PDB-4pc6: Elongation factor Tu:Ts complex with bound GDPNP

ID or keywords:

Entry

Database: PDB / ID: 4pc6

Title

Elongation factor Tu:Ts complex with bound GDPNP

Components

Elongation factor Ts
Elongation factor Tu

Keywords

TRANSLATION / G:GEF:nucleotide complex / Elongation factor / Protein synthesis

Function / homology

Function and homology information

protein-synthesizing GTPase / guanosine tetraphosphate binding / translation elongation factor activity / GTPase activity / GTP binding / cytoplasm / cytosol
Similarity search - Function

GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Elongation factor Ts, dimerisation domain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / GTP Cyclohydrolase I; Chain A, domain 1 ...
Similarity search - Domain/homology

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Thirup, S.S.

Citation

Journal: J.Struct.Biol. / Year: 2015
Title: Structural outline of the detailed mechanism for elongation factor Ts-mediated guanine nucleotide exchange on elongation factor Tu.
Authors: Thirup, S.S. / Van, L.B. / Nielsen, T.K. / Knudsen, C.R.

History

Deposition	Apr 14, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 6, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 1, 2015	Group: Database references
Revision 1.2	Jul 15, 2015	Group: Database references
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4pc6.cif.gz	514.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4pc6.ent.gz	425.1 KB	Display	PDB format
PDBx/mmJSON format	4pc6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4pc6_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	4pc6_full_validation.pdf.gz	1.3 MB	Display
Data in XML	4pc6_validation.xml.gz	50.1 KB	Display
Data in CIF	4pc6_validation.cif.gz	70.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pc/4pc6 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/4pc6	HTTPS FTP

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Related structure data

Related structure data	4pc1SC 4pc2C 4pc3C 4pc7C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4pc1-1 4pc2-1 4pc1-2 4pc3-2 4pc2-2 4pc3-1 1iyd-d 1iye-d 1i1m-d 1xmx-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#81 - Sep 2006 Elongation Factors similarity (23) #121 - Jan 2010 70S Ribosomes similarity (13) #157 - Jan 2013 Transfer-Messenger RNA similarity (13) #104 - Aug 2008 Selenocysteine Synthase similarity (6) #245 - May 2020 Spliceosomes similarity (6) #60 - Dec 2004 Ubiquitin similarity (1) #148 - Apr 2012 Ras Protein similarity (1)

Deposited unit

A: Elongation factor Tu

C: Elongation factor Ts

B: Elongation factor Tu

D: Elongation factor Ts

hetero molecules

149 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Elongation factor Tu

C: Elongation factor Ts

hetero molecules

defined by author&software
74.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Elongation factor Tu

D: Elongation factor Ts

hetero molecules

defined by author&software
74.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.969, 107.467, 193.339
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Elongation factor Tu / EF-Tu Mass: 43340.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / DH10B / Gene: tufA, tuf, ECDH10B_3514 / Production host: Escherichia coli (E. coli) / References: UniProt: B1X6I9, UniProt: A0A0M3KKV1*PLUS
#2: Protein	Elongation factor Ts / EF-Ts Mass: 30332.795 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: tsf, EcDH1_3433, ECDH1ME8569_0163 / Production host: Escherichia coli (E. coli) / References: UniProt: C9QRL8, UniProt: A0A0M3KKV2*PLUS
#3: Chemical	ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₃P₃ Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 468 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.75 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100mM MES, 18% PEG 6000, 5% glycerol, 152mM NH4CH3COO, 0.5mM GDPNP, 0.5mM pulvomycin, 5mM EDTA

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Data collection

Diffraction	Mean temperature: 292 K
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 17, 2002
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2 Å / Relative weight: 1
Reflection	Resolution: 2.2→29.6 Å / Num. obs: 79003 / % possible obs: 99.5 % / Redundancy: 7.7 % / R_merge(I) obs: 0.0103 / Net I/σ(I): 13.8
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 3.4 / % possible all: 98.5

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Processing

Software

Name: PHENIX / Version: (phenix.refine: dev_1702) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PC1

4pc1

Resolution: 2.2→29.542 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2231	3250	4.12 %	random
R_work	0.171	-	-	-
obs	0.173	78958	99.98 %	-

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.2→29.542 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9802	0	88	468	10358

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10069
X-RAY DIFFRACTION	f_angle_d	0.809	13599
X-RAY DIFFRACTION	f_dihedral_angle_d	12.843	3781
X-RAY DIFFRACTION	f_chiral_restr	0.029	1558
X-RAY DIFFRACTION	f_plane_restr	0.003	1752

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2-2.2328	0.303	121	0.2616	3255	X-RAY DIFFRACTION	100
2.2328-2.2677	0.2677	110	0.2464	3255	X-RAY DIFFRACTION	100
2.2677-2.3049	0.2612	117	0.2343	3293	X-RAY DIFFRACTION	100
2.3049-2.3446	0.2516	105	0.2281	3264	X-RAY DIFFRACTION	100
2.3446-2.3872	0.2524	138	0.2209	3293	X-RAY DIFFRACTION	100
2.3872-2.4331	0.2924	139	0.2235	3235	X-RAY DIFFRACTION	100
2.4331-2.4827	0.2782	155	0.2131	3240	X-RAY DIFFRACTION	100
2.4827-2.5367	0.2438	165	0.2055	3247	X-RAY DIFFRACTION	100
2.5367-2.5957	0.2664	166	0.2044	3212	X-RAY DIFFRACTION	100
2.5957-2.6606	0.265	180	0.1996	3247	X-RAY DIFFRACTION	100
2.6606-2.7324	0.232	157	0.1942	3256	X-RAY DIFFRACTION	100
2.7324-2.8128	0.2484	186	0.1941	3212	X-RAY DIFFRACTION	100
2.8128-2.9035	0.2762	151	0.1888	3256	X-RAY DIFFRACTION	100
2.9035-3.0072	0.274	157	0.1847	3259	X-RAY DIFFRACTION	100
3.0072-3.1274	0.242	155	0.1816	3266	X-RAY DIFFRACTION	100
3.1274-3.2696	0.2124	189	0.1645	3255	X-RAY DIFFRACTION	100
3.2696-3.4417	0.211	199	0.1529	3241	X-RAY DIFFRACTION	100
3.4417-3.657	0.228	155	0.154	3274	X-RAY DIFFRACTION	100
3.657-3.9388	0.2067	139	0.1518	3328	X-RAY DIFFRACTION	100
3.9388-4.334	0.1783	96	0.1437	3391	X-RAY DIFFRACTION	100
4.334-4.9586	0.1352	79	0.1349	3400	X-RAY DIFFRACTION	100
4.9586-6.2377	0.1934	98	0.1644	3442	X-RAY DIFFRACTION	100
6.2377-29.5444	0.1651	93	0.1457	3587	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.596	0.601	0.7979	5.531	1.4172	3.9566	-0.2529	-0.2435	0.5399	0.0886	0.2863	-0.1188	-0.4823	0.0677	-0.038	0.4323	0.012	-0.0106	0.2931	-0.0422	0.3571	14.3425	60.0198	72.7712
2	1.7467	0.5091	0.1402	2.3379	1.2862	3.0742	-0.0711	-0.4843	0.2581	0.1431	-0.0665	0.0383	-0.1291	-0.0609	0.1177	0.264	0.0848	-0.0347	0.4309	-0.0801	0.3224	28.2056	36.5779	94.081
3	3.6797	0.0752	-0.8814	2.1363	0.8958	2.0688	0.0392	-0.1196	-0.1186	0.3035	0.092	-0.0708	-0.4866	-1.0204	-0.1167	0.6544	0.1142	-0.1374	0.7709	0.1911	0.5863	-7.0624	60.2641	57.0536
4	9.1532	-2.0645	-3.4844	0.6023	1.298	3.9109	0.082	0.3501	0.4862	-0.3022	0.0783	0.4483	0.0736	-0.7587	-0.2338	0.5851	-0.071	-0.0704	0.5782	0.2667	0.5187	-0.3822	53.8609	48.45
5	1.6449	-0.0576	0.5573	5.1326	0.1643	1.656	-0.0969	0.254	0.0663	-0.0687	0.1797	0.0165	-0.1476	-0.1024	-0.0853	0.1917	-0.0586	0.0267	0.3232	0.0413	0.2496	7.5782	32.2984	54.9293
6	8.1054	-0.1728	-2.2143	2.1715	0.1105	2.6274	0.0018	0.4963	-0.3412	-0.3371	-0.093	-0.1962	0.2003	0.0653	0.1263	0.3659	0.0582	-0.0015	0.289	-0.0437	0.2809	31.0084	16.1223	53.8592
7	6.7706	-2.081	2.5337	6.6497	-3.5828	2.3628	0.3619	0.3827	-0.4472	-0.4797	-0.2738	-0.1269	0.7787	0.2336	-0.1033	0.5435	0.0213	-0.0024	0.6205	-0.1069	0.3691	42.6231	11.4918	53.0573
8	4.0351	0.0313	0.5574	4.8836	-0.3412	3.7641	0.1762	0.1943	-0.6433	0.162	-0.1064	-0.1491	0.7092	0.0797	-0.0579	0.2794	-0.0586	-0.0393	0.2277	-0.0341	0.3151	20.7664	12.0713	61.6828
9	1.13	2.0424	1.8327	3.7679	3.4454	3.1211	-0.2715	0.1044	0.1206	-1.2084	0.8732	-1.165	-0.6693	0.6757	-0.6205	0.4815	-0.1947	0.2267	0.5304	-0.1928	0.655	26.0797	49.7959	59.7632
10	2.8504	0.0783	0.2718	5.406	1.8302	2.2882	0.0052	0.1427	-0.1743	0.0663	0.0393	0.8365	0.2487	-0.5457	0.0129	0.5297	-0.161	-0.0603	0.3614	0.0536	0.6209	39.2243	-16.2942	76.75
11	4.1983	1.5895	-0.7514	4.6738	-1.1894	2.9706	0.0215	-0.2143	-0.6113	0.0877	-0.0164	0.1618	0.4862	0.0256	-0.0224	0.5065	-0.0768	-0.0044	0.2866	0.0316	0.4436	50.4534	-17.4469	80.1501
12	1.8838	0.697	-1.6382	0.749	0.7465	5.1175	-0.5931	-0.1038	-0.6517	0.6945	0.5081	0.8388	0.2659	-0.5657	0.353	0.4792	0.0078	0.1463	0.7931	0.1733	0.5712	23.5825	-2.3672	99.3855
13	3.334	0.6601	-0.6543	3.1851	-0.7167	2.9336	0.0842	-0.741	-0.4004	0.513	-0.0864	0.1699	0.1629	-0.2826	0.1235	0.2982	-0.0644	0.0269	0.4579	0.0603	0.321	30.6949	8.3333	94.2259
14	7.9213	-5.0839	-1.1089	3.713	0.9176	4.1701	-0.3264	-0.4043	-1.225	-0.2848	0.2937	-0.5374	0.6494	1.1991	-0.0107	0.6745	0.2289	0.0346	0.6968	-0.0467	0.9916	73.6501	-21.9209	71.0461
15	9.8562	-4.7247	3.51	4.6972	-2.209	9.2899	0.4095	0.1967	-0.6421	-0.1288	-0.0574	-0.7827	0.7727	1.0616	-0.3655	0.571	0.0543	0.0408	0.4432	-0.1913	0.6305	72.234	-14.1694	61.8237
16	2.7973	0.4133	-1.0347	4.3057	-1.4381	1.9335	-0.112	0.0592	0.0182	0.1158	0.2189	-0.1793	-0.1237	0.1973	-0.1013	0.2249	-0.0482	-0.0053	0.2579	-0.0881	0.1789	63.1926	7.8066	66.6005
17	2.4144	-1.3698	-0.8409	7.2303	0.749	2.2481	-0.0505	0.1424	0.1621	-0.1987	0.1975	-0.4231	0.0035	0.2378	-0.1167	0.1694	-0.0714	-0.0311	0.3045	-0.0522	0.2085	62.772	10.7606	64.2384
18	3.6526	-0.8346	3.2726	7.1912	-1.3468	3.9736	0.0261	0.1795	0.5367	-0.1157	-0.0988	-0.1918	-0.0966	0.2548	0.2157	0.2201	-0.0299	0.0643	0.2994	-0.0251	0.3571	50.8867	27.129	64.5304
19	7.5796	1.6387	2.3487	6.1108	1.0757	1.6931	0.4748	0.5756	0.4359	-0.4082	-0.3354	0.3562	0.1253	-0.3301	-0.1041	0.5948	0.0963	0.015	0.6711	0.0818	0.4059	31.8882	27.9581	48.047
20	3.2334	-0.2786	0.1809	1.9316	0.1989	3.3489	-0.0011	0.0256	0.6111	0.0608	-0.032	0.1154	-0.637	-0.1451	0.018	0.3439	-0.0506	0.0291	0.2121	-0.0121	0.4093	49.1717	30.4357	66.7358
21	3.2863	4.5998	-3.2651	6.4906	-4.5973	3.2541	-0.5332	0.1176	0.316	-1.5992	0.9581	1.5446	0.7246	-0.8152	-0.3634	0.583	-0.2097	-0.2017	0.6015	0.1363	0.604	42.7444	-6.44	63.5098

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 8:198)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 199:393)
3	X-RAY DIFFRACTION	3	chain 'C' and (resseq 1:32)
4	X-RAY DIFFRACTION	4	chain 'C' and (resseq 33:53)
5	X-RAY DIFFRACTION	5	chain 'C' and (resseq 54:161)
6	X-RAY DIFFRACTION	6	chain 'C' and (resseq 162:207)
7	X-RAY DIFFRACTION	7	chain 'C' and (resseq 208:225)
8	X-RAY DIFFRACTION	8	chain 'C' and (resseq 226:259)
9	X-RAY DIFFRACTION	9	chain 'C' and (resseq 260:282)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 8:66)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 67:198)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 199:223)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 224:393)
14	X-RAY DIFFRACTION	14	chain 'D' and (resseq 1:32)
15	X-RAY DIFFRACTION	15	chain 'D' and (resseq 33:51)
16	X-RAY DIFFRACTION	16	chain 'D' and (resseq 52:106)
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 107:161)
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 162:186)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 187:225)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 226:259)
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 260:282)

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