4V5J: 70S ribosome

Name: PDB 4V5J: Structure of the 70S ribosome bound to Release factor 2 and a substrate analog provides insights into catalysis of peptide release
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the 70S ribosome bound to Release factor 2 and a substrate analog provides insights into catalysis of peptide release. Determined by X-ray diffraction at 3.1 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: THERMUS THERMOPHILUS, ESCHERICHIA COLI, synthetic construct
Chains: 118
Atoms: 305,067
Mol. weight: 4650.65 kDa
Ligands: MG, ZN
Released: 9 Jul 2014

Explore 4V5J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V5J contains 445 α-helices and 644 β-strands across 106 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: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
β-strand	19	1	9
β-strand	32-34	3	10
α-helix	36-38	3
β-strand	40	1	9
β-strand	41-42	2	10
α-helix	44-62	19
β-strand	68-71	4	11
α-helix	75-86	12
β-strand	92-93	2	11
α-helix	105-109	5
α-helix	112-115	4
α-helix	119-121	3
α-helix	132-134	3
α-helix	135-143	9
α-helix	145-148	4
β-strand	161-164	4	11
α-helix	171-179	9
β-strand	185-186	2	11
β-strand	199-200	2	11
α-helix	208-223	16

Chains AC and CC: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	29-45	17
β-strand	55-56	2	15
β-strand	63-64	2	16
β-strand	67-70	4	15
α-helix	74-76	3
α-helix	83-92	10
β-strand	98-99	2	16
β-strand	102-105	4	15
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-141	12
β-strand	148-153	6	17
α-helix	157-159	3
β-strand	166	1	17
β-strand	169-170	2	17
β-strand	182-187	6	17
β-strand	198-203	6	17

Chain AD: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
α-helix	39	1
α-helix	53-67	15
α-helix	72-84	13
α-helix	89-98	10
β-strand	100	1	26
α-helix	114-122	9
β-strand	126	1	27
β-strand	127	1	28
β-strand	132	1	28
β-strand	139	1	26
β-strand	145	1	29
β-strand	148	1	27
α-helix	150-153	4
α-helix	156-163	8
β-strand	175	1	29
α-helix	178-180	3
β-strand	184	1	29
α-helix	200-206	7

Chains AE and CE: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-19	11	34
β-strand	24-35	12	34
β-strand	40-48	9	34
α-helix	51-62	12
β-strand	66-68	3	34
β-strand	80-84	5	35
β-strand	87-93	7	35
β-strand	99-101	3	35
α-helix	106-111	6
β-strand	117-125	9	35
α-helix	128-139	12
α-helix	145-150	6

Chains AF and CF: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	42
β-strand	4	1	43
β-strand	9-10	2	44
α-helix	18-32	15
β-strand	36-37	2	42
β-strand	41-52	12	44
β-strand	55-62	8	44
β-strand	65-67	3	42
α-helix	69-79	11
β-strand	92	1	43
β-strand	98-99	2	45

Chain AG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
α-helix	25-29	5
α-helix	37-50	14
α-helix	60-63	4
β-strand	73-75	3	55
β-strand	88-90	3	55
α-helix	93-108	16
α-helix	117-128	12
α-helix	133-144	12
α-helix	149-154	6

Chains AH and CH: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
α-helix	30-40	11
β-strand	45-49	5	65
β-strand	52-53	2	66
β-strand	56-57	2	66
β-strand	60-63	4	65
β-strand	65	1	67
β-strand	78	1	67
β-strand	83-85	3	68
β-strand	88	1	69
β-strand	91	1	69
β-strand	95	1	68
α-helix	97-99	3
α-helix	103-106	4
β-strand	109-114	6	68
β-strand	117-119	3	68
α-helix	121-126	6
β-strand	131-137	7	68

Chains AI and CI: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	76
β-strand	14-20	7	76
β-strand	26-28	3	76
β-strand	32	1	76
α-helix	33-36	4
β-strand	60-66	7	76
α-helix	70-79	10
α-helix	84-87	4
α-helix	90-92	3
α-helix	122-125	4

59 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, CA	RNA	1522	THERMUS THERMOPHILUS
30S ribosomal protein S2	AB, CB	protein	256	THERMUS THERMOPHILUS	P80371 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	239	THERMUS THERMOPHILUS	P80372 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	209	THERMUS THERMOPHILUS	P80373 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	162	THERMUS THERMOPHILUS	Q5SHQ5 (AlphaFold model)
30S ribosomal protein S6	AF, CF	protein	101	THERMUS THERMOPHILUS	Q5SLP8
30S ribosomal protein S7	AG, CG	protein	156	THERMUS THERMOPHILUS	P17291
30S ribosomal protein S8	AH, CH	protein	138	THERMUS THERMOPHILUS	Q5SHQ2
30S ribosomal protein S9	AI, CI	protein	128	THERMUS THERMOPHILUS	P62669
30S ribosomal protein S10	AJ, CJ	protein	105	THERMUS THERMOPHILUS	Q5SHN7
30S ribosomal protein S11	AK, CK	protein	129	THERMUS THERMOPHILUS	P80376
30S ribosomal protein S12	AL, CL	protein	132	THERMUS THERMOPHILUS	Q5SHN3

46 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V5J_1 16S Ribosomal RNA (chains AA, CA)
UUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCA
AGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUG
GGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGA
CCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAU
CAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAU
GGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAA
UCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGG
GGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUA
AUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCC
GGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACG
GCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAA
UUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCC
ACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACC
CGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGC
UAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUG
ACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUU
ACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGC
CCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCC
CGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGA
CUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCC
UGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCU
AAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGG
AAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACAC
ACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGG
CGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGU
GCGGCUGGAUCACCUCCUUUCU

Sequence of entity 2 (AB, CB), FASTA

>4V5J_2 30S RIBOSOMAL PROTEIN S2 (chains AB, CB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (AC, CC), FASTA

>4V5J_3 30S RIBOSOMAL PROTEIN S3 (chains AC, CC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (AD, CD), FASTA

>4V5J_4 30S RIBOSOMAL PROTEIN S4 (chains AD, CD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE, CE), FASTA

>4V5J_5 30S RIBOSOMAL PROTEIN S5 (chains AE, CE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (AF, CF), FASTA

>4V5J_6 30S RIBOSOMAL PROTEIN S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG, CG), FASTA

>4V5J_7 30S RIBOSOMAL PROTEIN S7 (chains AG, CG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH, CH), FASTA

>4V5J_8 30S RIBOSOMAL PROTEIN S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI, CI), FASTA

>4V5J_9 30S RIBOSOMAL PROTEIN S9 (chains AI, CI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (AJ, CJ), FASTA

>4V5J_10 30S RIBOSOMAL PROTEIN S10 (chains AJ, CJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (AK, CK), FASTA

>4V5J_11 30S RIBOSOMAL PROTEIN S11 (chains AK, CK)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (AL, CL), FASTA

>4V5J_12 30S RIBOSOMAL PROTEIN S12 (chains AL, CL)
MPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSG
YEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTK
KPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1094
ZN	Zinc ion	Zn	6

Primary citation

Structure of the 70S ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release. Jin, H., Kelley, A.C., Loakes, D. et al. Proc Natl Acad Sci U S A (2010) 107:8593-8598. DOI 10.1073/pnas.1003995107 · PubMed

Other PDB entries of the same protein (UniProt P80371 (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…

Browse structure collections

About this viewer

MolViewer shows 4V5J 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.