514
α-helix411-43020

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
5S ribosomal RNAA7RNA120Escherichia coli
23S ribosomal RNAA8RNA2904Escherichia coli
Preprotein translocase secy subunitAAprotein442Escherichia coli
Preprotein translocase sece subunitABprotein65Escherichia coli
Preprotein translocase subunit secGACprotein53Methanocaldococcus jannaschiiP60460 (AlphaFold model)
50S ribosomal protein L1A5protein234Escherichia coli K-12P0A7L0 (AlphaFold model)
50S ribosomal protein L2A6protein273Escherichia coli K-12P60422 (AlphaFold model)
50S ribosomal protein L3ADprotein209Escherichia coli K-12P60438 (AlphaFold model)
50S ribosomal protein L4AEprotein201Escherichia coli K-12P60723
50S ribosomal protein L5AFprotein179Escherichia coli K-12P62399
50S ribosomal protein L6AGprotein177Escherichia coli K-12P0AG55
50S ribosomal protein L9AHprotein149Escherichia coli K-12P0A7R1

44 more molecules are not listed.

Sequence of entity 1 (A7), FASTA
>4V7I_1 5S ribosomal RNA (chains A7)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU
Sequence of entity 2 (A8), FASTA
>4V7I_2 23S ribosomal RNA (chains A8)
GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUG
CUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAU
GGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCG
AACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC
AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAA
GCGUCUGGAAAGGCGCGCGAUACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGU
GAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUGAAUAUGGGGGGACCAUCCUC
CAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA
GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGC
ACGCUUAGGCGUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAG
CAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUCUUAACUGGGCGUUAAGUUGC
AGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU
AACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUG
AAAGGCCAAUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUC
GUGAAUUCAUCUCCGGGGGUAGAGCACUGUUUCGGCAAGGGGGUCAUCCCGACUUACCAA
CCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACACGGCGGGUGCUAA
CGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUA
AGUGGGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCA
UUUAAAGAAAGCGUAAUAGCUCACUGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGC
UAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUUGGGUAGGGGAGCGUUC
UGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGA
CAUAAGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCC
AACGUUAAUCGGGGCAGGGUGAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUG
GGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGGGGACGGAGAAGGCUAU
GUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCG
GAAAAUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUG
CUUCCAGGAAAAGCCUCUAAGCAUCAGGUAACAUCAAAUCGUACCCCAAACCGACACAGG
UGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAU
GGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG
CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGC
AAACACGAAAGUGGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUG
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAACCUU
Sequence of entity 3 (AA), FASTA
>4V7I_3 PREPROTEIN TRANSLOCASE SECY SUBUNIT (chains AA)
KKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWQT
ITASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFV
EAVLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQT
IFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRRRIVVNYAKRQ
QGRRVYAAQSTHLPLKVVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVD
GIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIKKSGA
FVPGIRPGEQTAKYIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIV
YRMYEQLLREKVSELHPAIAKL
Sequence of entity 4 (AB), FASTA
>4V7I_4 PREPROTEIN TRANSLOCASE SECE SUBUNIT (chains AB)
TKGKATVAFAREARTEVRKVIWPTRKPTKDEYLAVAKVTALGISLLGIIGYIIHVPATYI
KGILK
Sequence of entity 5 (AC), FASTA
>4V7I_5 Preprotein translocase subunit secG (chains AC)
MSKREETGLATSAGLIRYMDETFSKIRVKPEHVIGVTVAFVIIEAILTYGRFL
Sequence of entity 6 (A5), FASTA
>4V7I_6 50S ribosomal protein L1 (chains A5)
MAKLTKRMRVIREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVR
GATVLPHGTGRSVRVAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMNFDVVIASPDA
MRVVGQLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDF
DADKLKENLEALLVALKKAKPTQAKGVYIKKVSISTTMGAGVAVDQAGLSASVN
Sequence of entity 7 (A6), FASTA
>4V7I_7 50S ribosomal protein L2 (chains A6)
MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQ
AYRIVDFKRNKDGIPAVVERLEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGV
DAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGTYVQIVARDGAYVTLRLRSGE
MRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF
GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK
Sequence of entity 8 (AD), FASTA
>4V7I_8 50S ribosomal protein L3 (chains AD)
MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV
TKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAG
TVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRV
DAERNLLLVKGAVPGATGSDLIVKPAVKA
Sequence of entity 9 (AE), FASTA
>4V7I_9 50S ribosomal protein L4 (chains AE)
MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPW
RQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIV
VEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSL
IAFDKVVMTADAVKQVEEMLA
Sequence of entity 10 (AF), FASTA
>4V7I_10 50S ribosomal protein L5 (chains AF)
MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAI
SGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAK
SFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK
Sequence of entity 11 (AG), FASTA
>4V7I_11 50S ribosomal protein L6 (chains AG)
MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK
Sequence of entity 12 (AH), FASTA
>4V7I_12 50S ribosomal protein L9 (chains AH)
MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAE
VLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNG
VLRTTGEHEVSFQVHSEVFAKVIVNVVAE

Primary citation

Regulation of the protein-conducting channel by a bound ribosome. Gumbart, J., Trabuco, L.G., Schreiner, E. et al. Structure (2009) 17:1453-1464. DOI 10.1016/j.str.2009.09.010 · PubMed

Other PDB entries of the same protein (UniProt P60460 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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