6ZVH: EDF1-ribosome complex
EDF1-ribosome complex. Determined by electron microscopy at 2.9 Å resolution. Released 19 Aug 2020.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organism
- Homo sapiens
- Chains
- 37
- Atoms
- 79,014
- Mol. weight
- 1169.79 kDa
- Ligands
- MG, ZN
- Released
- 19 Aug 2020
Explore 6ZVH in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6ZVH contains 209 α-helices and 252 β-strands across 35 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 | 20-22 | 3 | 58 |
| β-strand | 28 | 1 | 59 |
| β-strand | 29-31 | 3 | 58 |
| β-strand | 36-40 | 5 | 60 |
| β-strand | 43 | 1 | 61 |
| α-helix | 47-49 | 3 | |
| α-helix | 50-56 | 7 | |
| β-strand | 57 | 1 | 4 |
| α-helix | 63-65 | 3 | |
| β-strand | 66 | 1 | 61 |
| β-strand | 69-73 | 5 | 60 |
| α-helix | 75-80 | 6 | |
| α-helix | 89-92 | 4 | |
| α-helix | 96-99 | 4 | |
Chain A: 8 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-21 | 9 | |
| β-strand | 25 | 1 | 1 |
| β-strand | 38-41 | 4 | 1 |
| β-strand | 47-49 | 3 | 1 |
| α-helix | 51-66 | 16 | |
| α-helix | 71-73 | 3 | |
| β-strand | 74-78 | 5 | 2 |
| α-helix | 84-94 | 11 | |
| β-strand | 97-100 | 4 | 2 |
| β-strand | 121-124 | 4 | 2 |
| α-helix | 131-139 | 9 | |
| β-strand | 144-146 | 3 | 2 |
| β-strand | 147 | 1 | 3 |
| β-strand | 161 | 1 | 3 |
| α-helix | 168-185 | 18 | |
| α-helix | 199-202 | 4 | |
| α-helix | 207-222 | 16 | |
Chain b: 1 helix, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-17 | 6 | |
| β-strand | 32-36 | 5 | 27 |
| β-strand | 43-47 | 5 | 27 |
| β-strand | 55 | 1 | 28 |
| β-strand | 62 | 1 | 28 |
| β-strand | 64-65 | 2 | 29 |
| β-strand | 72-73 | 2 | 29 |
| β-strand | 78-81 | 4 | 27 |
Chain B: 9 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-26 | 3 | |
| β-strand | 28-34 | 7 | 5 |
| β-strand | 43-50 | 8 | 5 |
| α-helix | 51-52 | 2 | |
| β-strand | 53 | 1 | 6 |
| β-strand | 56 | 1 | 6 |
| α-helix | 58-62 | 5 | |
| β-strand | 66 | 1 | 5 |
| β-strand | 69-70 | 2 | 7 |
| β-strand | 82-84 | 3 | 7 |
| β-strand | 87-91 | 5 | 5 |
| β-strand | 95-99 | 5 | 5 |
| β-strand | 102-105 | 4 | 7 |
| α-helix | 107-113 | 7 | |
| β-strand | 118 | 1 | 8 |
| β-strand | 120-127 | 8 | 7 |
| β-strand | 135-142 | 8 | 7 |
| β-strand | 143 | 1 | 9 |
| β-strand | 154 | 1 | 8 |
| α-helix | 158-176 | 19 | |
| α-helix | 181-188 | 8 | |
| α-helix | 192-200 | 9 | |
| α-helix | 201-203 | 3 | |
| β-strand | 207 | 1 | 9 |
| β-strand | 211-217 | 7 | 7 |
| α-helix | 225-232 | 8 | |
Chain c: 0 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-14 | 5 | 62 |
| β-strand | 20-21 | 2 | 26 |
| β-strand | 27-29 | 3 | 26 |
| β-strand | 32-33 | 2 | 62 |
| β-strand | 41-42 | 2 | 62 |
| β-strand | 45-47 | 3 | 26 |
| β-strand | 55-58 | 4 | 62 |
Chain C: 13 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-71 | 7 | |
| α-helix | 79-83 | 5 | |
| α-helix | 86-88 | 3 | |
| α-helix | 91-97 | 7 | |
| β-strand | 103-116 | 14 | 70 |
| β-strand | 119-131 | 13 | 70 |
| β-strand | 136-137 | 2 | 71 |
| β-strand | 138-144 | 7 | 70 |
| α-helix | 147-160 | 14 | |
| β-strand | 163-164 | 2 | 71 |
| β-strand | 168 | 1 | 72 |
| β-strand | 179 | 1 | 72 |
| β-strand | 184-188 | 5 | 73 |
| β-strand | 191-197 | 7 | 73 |
| β-strand | 204-205 | 2 | 73 |
| α-helix | 208-217 | 10 | |
| β-strand | 222-227 | 6 | 73 |
| α-helix | 233-249 | 17 | |
| α-helix | 253-255 | 3 | |
| α-helix | 258-259 | 2 | |
| α-helix | 262-264 | 3 | |
| α-helix | 265-268 | 4 | |
| α-helix | 270-272 | 3 | |
| α-helix | 273-277 | 5 | |
Chain d: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 30-31 | 2 | 63 |
| α-helix | 33-35 | 3 | |
| β-strand | 38-39 | 2 | 63 |
| α-helix | 40-50 | 11 | |
| β-strand | 53-54 | 2 | 54 |
Chain D: 10 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-28 | 22 | |
| α-helix | 30-32 | 3 | |
| β-strand | 37-40 | 4 | 12 |
| β-strand | 46-50 | 5 | 12 |
| α-helix | 64-76 | 13 | |
| α-helix | 79-80 | 2 | |
| β-strand | 84-88 | 5 | 12 |
| α-helix | 90-91 | 2 | |
| α-helix | 94-96 | 3 | |
| α-helix | 98-111 | 14 | |
| α-helix | 115-129 | 15 | |
| β-strand | 133-140 | 8 | 13 |
| β-strand | 148-151 | 4 | 13 |
| β-strand | 154-155 | 2 | 13 |
| β-strand | 168-176 | 9 | 13 |
| β-strand | 181-189 | 9 | 13 |
| α-helix | 190-191 | 2 | |
| β-strand | 209-210 | 2 | 14 |
| α-helix | 211-213 | 3 | |
| β-strand | 223 | 1 | 15 |
| β-strand | 226 | 1 | 16 |
27 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 |
|---|
| 18S rRNA | 2 | RNA | 1740 | Homo sapiens | |
| 40S ribosomal protein SA | A | protein | 221 | Homo sapiens | P08865 (AlphaFold model) |
| 40S ribosomal protein S3a | B | protein | 264 | Homo sapiens | P61247 (AlphaFold model) |
| 40S ribosomal protein S3 | D | protein | 227 | Homo sapiens | P23396 (AlphaFold model) |
| 40S ribosomal protein S4, X isoform | E | protein | 262 | Homo sapiens | P62701 (AlphaFold model) |
| 40S ribosomal protein S5 | F | protein | 189 | Homo sapiens | P46782 |
| 40S ribosomal protein S7 | H | protein | 189 | Homo sapiens | P62081 |
| 40S ribosomal protein S8 | I | protein | 206 | Homo sapiens | P62241 |
| 40S ribosomal protein S10 | K | protein | 98 | Homo sapiens | P46783 |
| 40S ribosomal protein S11 | L | protein | 153 | Homo sapiens | P62280 |
| 40S ribosomal protein S15 | P | protein | 129 | Homo sapiens | P62841 |
| 40S ribosomal protein S16 | Q | protein | 144 | Homo sapiens | P62249 |
25 more molecules are not listed.
Sequence of entity 1 (2), FASTA
>6ZVH_1 18S rRNA (chains 2)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCCACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGUGGUGACUCUAGAUA
ACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAU
CAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGG
UUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGC
GCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUU
UCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUCCGCGAGGAUCCAUUGGAGG
GCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCU
GCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGUCCCCGCCCUCUCGGCCGGGG
CCCGAAGCAUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUA
CCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAG
GCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUU
GGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAG
AACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUG
CCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAA
AGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAA
GGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCG
GCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGU
GCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAC
UCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAG
GGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAU
GUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCA
GGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCC
AUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCC
UUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGG
CCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUA
UCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
Sequence of entity 2 (A), FASTA
>6ZVH_2 40S ribosomal protein SA (chains A)
GALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAA
RAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLL
VVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREV
LRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVT
Sequence of entity 3 (B), FASTA
>6ZVH_3 40S ribosomal protein S3a (chains B)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV
Sequence of entity 4 (D), FASTA
>6ZVH_4 40S ribosomal protein S3 (chains D)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQK
Sequence of entity 5 (E), FASTA
>6ZVH_5 40S ribosomal protein S4, X isoform (chains E)
ARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEV
KKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKY
KLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNLC
MVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPRG
KGIRLTIAEERDKRLAAKQSSG
Sequence of entity 6 (F), FASTA
>6ZVH_6 40S ribosomal protein S5 (chains F)
DIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIVERLTNS
MMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGTVR
RQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINAAKGSSNSYAIKKKDE
LERVAKSNR
Sequence of entity 7 (H), FASTA
>6ZVH_7 40S ribosomal protein S7 (chains H)
SAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFV
PVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTA
VHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKD
VNFEFPEFQ
Sequence of entity 8 (I), FASTA
>6ZVH_8 40S ribosomal protein S8 (chains I)
GISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLD
VGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPL
GRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQ
CGRADGYVLEGKELEFYLRKIKARKG
Sequence of entity 9 (K), FASTA
>6ZVH_9 40S ribosomal protein S10 (chains K)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSR
Sequence of entity 10 (L), FASTA
>6ZVH_10 40S ribosomal protein S11 (chains L)
ADIQTERAYQKQPTIFQNKKRVLLGETGKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCP
FTGNVSIRGRILSGVVTKMKMQRTIVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQ
IGDIVTVGECRPLSKTVRFNVLKVTKAAGTKKQ
Sequence of entity 11 (P), FASTA
>6ZVH_11 40S ribosomal protein S15 (chains P)
RTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRLRKAKKEAPP
MEKPEVVKTHLRDMIILPEMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHG
RPGIGATHS
Sequence of entity 12 (Q), FASTA
>6ZVH_12 40S ribosomal protein S16 (chains Q)
SKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKER
FAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVA
DPRRCESKKFGGPGARARYQKSYR
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 30 |
| ZN | Zinc ion | Zn | 3 |
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 P08865 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
- 8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
- 9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
- 8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline
- 9C3H 2.0 Å, Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.
- 29IZ 2.08 Å, Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2
- 9TV2 2.1 Å, 80S ribosomes from primary B-cells infected with delta v-snoRNA1 EBV
- 3BCH 2.15 Å, Crystal Structure of the Human Laminin Receptor Precursor
- 7R4X 2.15 Å, Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map
- 9I2D 2.19 Å, NMT1-NAC bound human RNC with 10 amino acid ARF1-linker
- 9PBE 2.19 Å, In situ human 80S ribosome (composite map)
- 8YOP 2.2 Å, Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline
Browse structure collections
About this viewer
MolViewer shows 6ZVH directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.