PDB-4pc2: Elongation factor Tu:Ts complex with a bound GDP

ID or keywords:

Entry

Database: PDB / ID: 4pc2

Title

Elongation factor Tu:Ts complex with a bound GDP

Components

(Elongation factor ...) x 2

Keywords

TRANSLATION / G:GEF:GDP complex / Elongation Factor Tu / Elongation factor Ts

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: 2.1999 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	Mar 7, 2018	Group: Database references / Derived calculations / Source and taxonomy Category: citation / entity_src_gen / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4pc2.cif.gz	737.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4pc2.ent.gz	624.4 KB	Display	PDB format
PDBx/mmJSON format	4pc2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4pc2_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4pc2_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4pc2_validation.xml.gz	51 KB	Display
Data in CIF	4pc2_validation.cif.gz	74.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pc/4pc2 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/4pc2	HTTPS FTP

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Related structure data

Related structure data	4pc1SC 4pc3C 4pc6C 4pc7C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4pc6-1 4pc3-2 4pc1-2 4pc1-1 4pc3-1 4pc6-2 1i1m-d 1xmx-2 1a3g-d 1iyd-d 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 (22) #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 (5) #60 - Dec 2004 Ubiquitin 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
74.4 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
74.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.927, 108.510, 193.750
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Elongation factor ... , 2 types, 4 molecules ABCD

#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) / Gene: tsf, BN17_45931, ECs0172, LF82_2325 / Production host: Escherichia coli (E. coli) / References: UniProt: C3TPM7

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Non-polymers , 4 types, 718 molecules

#3: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.63 Å³/Da / Density % sol: 53.27 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM Hepes 73 mM Tris 17% PEG 6000 5% glycerol 150mM NaCl 1mM GDP 5mM EDTA

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.944 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 22, 2002
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.944 Å / Relative weight: 1
Reflection	Resolution: 2.1999→35 Å / Num. obs: 78193 / % possible obs: 97.8 % / Redundancy: 5 % / R_merge(I) obs: 0.044 / Net I/σ(I): 18.1
Reflection shell	Resolution: 2.1999→2.28 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.252 / Mean I/σ(I) obs: 4.2 / % possible all: 85.3

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Processing

Software

Name: PHENIX / Version: (phenix.refine: dev_1593) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PC1

4pc1

Resolution: 2.1999→34.989 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 19.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2136	4290	5.62 %	random
R_work	0.1652	-	-	-
obs	0.1679	76340	95.55 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1999→34.989 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9895	0	73	709	10677

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	10155
X-RAY DIFFRACTION	f_angle_d	1.149	13717
X-RAY DIFFRACTION	f_dihedral_angle_d	14.543	3827
X-RAY DIFFRACTION	f_chiral_restr	0.044	1577
X-RAY DIFFRACTION	f_plane_restr	0.005	1779

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 (%)
2.1999-2.2249	0.2275	104	0.211	1694	X-RAY DIFFRACTION	68
2.2249-2.2511	0.2123	107	0.1836	2054	X-RAY DIFFRACTION	82
2.2511-2.2786	0.2179	129	0.1849	2105	X-RAY DIFFRACTION	86
2.2786-2.3074	0.2314	126	0.1892	2216	X-RAY DIFFRACTION	88
2.3074-2.3377	0.2519	134	0.186	2298	X-RAY DIFFRACTION	93
2.3377-2.3698	0.2391	127	0.1751	2333	X-RAY DIFFRACTION	93
2.3698-2.4036	0.2147	138	0.1778	2335	X-RAY DIFFRACTION	94
2.4036-2.4395	0.249	147	0.181	2380	X-RAY DIFFRACTION	95
2.4395-2.4776	0.2202	153	0.178	2340	X-RAY DIFFRACTION	95
2.4776-2.5182	0.212	155	0.1815	2387	X-RAY DIFFRACTION	96
2.5182-2.5616	0.2233	163	0.1766	2356	X-RAY DIFFRACTION	96
2.5616-2.6082	0.245	170	0.1825	2364	X-RAY DIFFRACTION	97
2.6082-2.6583	0.243	164	0.1844	2427	X-RAY DIFFRACTION	97
2.6583-2.7126	0.2286	135	0.1776	2422	X-RAY DIFFRACTION	97
2.7126-2.7715	0.2367	151	0.1823	2435	X-RAY DIFFRACTION	98
2.7715-2.836	0.2259	192	0.1854	2423	X-RAY DIFFRACTION	98
2.836-2.9069	0.2602	146	0.1839	2449	X-RAY DIFFRACTION	99
2.9069-2.9854	0.2513	176	0.1804	2439	X-RAY DIFFRACTION	99
2.9854-3.0732	0.2555	160	0.1847	2480	X-RAY DIFFRACTION	99
3.0732-3.1723	0.1959	154	0.1826	2468	X-RAY DIFFRACTION	99
3.1723-3.2856	0.2273	177	0.174	2479	X-RAY DIFFRACTION	99
3.2856-3.4171	0.2393	219	0.1703	2411	X-RAY DIFFRACTION	100
3.4171-3.5725	0.2033	155	0.1618	2521	X-RAY DIFFRACTION	100
3.5725-3.7606	0.2141	129	0.1554	2550	X-RAY DIFFRACTION	100
3.7606-3.9959	0.2016	116	0.1547	2535	X-RAY DIFFRACTION	99
3.9959-4.3039	0.1911	122	0.143	2561	X-RAY DIFFRACTION	100
4.3039-4.7361	0.1411	103	0.127	2591	X-RAY DIFFRACTION	100
4.7361-5.4192	0.1837	100	0.1392	2614	X-RAY DIFFRACTION	100
5.4192-6.8194	0.1856	115	0.1726	2637	X-RAY DIFFRACTION	100
6.8194-34.9935	0.175	123	0.1543	2746	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	2.1636	0.5407	-0.1872	4.7025	-2.1691	2.5023	-0.3601	0.0602	-0.3494	-0.2947	0.4145	0.0221	0.3435	-0.2757	-0.0578	0.429	-0.0538	0.0627	0.4343	-0.0259	0.3355	59.5898	-6.0664	72.9857
2	1.2033	0.4078	-0.0802	1.9512	-1.3193	2.5302	-0.0226	-0.3202	-0.1542	0.1132	-0.0575	0.0247	0.0514	0.0407	0.0667	0.2154	0.0761	0.0253	0.3229	0.0302	0.2739	45.7533	17.4086	94.1794
3	2.8634	-0.2282	-2.7136	3.9997	1.6281	3.119	-0.2735	-0.4812	0.1248	0.8798	0.4729	-0.1999	0.7522	0.8913	-0.2183	0.4927	0.1303	0.0758	0.5784	-0.09	0.4094	81.4494	-6.8631	57.1729
4	4.4164	-5.6418	0.1741	7.3646	-0.1632	0.5353	0.6725	0.0438	0.1589	-0.6749	-0.2292	-0.4438	-0.0899	0.4262	-0.3963	0.4227	0.0122	0.0552	0.3852	-0.1253	0.3133	75.0029	-0.3511	48.6022
5	1.4977	1.4013	-0.3666	6.9712	-1.3311	1.062	-0.0663	0.172	-0.0972	0.2974	0.0835	-0.0997	0.0374	-0.0346	-0.0066	0.1952	-0.0186	0.0146	0.2143	-0.0469	0.2134	66.7031	20.1827	55.7559
6	1.1611	-1.007	-0.5663	6.3145	1.5948	2.3368	-0.025	0.0522	0.0023	-0.1253	0.1199	-0.1421	0.0225	0.1554	-0.0882	0.1026	-0.0538	-0.0194	0.2504	-0.03	0.208	65.5562	22.872	53.9511
7	8.0463	0.9025	6.0683	3.6076	0.0805	9.4711	-0.0488	0.2298	0.2039	0.1345	0.0528	0.1309	-0.3357	0.1993	0.0379	0.1999	0.0024	0.0837	0.2012	-0.0054	0.2266	54.0247	38.7808	58.9632
8	5.4156	5.4771	-6.7913	7.4112	-5.9533	9.3445	-0.0909	0.8031	0.0463	-0.4329	-0.0182	0.0694	0.1787	-0.1409	0.105	0.4048	0.0867	-0.0623	0.3874	-0.0102	0.2883	31.1606	36.7288	47.0925
9	6.4225	0.9667	-1.2441	4.3933	1.8936	1.584	0.3461	0.4658	0.3908	-0.3205	-0.0406	0.0572	-0.3213	-0.1893	-0.2326	0.3971	0.0106	0.0391	0.372	0.0744	0.2928	30.063	42.2464	52.9809
10	3.5736	0.7017	-0.5254	4.0903	0.1522	3.8027	0.1013	-0.0743	0.37	0.0933	-0.0016	-0.0073	-0.5208	-0.0705	-0.0962	0.208	-0.0194	0.029	0.1761	0.004	0.2363	53.1649	42.0542	61.6846
11	3.0391	5.0657	-2.7703	8.48	-4.6023	2.5317	-0.0404	-0.3494	-0.2895	-1.0039	0.462	0.8789	0.7678	-0.6988	-0.3521	0.5559	-0.1959	-0.2289	0.5356	0.2137	0.6256	47.7781	3.1086	60.2431
12	0.7162	0.5328	-0.5675	4.6049	-0.2469	1.6315	-0.0718	0.2121	0.0171	-0.0118	0.0145	-0.671	-0.0888	0.3331	0.0408	0.3926	-0.1052	-0.0385	0.405	0.0182	0.4931	34.6622	67.364	78.2806
13	4.9336	1.0521	1.0351	4.2904	0.4925	3.5648	-0.1274	-0.028	0.717	0.01	-0.0741	0.4326	-0.4385	-0.2085	0.1303	0.4181	-0.0129	-0.0293	0.3241	-0.0302	0.3988	19.8064	74.4008	80.2151
14	2.0392	0.7835	0.691	2.5264	0.6255	2.0751	0.1137	-0.3766	0.1584	0.3715	-0.1091	-0.2265	-0.0314	0.1106	0.0102	0.2383	-0.0178	-0.0173	0.3357	-0.006	0.2905	44.1286	47.1622	95.023
15	6.924	-6.259	0.0193	7.3685	-0.9929	2.2368	-0.6116	-0.7534	1.2493	0.3093	0.2007	0.3537	-0.7985	-0.6272	0.2098	0.5839	0.1753	-0.1591	0.5413	-0.1062	0.9077	0.4112	76.5042	71.3408
16	4.1559	-5.5937	-2.1258	8.6988	1.9245	8.0345	-0.0801	-0.2246	0.4699	-0.2621	0.1259	0.5679	-0.6885	-0.6446	-0.0814	0.43	-0.0024	-0.108	0.3579	0.0679	0.4221	1.8815	68.6326	62.0424
17	2.9661	1.2097	0.6814	4.2504	1.4022	1.2201	-0.0352	0.0191	-0.0436	0.2096	0.0206	-0.0558	-0.0006	-0.0537	0.0038	0.2165	-0.0299	-0.0229	0.183	0.0426	0.1528	10.7738	46.4105	66.548
18	1.7092	-1.9463	0.62	7.245	-1.4446	1.9962	-0.0839	0.0248	-0.125	-0.0903	0.1706	0.363	-0.0109	-0.1028	-0.0746	0.1546	-0.0394	0.0372	0.251	0.0421	0.1875	11.4376	43.6156	64.3314
19	6.1195	0.4777	-2.8107	4.6416	-0.4056	4.6928	-0.0769	-0.0559	-0.6058	0.0873	0.0268	-0.0064	0.1492	-0.154	0.0884	0.163	0.0103	-0.0296	0.1861	0.0101	0.3151	23.0623	27.1255	64.5632
20	3.3177	3.0655	1.2876	3.017	0.7658	2.6159	-0.1252	1.3481	-0.3754	-0.2214	0.1916	-0.0777	-0.0638	0.0269	-0.0439	0.4142	0.0479	0.0384	0.4398	-0.049	0.3052	41.7786	28.8801	45.5625
21	9.1865	-0.3795	-6.9274	5.2084	-1.5908	7.4799	0.27	0.6173	-0.5989	-0.1807	-0.1112	0.0995	0.6075	-0.3599	-0.1463	0.4108	0.0302	-0.1238	0.4268	-0.0833	0.3915	42.1618	23.0758	50.9399
22	3.3555	0.1725	0.3217	3.6762	-0.6751	3.6418	0.124	-0.1224	-0.6788	0.0604	-0.0495	-0.0961	0.4353	0.1543	-0.0634	0.2157	-0.0039	-0.0105	0.1968	0.0112	0.2973	24.7891	23.8709	66.8093
23	2.6452	3.4091	2.2733	4.3898	2.9272	1.9509	-0.4384	0.3228	-0.1843	-1.0893	0.5861	-1.0698	-0.6252	0.8785	-0.1245	0.5472	-0.213	0.1425	0.6309	-0.0079	0.4886	31.8179	61.45	63.7186

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 33:51)
5	X-RAY DIFFRACTION	5	chain 'C' and (resseq 52:106)
6	X-RAY DIFFRACTION	6	chain 'C' and (resseq 107:161)
7	X-RAY DIFFRACTION	7	chain 'C' and (resseq 162:186)
8	X-RAY DIFFRACTION	8	chain 'C' and (resseq 187:204)
9	X-RAY DIFFRACTION	9	chain 'C' and (resseq 205:225)
10	X-RAY DIFFRACTION	10	chain 'C' and (resseq 226:259)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 260:282)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 8:106)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 107:198)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 199:393)
15	X-RAY DIFFRACTION	15	chain 'D' and (resseq 1:32)
16	X-RAY DIFFRACTION	16	chain 'D' and (resseq 33:51)
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 52:106)
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 107:161)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 162:186)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 187:207)
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 208:225)
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 226:259)
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 260:282)

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Elongation factor ... , 2 types, 4 molecules ABCD

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Non-polymers , 4 types, 718 molecules

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-Elongation factor ... , 2 types, 4 molecules ABCD

-Non-polymers , 4 types, 718 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

-
Validation report

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Related structure data

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Links

-
Assembly

-
Components

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Elongation factor ... , 2 types, 4 molecules ABCD

-
Non-polymers , 4 types, 718 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi