4V5P: EF-Tu and A9C-tRNA-Trp

Name: PDB 4V5P: The crystal structure of EF-Tu and A9C-tRNA-Trp bound to a near- cognate codon on the 70S ribosome
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

The crystal structure of EF-Tu and A9C-tRNA-Trp bound to a near- cognate codon on the 70S ribosome. 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
Chains: 118
Atoms: 307,322
Mol. weight: 4667.24 kDa
Ligands: ZN, GDP, KIR
Released: 9 Jul 2014

Explore 4V5P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V5P contains 439 α-helices and 731 β-strands across 104 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: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	28-31	4
β-strand	34-36	3	5
β-strand	39-41	3	5
α-helix	42	1
α-helix	44-64	21
β-strand	68-71	4	6
α-helix	78-86	9
β-strand	92-93	2	6
α-helix	105-122	18
α-helix	125-127	3
α-helix	134-148	15
β-strand	161-164	4	6
α-helix	171-179	9
β-strand	184-188	5	6
α-helix	194-196	3
β-strand	199-202	4	6
α-helix	208-226	19

Chain AC: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	13
α-helix	30-45	16
β-strand	52-56	5	14
β-strand	57-58	2	13
β-strand	63-64	2	15
β-strand	67-70	4	14
α-helix	73-77	5
α-helix	82-93	12
β-strand	98-99	2	15
β-strand	102-105	4	14
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-143	14
β-strand	148-155	8	16
α-helix	157-159	3
β-strand	164-166	3	16
β-strand	169-171	3	16
β-strand	182-191	10	16
β-strand	194-203	10	16

Chains AD and CD: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
α-helix	49-52	4
α-helix	53-67	15
α-helix	72-84	13
α-helix	89-99	11
β-strand	100	1	25
α-helix	101-106	6
α-helix	114-122	9
β-strand	126-127	2	26
β-strand	132	1	26
β-strand	139	1	25
β-strand	145	1	27
β-strand	147-148	2	26
α-helix	156-163	8
β-strand	174	1	28
β-strand	184	1	27
β-strand	185	1	28
α-helix	200-204	5

Chain AE: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	9-20	12	33
β-strand	23-35	13	33
β-strand	40	1	34
β-strand	41-48	8	33
α-helix	51-62	12
β-strand	68	1	34
β-strand	72	1	35
β-strand	75	1	35
β-strand	80-84	5	36
β-strand	87-93	7	36
β-strand	99-101	3	36
α-helix	104-113	10
β-strand	117-124	8	36
α-helix	128-140	13
α-helix	145-152	8

Chains AF and CF: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	43
α-helix	16-32	17
β-strand	37-40	4	43
β-strand	44-52	9	43
β-strand	55-60	6	43
β-strand	63-67	5	43
α-helix	72-80	9
β-strand	85-92	8	43
α-helix	93	1
α-helix	95-97	3
β-strand	98-99	2	44

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

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	21-30	10
α-helix	36-51	16
α-helix	58-69	12
β-strand	73-77	5	53
β-strand	86-90	5	53
α-helix	93-108	16
α-helix	116-129	14
α-helix	133-147	15
α-helix	149-154	6

Chain AH: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
β-strand	23-27	5	70
α-helix	30-41	12
β-strand	45-53	9	70
β-strand	56-63	8	70
β-strand	65	1	71
α-helix	75-77	3
β-strand	78	1	71
β-strand	83-85	3	72
β-strand	88	1	73
β-strand	91	1	73
β-strand	94-95	2	72
α-helix	103-106	4
β-strand	109-114	6	72
β-strand	117-120	4	72
α-helix	121-126	6
β-strand	131-137	7	72

Chain AI: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	77
β-strand	13-17	5	77
β-strand	20	1	78
β-strand	26-27	2	79
β-strand	32	1	79
α-helix	33-36	4
α-helix	43-45	3
α-helix	49-51	3
β-strand	60	1	78
β-strand	61-62	2	79
β-strand	63-66	4	77
α-helix	70-87	18
α-helix	97-99	3
α-helix	110-113	4
α-helix	121-125	5

62 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	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	P0DOY9
30S ribosomal protein S9	AI, CI	protein	128	THERMUS THERMOPHILUS	P80374
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	135	THERMUS THERMOPHILUS	Q5SHN3

46 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4V5P_1 16S RRNA (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

>4V5P_2 30S RIBOSOMAL PROTEIN S2 (chains AB, CB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (AC, CC), FASTA

>4V5P_3 30S RIBOSOMAL PROTEIN S3 (chains AC, CC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (AD, CD), FASTA

>4V5P_4 30S RIBOSOMAL PROTEIN S4 (chains AD, CD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE, CE), FASTA

>4V5P_5 30S RIBOSOMAL PROTEIN S5 (chains AE, CE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (AF, CF), FASTA

>4V5P_6 30S RIBOSOMAL PROTEIN S6 (chains AF, CF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG, CG), FASTA

>4V5P_7 30S RIBOSOMAL PROTEIN S7 (chains AG, CG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH, CH), FASTA

>4V5P_8 30S RIBOSOMAL PROTEIN S8 (chains AH, CH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI, CI), FASTA

>4V5P_9 30S RIBOSOMAL PROTEIN S9 (chains AI, CI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGHFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (AJ, CJ), FASTA

>4V5P_10 30S RIBOSOMAL PROTEIN S10 (chains AJ, CJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (AK, CK), FASTA

>4V5P_11 30S RIBOSOMAL PROTEIN S11 (chains AK, CK)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (AL, CL), FASTA

>4V5P_12 30S RIBOSOMAL PROTEIN S12 (chains AL, CL)
MVALPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL
TSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKY
GTKKPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
KIR	Kirromycin	C43 H60 N2 O12	2

Primary citation

How Mutations in tRNA Distant from the Anticodon Affect the Fidelity of Decoding. Schmeing, T.M., Voorhees, R.M., Kelley, A.C. et al. Nat Struct Mol Biol (2011) 18:432. DOI 10.1038/NSMB.2003 · 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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