4V63: Translation termination on the 70S ribosome

Name: PDB 4V63: Structural basis for translation termination on the 70S ribosome.
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structural basis for translation termination on the 70S ribosome. Determined by X-ray diffraction at 3.21 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.21 Å
Organisms: Thermus thermophilus, Escherichia coli
Chains: 112
Atoms: 299,961
Mol. weight: 4627.22 kDa
Ligands: ZN, MG
Released: 9 Jul 2014

Explore 4V63 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V63 contains 418 α-helices and 662 β-strands across 100 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.

Chains AB and CB: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
α-helix	26-29	4
β-strand	32-34	3	38
β-strand	41-42	2	38
α-helix	44-64	21
β-strand	68-71	4	39
α-helix	75-86	12
β-strand	92-93	2	39
α-helix	96-98	3
α-helix	105-120	16
α-helix	132-149	18
β-strand	161-164	4	39
α-helix	171-179	9
β-strand	184-187	4	39
α-helix	194-196	3
β-strand	199-201	3	39
α-helix	208-224	17
α-helix	231-233	3
α-helix	236-239	4

Chain AC: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	20-22	3	46
α-helix	29-45	17
α-helix	48-50	3
β-strand	52-55	4	47
β-strand	57-59	3	46
β-strand	63-65	3	46
β-strand	68-70	3	47
α-helix	73-75	3
α-helix	83-93	11
β-strand	98-100	3	46
β-strand	103-104	2	47
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-144	15
β-strand	148-155	8	48
β-strand	165-171	7	48
α-helix	182	1
β-strand	183-184	2	48
β-strand	187	1	48
β-strand	191	1	49
β-strand	194	1	49
β-strand	196-202	7	48

Chain AD: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
α-helix	24-27	4
α-helix	53-67	15
α-helix	72-84	13
α-helix	89-99	11
β-strand	100	1	60
α-helix	101-106	6
α-helix	114-122	9
β-strand	126	1	61
β-strand	128	1	62
β-strand	131	1	62
β-strand	139	1	60
β-strand	145-147	3	63
β-strand	148	1	61
α-helix	150-153	4
α-helix	156-164	9
β-strand	174-177	4	63
α-helix	178-180	3
β-strand	182-185	4	63
α-helix	200-207	8

Chains AE and CE: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	7-17	11	72
β-strand	26-35	10	72
β-strand	41-48	8	72
α-helix	51-64	14
β-strand	67	1	72
β-strand	75	1	73
β-strand	80-84	5	73
β-strand	87-93	7	73
β-strand	99-101	3	73
α-helix	104-111	8
β-strand	117-125	9	73
α-helix	128-141	14
α-helix	145-153	9

Chains AF and CF: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	79
α-helix	16-33	18
β-strand	36-40	5	79
β-strand	44-45	2	79
β-strand	52	1	80
β-strand	55	1	80
β-strand	59-66	8	79
α-helix	72-81	10
β-strand	85-92	8	79
β-strand	98-99	2	81

Chains AG and CG: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-30	10
α-helix	36-53	18
α-helix	58-68	11
β-strand	73-79	7	94
β-strand	84-90	7	94
α-helix	93-108	16
α-helix	116-129	14
α-helix	133-147	15
α-helix	148-153	6

Chains AH and CH: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
β-strand	23-24	2	102
α-helix	30-41	12
β-strand	45-52	8	102
β-strand	57-63	7	102
β-strand	65	1	103
α-helix	76-77	2
β-strand	78	1	103
β-strand	83-85	3	104
β-strand	94-95	2	104
α-helix	97-99	3
α-helix	103-106	4
β-strand	109-114	6	104
β-strand	117-119	3	104
α-helix	123-127	5
β-strand	131-137	7	104

Chains AI and CI: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	114
β-strand	14-21	8	114
β-strand	27-28	2	114
α-helix	33-36	4
α-helix	41-46	6
α-helix	48-52	5
β-strand	59-66	8	114
α-helix	71-87	17
α-helix	91-93	3
α-helix	109-111	3
β-strand	118	1	115
β-strand	121	1	115

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 rRNA	AA, CA	RNA	1525	Thermus thermophilus
P and E-site tRNA(fMet)	AY, AZ, CY, CZ	RNA	77	Escherichia coli
mRNA	AV, CV	RNA	27
30S ribosomal protein S2	AB, CB	protein	256	Thermus thermophilus	P62662 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	239	Thermus thermophilus	P62663 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	209	Thermus thermophilus	P62664 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	162	Thermus thermophilus	P62665 (AlphaFold model)
30S ribosomal protein S6	AF, CF	protein	101	Thermus thermophilus	P62666
30S ribosomal protein S7	AG, CG	protein	156	Thermus thermophilus	P62667
30S ribosomal protein S8	AH, CH	protein	138	Thermus thermophilus	P62668
30S ribosomal protein S9	AI, CI	protein	128	Thermus thermophilus	P62669
30S ribosomal protein S10	AJ, CJ	protein	105	Thermus thermophilus	P62653

43 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V63_1 16S RRNA (chains AA, CA)
AUUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGC
AAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGU
GGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGG
ACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCA
UCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGA
UGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGA
AUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCG
GGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGAGGAGGGGACUGACGGUACCGGGGU
AAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACC
CGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCAC
GGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGA
AUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGC
CACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUAC
CCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAG
CUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUU
GACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCU
UACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAG
CCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUC
CCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGG
ACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGC
CUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGC
UAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCG
GAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACA
CACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAG
GCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGG
UGCGGCUGGAUCACCUCCUUUCUAA

Sequence of entity 2 (AY, AZ, CY, CZ), FASTA

>4V63_2 P and E-site tRNA(fMet) (chains AY, AZ, CY, CZ)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA

Sequence of entity 3 (AV, CV), FASTA

>4V63_3 mRNA (chains AV, CV)
GGCAAGGAGGUAAAAAUGUAAAAAAAA

Sequence of entity 4 (AB, CB), FASTA

>4V63_4 30S ribosomal protein S2 (chains AB, CB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 5 (AC, CC), FASTA

>4V63_5 30S ribosomal protein S3 (chains AC, CC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 6 (AD, CD), FASTA

>4V63_6 30S ribosomal protein S4 (chains AD, CD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 7 (AE, CE), FASTA

>4V63_7 30S ribosomal protein S5 (chains AE, CE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 8 (AF, CF), FASTA

>4V63_8 30S ribosomal protein S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 9 (AG, CG), FASTA

>4V63_9 30S ribosomal protein S7 (chains AG, CG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 10 (AH, CH), FASTA

>4V63_10 30S ribosomal protein S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 11 (AI, CI), FASTA

>4V63_11 30S ribosomal protein S9 (chains AI, CI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 12 (AJ, CJ), FASTA

>4V63_12 30S ribosomal protein S10 (chains AJ, CJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
MG	Magnesium ion	Mg	2577

Primary citation

Structural basis for translation termination on the 70S ribosome. Laurberg, M., Asahara, H., Korostelev, A. et al. Nature (2008) 454:852-857. DOI 10.1038/nature07115 · PubMed

Other PDB entries of the same protein (UniProt P62662 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5J4D 3.1 Å, E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated…
6N1D 3.2 Å, X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into…
5V8I 3.25 Å, Thermus thermophilus 70S ribosome lacking ribosomal protein uS17
4V84 3.4 Å, Crystal structure of a complex containing domain 3 of CrPV IGR IRES RNA bound to the 70S…
4V9N 3.4 Å, Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.
4V9Q 3.4 Å, Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome.
6B4V 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 bound to the 70S ribosome
6BOH 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304)…
4V83 3.5 Å, Crystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to…
4V9K 3.5 Å, 70S ribosome translocation intermediate GDPNP-I containing elongation factor EFG/GDPNP,…
4V9L 3.5 Å, 70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC…
6BOK 3.55 Å, E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome

Browse structure collections

About this viewer

MolViewer shows 4V63 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.