6ZVH: EDF1-ribosome complex

Name: PDB 6ZVH: EDF1-ribosome complex
Published: 2020-08-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

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

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