4V4R: Whole ribosomal complex

Name: PDB 4V4R: Crystal structure of the whole ribosomal complex.
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal structure of the whole ribosomal complex. Determined by X-ray diffraction at 5.9 Å resolution. Released 9 Jul 2014.

Method: X-ray diffraction
Resolution: 5.9 Å
Organisms: Thermus thermophilus, Escherichia coli
Chains: 56
Atoms: 142,780
Mol. weight: 2277.81 kDa
Released: 9 Jul 2014

Explore 4V4R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V4R contains 182 α-helices and 281 β-strands across 49 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	20
β-strand	32-35	4	21
β-strand	39	1	20
β-strand	40-42	3	21
α-helix	43	1
α-helix	44-62	19
β-strand	69	1	22
β-strand	70-71	2	23
α-helix	78-84	7
β-strand	92-93	2	23
α-helix	97-98	2
α-helix	105-120	16
α-helix	132-147	16
α-helix	149-152	4
β-strand	162-164	3	22
α-helix	171-180	10
β-strand	184-188	5	22
β-strand	199-202	4	22
α-helix	208-226	19

Chain AC: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	26
α-helix	29-46	18
β-strand	53-56	4	27
β-strand	57-58	2	26
β-strand	67-70	4	27
α-helix	74-77	4
α-helix	83-94	12
β-strand	102-105	4	27
α-helix	113-125	13
α-helix	130-143	14
β-strand	148-154	7	28
β-strand	165-171	7	28
β-strand	182-191	10	28
β-strand	194-203	10	28

Chain AD: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	39-40	2
α-helix	53-68	16
α-helix	72-84	13
α-helix	91-98	8
α-helix	101-107	7
α-helix	114-122	9
β-strand	127	1	35
β-strand	145	1	36
β-strand	147	1	35
α-helix	152-154	3
α-helix	156-164	9
β-strand	174-177	4	36
β-strand	182-185	4	36
α-helix	201-204	4

Chain AE: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	40
β-strand	15-16	2	40
β-strand	19	1	41
β-strand	24	1	41
β-strand	27-35	9	40
β-strand	41-48	8	40
α-helix	51-61	11
β-strand	66-67	2	40
β-strand	87	1	42
β-strand	92-93	2	43
β-strand	99-101	3	43
α-helix	105-108	4
α-helix	110-113	4
β-strand	117-119	3	43
β-strand	124	1	42
α-helix	128-134	7
α-helix	136-140	5
α-helix	145-152	8

Chain AF: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	46
α-helix	16-33	18
α-helix	35	1
β-strand	36-40	5	46
β-strand	44-52	9	46
β-strand	55-67	13	46
α-helix	69-71	3
α-helix	72-80	9
β-strand	85-92	8	46
β-strand	98-99	2	47

Chain AG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	21-30	10
α-helix	36-53	18
α-helix	58-67	10
β-strand	74-79	6	51
β-strand	84-89	6	51
α-helix	93-109	17
α-helix	116-129	14
α-helix	133-147	15
α-helix	150-154	5

Chain AH: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
β-strand	23-27	5	54
α-helix	30-40	11
β-strand	47-54	8	54
β-strand	56-62	7	54
β-strand	84-85	2	55
β-strand	94-95	2	55
α-helix	103-106	4
β-strand	109-114	6	55
β-strand	117-120	4	55
α-helix	121-125	5
β-strand	131-137	7	55

Chain AI: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	60
β-strand	15-21	7	60
β-strand	26-28	3	60
α-helix	33-36	4
α-helix	41-50	10
β-strand	59-65	7	60
α-helix	70-88	19
α-helix	93-96	4
α-helix	122-124	3

41 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	1522	Thermus thermophilus
P-site tRNA (Phe)	AV	RNA	76	Escherichia coli
E-site tRNA (Phe)	AW	RNA	76	Escherichia coli
5'-r(apupgpupupcpupapgpupapcpapapupapapu)-3'	AX	RNA	18
30S ribosomal protein S2	AB	protein	256	Thermus thermophilus	P80371 (AlphaFold model)
30S ribosomal protein S3	AC	protein	239	Thermus thermophilus	P80372 (AlphaFold model)
30S ribosomal protein S4	AD	protein	209	Thermus thermophilus	P80373 (AlphaFold model)
30S ribosomal protein S5	AE	protein	162	Thermus thermophilus	Q5SHQ5 (AlphaFold model)
30S ribosomal protein S6	AF	protein	101	Thermus thermophilus	Q5SLP8
30S ribosomal protein S7	AG	protein	156	Thermus thermophilus	P17291
30S ribosomal protein S8	AH	protein	138	Thermus thermophilus	P0DOY9
30S ribosomal protein S9	AI	protein	128	Thermus thermophilus	P80374

44 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>4V4R_1 16S ribosomal RNA (chains AA)
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 (AV), FASTA

>4V4R_2 P-site tRNA (Phe) (chains AV)
GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUC
CACAGAAUUCGCACCA

Sequence of entity 3 (AW), FASTA

>4V4R_3 E-site tRNA (Phe) (chains AW)
GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUC
CACAGAAUUCGCACCA

Sequence of entity 4 (AX), FASTA

>4V4R_4 5'-R(*AP*UP*GP*UP*UP*CP*UP*AP*GP*UP*AP*CP*AP*AP*UP*AP*AP*U)-3' (chains AX)
AUGUUCUAGUACAAUAAU

Sequence of entity 5 (AB), FASTA

>4V4R_5 30S ribosomal protein S2 (chains AB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 6 (AC), FASTA

>4V4R_6 30S ribosomal protein S3 (chains AC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 7 (AD), FASTA

>4V4R_7 30S ribosomal protein S4 (chains AD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 8 (AE), FASTA

>4V4R_8 30S ribosomal protein S5 (chains AE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 9 (AF), FASTA

>4V4R_9 30S ribosomal protein S6 (chains AF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 10 (AG), FASTA

>4V4R_10 30S ribosomal protein S7 (chains AG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 11 (AH), FASTA

>4V4R_11 30S ribosomal protein S8 (chains AH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 12 (AI), FASTA

>4V4R_12 30S ribosomal protein S9 (chains AI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Primary citation

Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop Codon. Petry, S., Brodersen, D.E., Murphy IV, F.V. et al. Cell (2005) 123:1255-1266. DOI 10.1016/j.cell.2005.09.039 · 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…

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