4V9N: 70S ribosome

Name: PDB 4V9N: Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2. Determined by X-ray diffraction at 3.4 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Thermus thermophilus
Chains: 110
Atoms: 294,074
Mol. weight: 4435.85 kDa
Ligands: MG, ZN
Released: 9 Jul 2014

Explore 4V9N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V9N contains 486 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	9-13	5
α-helix	29-31	3
β-strand	32-34	3	35
α-helix	36-38	3
β-strand	41-42	2	35
α-helix	44-63	20
β-strand	69-71	3	36
α-helix	75-77	3
α-helix	78-87	10
β-strand	92-93	2	36
α-helix	105-121	17
α-helix	132-149	18
β-strand	162-164	3	36
α-helix	171-179	9
β-strand	184-187	4	36
α-helix	194-196	3
β-strand	199-201	3	36
α-helix	208-225	18
α-helix	231-233	3

Chains AC and CC: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	20-21	2	48
α-helix	29-45	17
α-helix	48-50	3
β-strand	55	1	49
β-strand	57-58	2	48
β-strand	63	1	50
β-strand	67-68	2	49
α-helix	74-77	4
α-helix	83-94	12
β-strand	98	1	50
β-strand	102-103	2	49
α-helix	109-111	3
α-helix	113-125	13
α-helix	132-143	12
β-strand	148-155	8	51
α-helix	157-159	3
β-strand	164-171	8	51
β-strand	182-187	6	51
β-strand	197-203	7	51

Chain AD: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	25-27	3
α-helix	33-35	3
α-helix	53-67	15
α-helix	72-84	13
α-helix	89-98	10
β-strand	100	1	58
α-helix	101-107	7
α-helix	114-122	9
β-strand	126-128	3	59
β-strand	131-132	2	59
β-strand	139	1	58
β-strand	146-148	3	59
α-helix	149	1
α-helix	150-152	3
α-helix	156-162	7
β-strand	174-175	2	60
β-strand	184-185	2	60
α-helix	188-190	3
α-helix	200-206	7

Chains AE and CE: 4 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	68
β-strand	17-18	2	69
β-strand	25-26	2	69
β-strand	28	1	70
β-strand	31-35	5	68
β-strand	40-45	6	68
β-strand	48	1	70
α-helix	51-64	14
β-strand	67-68	2	68
β-strand	80-84	5	71
β-strand	87-91	5	71
β-strand	92-93	2	72
β-strand	100-101	2	72
α-helix	104-111	8
β-strand	118-119	2	72
β-strand	122-124	3	71
α-helix	128-140	13
α-helix	145-151	7

Chains AF and CF: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	84
β-strand	7-10	4	85
α-helix	16-32	17
β-strand	36-37	2	84
β-strand	41-52	12	85
β-strand	55-62	8	85
β-strand	65-67	3	84
α-helix	69-71	3
α-helix	72-80	9
β-strand	85	1	85
β-strand	89	1	85
β-strand	92	1	84
β-strand	99	1	86

Chains AG and CG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	13-15	3
α-helix	21-30	10
α-helix	36-53	18
α-helix	58-68	11
β-strand	74-77	4	100
β-strand	86-89	4	100
α-helix	93-110	18
α-helix	116-129	14
α-helix	133-147	15
α-helix	148-153	6

Chains AH and CH: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	23-24	2	108
β-strand	27	1	108
α-helix	30-41	12
β-strand	45-53	9	108
β-strand	56-63	8	108
β-strand	65	1	109
α-helix	75-77	3
β-strand	78	1	109
β-strand	83-85	3	110
β-strand	88	1	111
β-strand	91	1	111
β-strand	94	1	112
β-strand	109-111	3	110
β-strand	112-113	2	113
β-strand	118-119	2	113
α-helix	121-127	7
β-strand	132	1	112
β-strand	135-137	3	110

Chains AI and CI: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	124
β-strand	13-21	9	124
β-strand	26-28	3	124
α-helix	33-36	4
α-helix	41-45	5
α-helix	48-53	6
α-helix	55-57	3
β-strand	59-66	8	124
α-helix	70-87	18
α-helix	90-95	6
α-helix	109-113	5

51 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 (1504-mer)	AA, CA	RNA	1504	Thermus thermophilus
messenger RNA (5'-R(APAPUPGPUPAP*G)-3')	AV, CV	RNA	10	Thermus thermophilus
P-site tRNA-fMet	AW, CW	RNA	77	Thermus thermophilus
Bacterial peptide chain release factor 2 (RF-2)	AY, CY	protein	362	Thermus thermophilus	Q72GJ6 (AlphaFold model)
30S ribosomal protein S2	AB, CB	protein	234	Thermus thermophilus	P62662 (AlphaFold model)
30S ribosomal protein S3	AC, CC	protein	206	Thermus thermophilus	P62663 (AlphaFold model)
30S ribosomal protein S4	AD, CD	protein	208	Thermus thermophilus	P62664 (AlphaFold model)
30S ribosomal protein S5	AE, CE	protein	151	Thermus thermophilus	P62665
30S ribosomal protein S6	AF, CF	protein	101	Thermus thermophilus	P62666
30S ribosomal protein S7	AG, CG	protein	155	Thermus thermophilus	P62667
30S ribosomal protein S8	AH, CH	protein	138	Thermus thermophilus	P62668
30S ribosomal protein S9	AI, CI	protein	127	Thermus thermophilus	P62669

43 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V9N_1 16S rRNA (1504-MER) (chains AA, CA)
UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCG
UGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGA
CCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGC
CCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCU
AGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCG
GCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUC
CGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGU
AAACUCCUGAACCCGGGACGAAACCCCCGAGGAGGGGACUGACGGUACCGGGGUAAUAGC
GCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUU
CACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCA
ACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCC
GGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUG
GUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGU
AGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACG
CGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGG
GGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAG
GCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAG
CACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAA
CGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCC
CGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGC
GACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCG
CAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCG
CUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGC
CCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCG
AGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGC
UGGA

Sequence of entity 2 (AV, CV), FASTA

>4V9N_2 messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3') (chains AV, CV)
AAUGUAAAAA

Sequence of entity 3 (AW, CW), FASTA

>4V9N_3 P-site tRNA-fMet (chains AW, CW)
CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAA
UCCGGCCCCCGCAACCA

Sequence of entity 4 (AY, CY), FASTA

>4V9N_4 Bacterial peptide chain release factor 2 (RF-2) (chains AY, CY)
NASRNAWKASGGIFDIPQKETRLKELERRLEDPSLWNDPEAARKVSQEAARLRRTVDTFR
SLESDLQGLLELMEELPAEEREALKPELEEAAKKLDELYHQTLLNFPHAEKNAILTIQPG
AGGTEACDWAEMLLRMYTRFAERQGFQVEVVDLTPGPEAGIDYAQILVKGENAYGLLSPE
AGVHRLVRPSPFDASGRRHTSFAGVEVIPEVDEEVEVVLKPEELRIDVMRASGPGGPGVN
TTDSAVRVVHLPTGITVTCQTTRSQIKNKELALKILKARLYELERKKREEELKALRGEVR
PIEWGSQIRSYVLDKNYVKDHRTGLMRHDPENVLDGDLMDLIWAGLEWKAGRRQGTEEVE
AE

Sequence of entity 5 (AB, CB), FASTA

>4V9N_5 30S ribosomal protein S2 (chains AB, CB)
VKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIEDLAMRGG
TILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEALFASPE
IEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKLFIPVIA
LADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ

Sequence of entity 6 (AC, CC), FASTA

>4V9N_6 30S ribosomal protein S3 (chains AC, CC)
GNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERAA
DNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRVA
EQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRAN
IDYGFALARTTYGVLGVKAYIFLGEV

Sequence of entity 7 (AD, CD), FASTA

>4V9N_7 30S ribosomal protein S4 (chains AD, CD)
GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREK
QKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLV
RHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGM
KGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 8 (AE, CE), FASTA

>4V9N_8 30S ribosomal protein S5 (chains AE, CE)
DFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYARR
NMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTKELG
SRNPINIAYATMEALRQLRTKADVERLRKGE

Sequence of entity 9 (AF, CF), FASTA

>4V9N_9 30S ribosomal protein S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 10 (AG, CG), FASTA

>4V9N_10 30S ribosomal protein S7 (chains AG, CG)
ARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLKV
FKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRIA
HELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 11 (AH, CH), FASTA

>4V9N_11 30S ribosomal protein S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 12 (AI, CI), FASTA

>4V9N_12 30S ribosomal protein S9 (chains AI, CI)
EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFDA
YITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARR
APQYSKR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2410
ZN	Zinc ion	Zn	4

Primary citation

Crystal Structure of the 70S Ribosome Bound with the Q253P Mutant Form of Release Factor RF2. Santos, N., Zhu, J., Donohue, J.P. et al. Structure (2013) 21:1258-1263. DOI 10.1016/j.str.2013.04.028 · PubMed

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