4V5L: EF-Tu and aminoacyl-tRNA

Name: PDB 4V5L: The structure of EF-Tu and aminoacyl-tRNA bound to the 70S ribosome with a GTP analog
Published: 2014-07-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

The structure of EF-Tu and aminoacyl-tRNA bound to the 70S ribosome with a GTP analog. 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: 59
Atoms: 153,628
Mol. weight: 2325.01 kDa
Ligands: PAR, ZN, GCP, MG
Released: 9 Jul 2014

Explore 4V5L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V5L contains 210 α-helices and 370 β-strands across 52 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
β-strand	32-34	3	6
α-helix	36-38	3
β-strand	41-42	2	6
α-helix	44-63	20
β-strand	68-71	4	7
α-helix	78-86	9
β-strand	92-93	2	7
α-helix	105-108	4
α-helix	111-122	12
α-helix	132-135	4
α-helix	138-140	3
α-helix	142-147	6
β-strand	161-164	4	7
α-helix	171-179	9
β-strand	184-186	3	7
β-strand	190	1	8
β-strand	192	1	8
β-strand	199	1	7
α-helix	208-226	19

Chain AC: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
β-strand	21	1	12
α-helix	26-45	20
α-helix	48-50	3
β-strand	52	1	13
β-strand	56	1	13
β-strand	58	1	12
β-strand	63-64	2	14
β-strand	67-70	4	13
α-helix	73-76	4
α-helix	83-93	11
β-strand	98-99	2	14
β-strand	102-105	4	13
α-helix	106	1
α-helix	109-111	3
α-helix	113-125	13
α-helix	130-143	14
β-strand	148-152	5	15
β-strand	155	1	16
α-helix	157-159	3
β-strand	164	1	16
β-strand	167-171	5	15
β-strand	182-191	10	15
β-strand	194-203	10	15

Chain AD: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-15	7
α-helix	25-27	3
α-helix	49-52	4
α-helix	53-66	14
α-helix	72-84	13
α-helix	89-99	11
β-strand	100	1	20
α-helix	101-106	6
α-helix	114-122	9
β-strand	126-128	3	21
β-strand	131	1	21
β-strand	139	1	20
α-helix	140-141	2
β-strand	144-145	2	22
β-strand	146-148	3	21
α-helix	150-153	4
α-helix	156-164	9
β-strand	184-185	2	22
α-helix	200-206	7

Chain AE: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-19	11	26
β-strand	24-35	12	26
β-strand	40-48	9	26
α-helix	51-62	12
β-strand	66-68	3	26
β-strand	80-84	5	27
β-strand	87-93	7	27
β-strand	100-101	2	27
α-helix	104-113	10
β-strand	118-124	7	27
α-helix	128-140	13
α-helix	145-149	5

Chain AF: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	35
β-strand	4-5	2	36
β-strand	7-10	4	37
α-helix	16-33	18
β-strand	44-47	4	37
β-strand	57-62	6	37
β-strand	66-67	2	35
α-helix	69-71	3
α-helix	72-79	8
β-strand	85-88	4	37
β-strand	91-92	2	36
β-strand	98-99	2	38

Chain AG: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
α-helix	21-28	8
α-helix	36-51	16
α-helix	58-67	10
β-strand	73-75	3	44
β-strand	88-90	3	44
α-helix	93-108	16
α-helix	116-129	14
α-helix	135-144	10
α-helix	149-154	6

Chain AH: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	23-26	4	54
α-helix	30-41	12
β-strand	45-52	8	54
β-strand	57-63	7	54
β-strand	65	1	55
α-helix	75-77	3
β-strand	78	1	55
β-strand	83-85	3	56
β-strand	88	1	57
β-strand	91	1	57
β-strand	94-95	2	58
α-helix	97-99	3
α-helix	103-106	4
β-strand	112-114	3	58
β-strand	117-119	3	58
α-helix	121-127	7
β-strand	131-133	3	58
β-strand	135-137	3	56

Chain AI: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	59
β-strand	14-20	7	59
β-strand	26-28	3	59
β-strand	32	1	59
α-helix	33-36	4
α-helix	43-47	5
β-strand	60-66	7	59
α-helix	70-85	16
α-helix	100-102	3
α-helix	110-112	3
α-helix	122-125	4

44 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	RNA	1522	THERMUS THERMOPHILUS
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	P62667
30S ribosomal protein S8	AH	protein	138	THERMUS THERMOPHILUS	P0DOY9
30S ribosomal protein S9	AI	protein	128	THERMUS THERMOPHILUS	P62669
30S ribosomal protein S10	AJ	protein	105	THERMUS THERMOPHILUS	Q5SHN7
30S ribosomal protein S11	AK	protein	129	THERMUS THERMOPHILUS	P80376
30S ribosomal protein S12	AL	protein	135	THERMUS THERMOPHILUS	Q5SHN3

46 more molecules are not listed.

Sequence of entity 1 (AA), FASTA

>4V5L_1 16S RRNA (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 (AB), FASTA

>4V5L_2 30S RIBOSOMAL PROTEIN S2 (chains AB)
MPVEITVKELLEAGVHFGHERKRWNPKFARYIYAERNGIHIIDLQKTMEELERTFRFIED
LAMRGGTILFVGTKKQAQDIVRMEAERAGMPYVNQRWLGGMLTNFKTISQRVHRLEELEA
LFASPEIEERPKKEQVRLKHELERLQKYLSGFRLLKRLPDAIFVVDPTKEAIAVREARKL
FIPVIALADTDSDPDLVDYIIPGNDDAIRSIQLILSRAVDLIIQARGGVVEPSPSYALVQ
EAEATETPEGESEVEA

Sequence of entity 3 (AC), FASTA

>4V5L_3 30S RIBOSOMAL PROTEIN S3 (chains AC)
MGNKIHPIGFRLGITRDWESRWYAGKKQYRHLLLEDQRIRGLLEKELYSAGLARVDIERA
ADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVALNVQEVQNPNLSAPLVAQRV
AEQIERRFAVRRAIKQAVQRVMESGAKGAKVIVSGRIGGAEQARTEWAAQGRVPLHTLRA
NIDYGFALARTTYGVLGVKAYIFLGEVIGGQKPKARPELPKAEERPRRRRPAVRVKKEE

Sequence of entity 4 (AD), FASTA

>4V5L_4 30S RIBOSOMAL PROTEIN S4 (chains AD)
MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLRE
KQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQL
VRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEG
MKGKFLRLPDREDLALPVNEQLVIEFYSR

Sequence of entity 5 (AE), FASTA

>4V5L_5 30S RIBOSOMAL PROTEIN S5 (chains AE)
MPETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGY
YARRNMVEVPLQNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT
KELGSRNPINIAYATMEALRQLRTKADVERLRKGEAHAQAQG

Sequence of entity 6 (AF), FASTA

>4V5L_6 30S RIBOSOMAL PROTEIN S6 (chains AF)
MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYF
LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA

Sequence of entity 7 (AG), FASTA

>4V5L_7 30S RIBOSOMAL PROTEIN S7 (chains AG)
MARRRRAEVRQLQPDLVYGDVLVTAFINKIMRDGKKNLAARIFYDACKIIQEKTGQEPLK
VFKQAVENVKPRMEVRSRRVGGANYQVPMEVSPRRQQSLALRWLVQAANQRPERRAAVRI
AHELMDAAEGKGGAVKKKEDVERMAEANRAYAHYRW

Sequence of entity 8 (AH), FASTA

>4V5L_8 30S RIBOSOMAL PROTEIN S8 (chains AH)
MLTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLR
VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT
DREARKLGVGGELICEVW

Sequence of entity 9 (AI), FASTA

>4V5L_9 30S RIBOSOMAL PROTEIN S9 (chains AI)
MEQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD
AYITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKAR
RAPQYSKR

Sequence of entity 10 (AJ), FASTA

>4V5L_10 30S RIBOSOMAL PROTEIN S10 (chains AJ)
MPKIRIKLRGFDHKTLDASAQKIVEAARRSGAQVSGPIPLPTRVRRFTVIRGPFKHKDSR
EHFELRTHNRLVDIINPNRKTIEQLMTLDLPTGVEIEIKTVGGGR

Sequence of entity 11 (AK), FASTA

>4V5L_11 30S RIBOSOMAL PROTEIN S11 (chains AK)
MAKKPSKKKVKRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA
AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVDDTPVPHNGCR
PKKKFRKAS

Sequence of entity 12 (AL), FASTA

>4V5L_12 30S RIBOSOMAL PROTEIN S12 (chains AL)
MVALPTINQLVRKGREKVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRL
TSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKY
GTKKPKEAAKTAAKK

Ligands and cofactors

ID	Name	Formula	Copies
PAR	Paromomycin	C23 H45 N5 O14	1
ZN	Zinc ion	Zn	4
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
MG	Magnesium ion	Mg	1

Primary citation

The Mechanism for Activation of GTP Hydrolysis on the Ribosome. Voorhees, R.M., Schmeing, T.M., Kelley, A.C. et al. Science (2010) 330:835. DOI 10.1126/SCIENCE.1194460 · 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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