4V9H: Ribosome

Name: PDB 4V9H: Crystal structure of the ribosome bound to elongation factor G in the guanosine triphosphatase state
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal structure of the ribosome bound to elongation factor G in the guanosine triphosphatase state. Determined by X-ray diffraction at 2.86 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 2.86 Å
Organisms: Thermus thermophilus, Escherichia coli, Synthetic construct
Chains: 58
Atoms: 151,831
Mol. weight: 2306.03 kDa
Ligands: MG, GCP
Released: 9 Jul 2014

Explore 4V9H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V9H contains 255 α-helices and 365 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 AB: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-13	5
α-helix	26-31	6
β-strand	32-36	5	62
β-strand	39-42	4	62
α-helix	44-62	19
β-strand	68-71	4	63
α-helix	78-86	9
β-strand	92-93	2	63
α-helix	105-119	15
α-helix	132-148	17
β-strand	161-164	4	63
α-helix	171-180	10
β-strand	184-186	3	63
α-helix	194-196	3
β-strand	199-200	2	63
α-helix	208-226	19

Chain AC: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	66
α-helix	26-46	21
β-strand	52-59	8	66
β-strand	64-70	7	66
α-helix	73-77	5
α-helix	83-94	12
β-strand	99-105	7	66
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-143	14
β-strand	148-153	6	67
α-helix	157-159	3
β-strand	166	1	67
β-strand	169-171	3	67
β-strand	182-191	10	67
β-strand	194-203	10	67

Chain AD: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
α-helix	48-52	5
α-helix	53-68	16
α-helix	72-84	13
α-helix	89-97	9
β-strand	100	1	68
α-helix	101-107	7
α-helix	114-122	9
β-strand	126-128	3	69
β-strand	131-132	2	69
α-helix	138	1
β-strand	139	1	68
α-helix	140	1
β-strand	144-148	5	69
α-helix	156-164	9
α-helix	168-170	3
β-strand	174-177	4	69
β-strand	182-185	4	69
α-helix	201-206	6

Chain AE: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9-20	12	79
β-strand	23-35	13	79
β-strand	40-48	9	79
α-helix	51-63	13
β-strand	66-68	3	79
β-strand	72	1	80
β-strand	75	1	80
β-strand	80-84	5	81
β-strand	87-93	7	81
β-strand	100-101	2	81
α-helix	104-113	10
β-strand	118-124	7	81
α-helix	128-140	13
α-helix	145-151	7

Chain AF: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	83
α-helix	16-32	17
β-strand	36-40	5	83
β-strand	44-52	9	83
β-strand	55-67	13	83
α-helix	69-71	3
α-helix	72-81	10
β-strand	85-92	8	83
β-strand	98-99	2	48

Chain AG: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	12-15	4
α-helix	21-30	10
α-helix	36-52	17
α-helix	58-69	12
β-strand	73-79	7	86
β-strand	84-90	7	86
α-helix	93-108	16
α-helix	116-128	13
α-helix	133-142	10
α-helix	149-154	6

Chain AH: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	23-27	5	88
α-helix	30-41	12
β-strand	45-53	9	88
β-strand	56-63	8	88
β-strand	65	1	89
α-helix	75-77	3
β-strand	78	1	89
β-strand	83-85	3	90
β-strand	88	1	91
β-strand	91	1	91
β-strand	94-95	2	90
α-helix	97-99	3
α-helix	100-103	4
α-helix	104-106	3
β-strand	109-114	6	90
β-strand	117-120	4	90
α-helix	121-127	7
β-strand	131-137	7	90

Chain AI: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	95
β-strand	13-21	9	95
β-strand	26-28	3	95
β-strand	31-32	2	95
α-helix	33-36	4
α-helix	43-47	5
α-helix	48-51	4
β-strand	59-66	8	95
α-helix	70-87	18
α-helix	109-112	4
α-helix	122-124	3

45 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
16S ribosomal RNA	AA	RNA	1516	Thermus thermophilus
PE hybrid state tRNA Phe	AV	RNA	76	Escherichia coli
mRNA	AX	RNA	25	Synthetic construct
30S ribosomal protein S10	AJ	protein	98	Thermus thermophilus	Q5SHN7 (AlphaFold model)
30S ribosomal protein S11	AK	protein	119	Thermus thermophilus	P80376 (AlphaFold model)
30S ribosomal protein S12	AL	protein	124	Thermus thermophilus	Q5SHN3 (AlphaFold model)
30S ribosomal protein S13	AM	protein	124	Thermus thermophilus	P80377 (AlphaFold model)
30S ribosomal protein S14 TYPE Z	AN	protein	60	Thermus thermophilus	P0DOY6
30S ribosomal protein S15	AO	protein	88	Thermus thermophilus	Q5SJ76
30S ribosomal protein S16	AP	protein	83	Thermus thermophilus	Q5SJH3
30S ribosomal protein S17	AQ	protein	99	Thermus thermophilus	P0DOY7
30S ribosomal protein S18	AR	protein	70	Thermus thermophilus	Q5SLQ0

46 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>4V9H_1 16S ribosomal RNA (chains AA)
UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCG
UGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGA
CCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGC
CCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCU
AGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCG
GCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUC
CGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGU
AAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGC
GCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUU
CACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCA
ACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCC
GGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUG
GUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGU
AGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACG
CGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGG
GGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAG
GCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAG
CACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAA
CGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCC
CGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGC
GACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCG
CAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCG
CUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGC
CCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCG
AGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGC
UGGAUCACCUCCUUUC

Sequence of entity 2 (AV), FASTA

>4V9H_2 PE hybrid state tRNA Phe (chains AV)
GCCCGGAUAGCUCAGUCGGUAGAGCAGGGGAUUGAAAAUCCCCGUGUCCUUGGUUCGAUU
CCGAGUCCGGGCACCA

Sequence of entity 3 (AX), FASTA

>4V9H_3 mRNA (chains AX)
GGCAAGGAGGUAAAAAUGUUCAAAA

Sequence of entity 4 (AJ), FASTA

>4V9H_4 30S ribosomal protein S10 (chains AJ)
KIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSREH
FELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKT

Sequence of entity 5 (AK), FASTA

>4V9H_5 30S ribosomal protein S11 (chains AK)
KRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYAAQLAALDAAK
KAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCRPKKKFRKAS

Sequence of entity 6 (AL), FASTA

>4V9H_6 30S ribosomal protein S12 (chains AL)
PTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGY
EVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKK
PKEA

Sequence of entity 7 (AM), FASTA

>4V9H_7 30S ribosomal protein S13 (chains AM)
ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVE
NTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKK
KAPR

Sequence of entity 8 (AN), FASTA

>4V9H_8 30S ribosomal protein S14 TYPE Z (chains AN)
ARKALIEKAKRTPKFKVRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKASW

Sequence of entity 9 (AO), FASTA

>4V9H_9 30S ribosomal protein S15 (chains AO)
PITKEEKQKVIQEFARFPGDTGSTEVQVALLTLRINRLSEHLKVHKKDHHSHRGLLMMVG
QRRRLLRYLQREDPERYRALIEKLGIRG

Sequence of entity 10 (AP), FASTA

>4V9H_10 30S ribosomal protein S16 (chains AP)
MVKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLKVDVERARYWL
SVGAQPTDTARRLLRQAGVFRQE

Sequence of entity 11 (AQ), FASTA

>4V9H_11 30S ribosomal protein S17 (chains AQ)
PKKVLTGVVVSDKMQKTVTVLVERQFPHPLYGKVIKRSKKYLAHDPEEKYKLGDVVEIIE
SRPISKRKRFRVLRLVESGRMDLVEKYLIRRQNYESLSK

Sequence of entity 12 (AR), FASTA

>4V9H_12 30S ribosomal protein S18 (chains AR)
KAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSAKEQRILAKTIKRARILGL
LPFTEKLVRK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	138
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1

Primary citation

Elongation factor G bound to the ribosome in an intermediate state of translocation. Tourigny, D.S., Fernandez, I.S., Kelley, A.C. et al. Science (2013) 340:1235490-1235490. DOI 10.1126/science.1235490 · PubMed

Other PDB entries of the same protein (UniProt Q5SHN7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9NO7 2.13 Å, Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
4Y4O 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and…
8CVL 2.3 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
8FC6 2.35 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…
8VTW 2.35 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
4W2F 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin,…
6XHV 2.4 Å, Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex…
7RQA 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
7RQE 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y,…
8CVJ 2.4 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA,…
8VTU 2.4 Å, Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with…
8VTX 2.4 Å, Crystal structure of the A2058-N6-dimethylated Thermus thermophilus 70S ribosome in…

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