8R3V: Escherichia coli paused disome complex

Escherichia coli paused disome complex (non-rotated disome interface). Determined by electron microscopy at 3.28 Å resolution. Released 6 Mar 2024.

Method
Electron microscopy
Resolution
3.28 Å
Organism
Escherichia coli
Chains
65
Atoms
188,607
Mol. weight
3882.83 kDa
Ligands
ALA, MG, SPD, PUT
Released
6 Mar 2024

Explore 8R3V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R3V contains 269 α-helices and 292 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 12: 2 helices, 4 β-strands

ElementResiduesLengthSheet
β-strand13-1751
β-strand25-2951
β-strand33-4082
β-strand45-5282
α-helix53-6210
α-helix64-7411
Chain 32: 2 helices, 3 β-strands
ElementResiduesLengthSheet
β-strand3-865
α-helix17-2610
β-strand34-3855
α-helix41-499
β-strand54-5745
Chain 4: 2 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix7-82
β-strand10-1457
β-strand22-2657
α-helix56-638
Chain 62: 5 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix3-64
α-helix8-114
β-strand15-16212
β-strand22-24312
α-helix38-447
β-strand48-49212
α-helix50-512
α-helix55-617
Chain a2: 5 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix6-149
α-helix23-3311
β-strand4119
β-strand43-48610
α-helix55-573
β-strand60-64511
β-strand160-164511
β-strand170-171210
β-strand17719
α-helix182-19918
β-strand209-215710
α-helix219-2213
β-strand222-224310
Chain B: 12 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix8-125
β-strand16-19435
α-helix20-223
α-helix25-306
α-helix35-373
β-strand38-40335
α-helix43-6321
β-strand69136
α-helix74-8613
α-helix104-11916
α-helix133-14816
α-helix152-1543
β-strand161-162236
β-strand165137
α-helix167-1693
α-helix170-1778
β-strand183-184236
β-strand185138
β-strand187137
β-strand199138
α-helix208-22922
Chain b2: 9 helices, 29 β-strands
ElementResiduesLengthSheet
β-strand3-5314
α-helix6-72
β-strand17-19314
β-strand24115
α-helix31-333
β-strand34-35216
β-strand43117
β-strand49117
β-strand54118
α-helix611
β-strand62-63216
β-strand65115
β-strand76-82715
β-strand91-96615
β-strand101-105515
β-strand107119
β-strand115-116215
β-strand118120
β-strand129-131320
α-helix132-1343
α-helix1361
β-strand140-142320
β-strand144-145221
β-strand152-154321
β-strand162-168720
β-strand171-175520
β-strand181-185520
β-strand189-192420
β-strand195119
α-helix198-2025
β-strand204114
α-helix208-2136
β-strand216118
α-helix222-2243
β-strand245122
β-strand251122
α-helix264-2663
β-strand267-269320
Chain B2: 9 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix6-127
β-strand16-19440
α-helix25-306
β-strand31141
β-strand35140
β-strand38-40340
β-strand41141
α-helix43-6220
β-strand67-70442
α-helix74-8613
β-strand90-92342
α-helix104-12320
α-helix125-1295
α-helix133-14715
β-strand160-163442
α-helix172-1798
β-strand183-185342
β-strand199142
α-helix207-22822

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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
50S ribosomal protein L2812protein78Escherichia coliP0A7M2 (AlphaFold model)
50S ribosomal protein L3032protein59Escherichia coliP0AG51 (AlphaFold model)
Large ribosomal subunit protein bL31A4protein70Escherichia coliP0A7M9 (AlphaFold model)
50S ribosomal protein L3562protein65Escherichia coliP0A7Q1 (AlphaFold model)
23S ribosomal RNA71, 72RNA2904Escherichia coli
5S ribosomal RNA82RNA120Escherichia coli
16S ribosomal RNAA1, A2RNA1542Escherichia coli
Small ribosomal subunit protein uS2B, B2protein241Escherichia coliP0A7V0
Small ribosomal subunit protein uS3C1, C2protein233Escherichia coliP0A7V3
Small ribosomal subunit protein uS4D1, D2protein206Escherichia coliP0A7V8
Small ribosomal subunit protein uS5E1, E2protein167Escherichia coliP0A7W1
30S ribosomal protein S6F1, F2protein135Escherichia coliP02358

33 more molecules are not listed.

Sequence of entity 1 (12), FASTA
>8R3V_1 50S ribosomal protein L28 (chains 12)
MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVID
KKGIDTVLAELRARGEKY
Sequence of entity 2 (32), FASTA
>8R3V_2 50S ribosomal protein L30 (chains 32)
MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE
Sequence of entity 3 (4), FASTA
>8R3V_3 Large ribosomal subunit protein bL31A (chains 4)
MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRF
NKRFNIPGSK
Sequence of entity 4 (62), FASTA
>8R3V_4 50S ribosomal protein L35 (chains 62)
MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA
CLPYA
Sequence of entity 5 (71, 72), FASTA
>8R3V_5 23S ribosomal RNA (chains 71, 72)
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
GGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACXAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUG
AUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUG
UACCCGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUG
AGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGC
CGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUGACCCGUAAUCCGGGUU
GCGGACAGUGUCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCUAAAGAGUAACGGAGG
AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCA
GCUUGACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGG
UUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAU
ACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUC
CUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCU
GGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAG
GGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCA
UGCCAAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGC
ACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGA
AGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUAC
UAAUGAACCGUGAGGCUUAAUCUU
Sequence of entity 6 (82), FASTA
>8R3V_6 5S ribosomal RNA (chains 82)
UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAAC
GCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU
Sequence of entity 7 (A1, A2), FASTA
>8R3V_7 16S ribosomal RNA (chains A1, A2)
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAA
GUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAA
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAU
AACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
GGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGA
GGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
GGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCU
UCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUU
GACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAG
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCA
GAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUC
GUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACC
GGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCA
AACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCC
CUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCA
AGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAU
UCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAG
AAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGA
AAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGC
CGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUC
AUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCG
ACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAAC
UCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGU
UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGU
AGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAA
CAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA
Sequence of entity 8 (B, B2), FASTA
>8R3V_8 Small ribosomal subunit protein uS2 (chains B, B2)
MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKI
ASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQ
SQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLG
IPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEA
E
Sequence of entity 9 (C1, C2), FASTA
>8R3V_9 Small ribosomal subunit protein uS3 (chains C1, C2)
MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP
AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI
TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA
DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK
Sequence of entity 10 (D1, D2), FASTA
>8R3V_10 Small ribosomal subunit protein uS4 (chains D1, D2)
MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQK
VRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSH
KAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEG
TFKRKPERSDLSADINEHLIVELYSK
Sequence of entity 11 (E1, E2), FASTA
>8R3V_11 Small ribosomal subunit protein uS5 (chains E1, E2)
MAHIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAI
QKAMEKARRNMINVALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGV
HNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK
Sequence of entity 12 (F1, F2), FASTA
>8R3V_12 30S ribosomal protein S6 (chains F1, F2)
MRHYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYV
LMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANET
ADDAEAGDSEEEEEE

Ligands and cofactors

IDNameFormulaCopies
ALAAlanineC3 H7 N O21
MGMagnesium ionMg297
SPDSpermidineC7 H19 N31
PUT1,4-diaminobutaneC4 H12 N22
ZNZinc ionZn2

Primary citation

Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM. Flugel, T., Schacherl, M., Unbehaun, A. et al. Nat Commun (2024) 15:1756-1756. DOI 10.1038/s41467-024-46092-3 · PubMed

Other PDB entries of the same protein (UniProt P0A7M2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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