6ZVI: Mbf1-ribosome complex
Mbf1-ribosome complex. Determined by electron microscopy at 3.0 Å resolution. Released 9 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 38
- Atoms
- 80,088
- Mol. weight
- 1179.64 kDa
- Ligands
- ZN
- Released
- 9 Sept 2020
Explore 6ZVI in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6ZVI contains 200 α-helices and 246 β-strands across 34 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: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 15-16 | 2 | 66 |
| β-strand | 21-22 | 2 | 66 |
| β-strand | 27 | 1 | 67 |
| α-helix | 28-32 | 5 | |
| β-strand | 36 | 1 | 68 |
| β-strand | 38 | 1 | 68 |
| α-helix | 42-49 | 8 | |
| β-strand | 57 | 1 | 67 |
| α-helix | 63-74 | 12 | |
| α-helix | 76-79 | 4 | |
| β-strand | 88-89 | 2 | 69 |
| β-strand | 97-98 | 2 | 69 |
| α-helix | 104-115 | 12 | |
| α-helix | 122-129 | 8 | |
Chain B: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-8 | 3 | |
| α-helix | 11-25 | 15 | |
| β-strand | 40 | 1 | 70 |
| α-helix | 53-67 | 15 | |
| β-strand | 71 | 1 | 71 |
| α-helix | 73-80 | 8 | |
| β-strand | 83-86 | 4 | 72 |
| β-strand | 89-93 | 5 | 72 |
| β-strand | 96 | 1 | 70 |
| α-helix | 98-111 | 14 | |
| β-strand | 114-116 | 3 | 71 |
| β-strand | 122-124 | 3 | 71 |
| α-helix | 126-140 | 15 | |
Chain C: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-21 | 2 | 73 |
| β-strand | 23-28 | 6 | 74 |
| α-helix | 31-47 | 17 | |
| β-strand | 56-57 | 2 | 74 |
| α-helix | 58-60 | 3 | |
| β-strand | 61-65 | 5 | 75 |
| β-strand | 82-86 | 5 | 75 |
| β-strand | 87-91 | 5 | 74 |
| β-strand | 94-95 | 2 | 73 |
| α-helix | 97-106 | 10 | |
| β-strand | 112-117 | 6 | 74 |
Chain D: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2 | 1 | 76 |
| β-strand | 8 | 1 | 76 |
| α-helix | 13-15 | 3 | |
| β-strand | 16 | 1 | 77 |
| β-strand | 23 | 1 | 77 |
| β-strand | 32-37 | 6 | 78 |
| β-strand | 40 | 1 | 79 |
| β-strand | 43 | 1 | 79 |
| α-helix | 45-46 | 2 | |
| β-strand | 50-55 | 6 | 78 |
| α-helix | 57-62 | 6 | |
| α-helix | 65-74 | 10 | |
Chain E: 4 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-20 | 15 | |
| β-strand | 24-27 | 4 | 50 |
| α-helix | 32-43 | 12 | |
| β-strand | 50-54 | 5 | 50 |
| β-strand | 60-64 | 5 | 50 |
| β-strand | 72-74 | 3 | 80 |
| β-strand | 80-81 | 2 | 80 |
| α-helix | 86-93 | 8 | |
| β-strand | 96 | 1 | 81 |
| β-strand | 99 | 1 | 81 |
| β-strand | 101-106 | 6 | 80 |
| β-strand | 109-112 | 4 | 80 |
| α-helix | 113-117 | 5 | |
| β-strand | 123-129 | 7 | 80 |
Chain H: 6 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-23 | 12 | |
| α-helix | 27-34 | 8 | |
| α-helix | 36-39 | 4 | |
| β-strand | 48-57 | 10 | 1 |
| β-strand | 60 | 1 | 2 |
| α-helix | 61-62 | 2 | |
| β-strand | 68 | 1 | 2 |
| β-strand | 71-76 | 6 | 1 |
| β-strand | 82-86 | 5 | 1 |
| α-helix | 92-95 | 4 | |
| β-strand | 103-106 | 4 | 1 |
| β-strand | 122-126 | 5 | 1 |
| β-strand | 127 | 1 | 3 |
| β-strand | 131 | 1 | 3 |
| α-helix | 133-137 | 5 | |
Chain i: 12 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-7 | 3 | |
| α-helix | 14-19 | 6 | |
| β-strand | 24 | 1 | 9 |
| α-helix | 31-36 | 6 | |
| β-strand | 37-40 | 4 | 9 |
| α-helix | 42-44 | 3 | |
| β-strand | 46-48 | 3 | 9 |
| α-helix | 50-64 | 15 | |
| α-helix | 70-72 | 3 | |
| β-strand | 73-77 | 5 | 10 |
| α-helix | 80-82 | 3 | |
| α-helix | 83-87 | 5 | |
| α-helix | 89-92 | 4 | |
| β-strand | 97-99 | 3 | 10 |
| β-strand | 120-123 | 4 | 10 |
| α-helix | 130-136 | 7 | |
| β-strand | 143-145 | 3 | 10 |
| β-strand | 159 | 1 | 10 |
| α-helix | 167-183 | 17 | |
| α-helix | 199-202 | 4 | |
Chain I: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-15 | 10 | 4 |
| α-helix | 16-18 | 3 | |
| β-strand | 20-28 | 9 | 4 |
| α-helix | 37-48 | 12 | |
| β-strand | 55-57 | 3 | 4 |
| β-strand | 61-62 | 2 | 4 |
| α-helix | 63 | 1 | |
| β-strand | 69-76 | 8 | 4 |
| α-helix | 80-84 | 5 | |
| α-helix | 88-93 | 6 | |
| α-helix | 105-115 | 11 | |
| α-helix | 123-134 | 12 | |
26 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| A/P-site tRNA | d | RNA | 76 | Saccharomyces cerevisiae | |
| P/E-site tRNA | e | RNA | 77 | Saccharomyces cerevisiae | |
| mRNA | f | RNA | 35 | Saccharomyces cerevisiae | |
| 18S rRNA | h | RNA | 1758 | Saccharomyces cerevisiae | |
| 40S ribosomal protein S0-A | i | protein | 206 | Saccharomyces cerevisiae | P32905 (AlphaFold model) |
| RPS1A isoform 1 | j | protein | 216 | Saccharomyces cerevisiae | P33442 (AlphaFold model) |
| RPS2 isoform 1 | k | protein | 217 | Saccharomyces cerevisiae | P25443 (AlphaFold model) |
| RPS3 isoform 1 | l | protein | 223 | Saccharomyces cerevisiae | P05750 (AlphaFold model) |
| 40S ribosomal protein S4-A | m | protein | 260 | Saccharomyces cerevisiae | P0CX35 |
| Rps5p | n | protein | 206 | Saccharomyces cerevisiae | P26783 |
| 40S ribosomal protein S6-A | o | protein | 218 | Saccharomyces cerevisiae | P0CX37 |
| 40S ribosomal protein S7-A | p | protein | 185 | Saccharomyces cerevisiae | P26786 |
26 more molecules are not listed.
Sequence of entity 1 (d), FASTA
>6ZVI_1 A/P-site tRNA (chains d)
GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUAGGAAUCCCCGUGUCCUUGGUUCGAUU
CCGAGUCCGGGCACCA
Sequence of entity 2 (e), FASTA
>6ZVI_2 P/E-site tRNA (chains e)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA
Sequence of entity 3 (f), FASTA
>6ZVI_3 mRNA (chains f)
UUUUUUUUUUUUGACAAAUUUUUUUUUUAAACUGG
Sequence of entity 4 (h), FASTA
>6ZVI_4 18S rRNA (chains h)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAA
AAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCU
UUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAA
AUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAA
CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGA
AGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACG
AUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGG
AACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAU
AUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCGG
AUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUGUGGCUCUUGGCGAACCA
GGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAUUGCUCGAAUAUAUUAG
CAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAU
GAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUU
UAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGA
AAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGAC
UAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCU
UUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCA
CCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCA
GACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUG
GCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAA
CCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUUAGAGGGACUAUCGGUU
UCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCC
GCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGCCGAGAGGUCUUGGUAAU
CUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAA
UUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACC
GCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUCUGCAGAGCGGAGAA
UUUGGACAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAA
CCUGCGGAAGGAUCAUUA
Sequence of entity 5 (i), FASTA
>6ZVI_5 40S ribosomal protein S0-A (chains i)
SLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAA
RIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALVDRTQPWSIMPDLYFYRDP
Sequence of entity 6 (j), FASTA
>6ZVI_6 RPS1A isoform 1 (chains j)
VVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDALKGRVVEVCLADLQGSEDH
SFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLIEANVTVKTSDDYVLRIFA
IAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTLAQLTSKLIPEVINKEIEN
ATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEG
Sequence of entity 7 (k), FASTA
>6ZVI_7 RPS2 isoform 1 (chains k)
GWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKA
AFVAIGNTYGFLTPNLWAEQPLPVSPLDIYSDEASAQ
Sequence of entity 8 (l), FASTA
>6ZVI_8 RPS3 isoform 1 (chains l)
ALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGEN
GRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGV
VRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVL
GIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDY
Sequence of entity 9 (m), FASTA
>6ZVI_9 40S ribosomal protein S4-A (chains m)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQGL
Sequence of entity 10 (n), FASTA
>6ZVI_10 Rps5p (chains n)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR
Sequence of entity 11 (o), FASTA
>6ZVI_11 40S ribosomal protein S6-A (chains o)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSE
Sequence of entity 12 (p), FASTA
>6ZVI_12 40S ribosomal protein S7-A (chains p)
APQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIFV
PVPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAVH
DKILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIV
FEIPS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
EDF1 coordinates cellular responses to ribosome collisions. Sinha, N.K., Ordureau, A., Best, K. et al. Elife (2020) 9. DOI 10.7554/eLife.58828 · PubMed
Other PDB entries of the same protein (UniProt P32905 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9PN5 1.75 Å, Composite map of hypomethylated 80S ribosome treated with hygromycin B
- 8CCS 1.97 Å, 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
- 8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
- 8CEH 2.05 Å, Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2…
- 8EVT 2.2 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
- 8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
- 8CGN 2.28 Å, Non-rotated 80S S. cerevisiae ribosome with ligands
- 8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
- 8EVP 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
- 9DP7 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
- 7ZW0 2.4 Å, FAP-80S Complex - Rotated state
- 8BN3 2.4 Å, Yeast 80S, ES7s delta, eIF5A, Stm1 containing
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