PDB-6gvc: Structure of ArhGAP12 bound to G-Actin

ID or keywords:

Entry

Database: PDB / ID: 6gvc

Title

Structure of ArhGAP12 bound to G-Actin

Components

Actin, alpha skeletal muscle
Rho GTPase-activating protein 12

Keywords

HYDROLASE / GAP / RAC / Actin

Function / homology

Function and homology information

RHOV GTPase cycle / RHOF GTPase cycle / negative regulation of small GTPase mediated signal transduction / RHOD GTPase cycle / RAC1 GTPase cycle / cytoskeletal motor activator activity / phagocytosis, engulfment / tropomyosin binding / myosin heavy chain binding / mesenchyme migration ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Oryctolagus cuniculus (rabbit)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Mouilleron, S. / Treisman, R. / Diring, J.

Funding support

United Kingdom, 1items

Citation

Journal: Nat.Cell Biol. / Year: 2019
Title: RPEL-family rhoGAPs link Rac/Cdc42 GTP loading to G-actin availability.
Authors: Diring, J. / Mouilleron, S. / McDonald, N.Q. / Treisman, R.

History

Deposition	Jun 20, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6gvc.cif.gz	905.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6gvc.ent.gz	750.8 KB	Display	PDB format
PDBx/mmJSON format	6gvc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6gvc_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	6gvc_full_validation.pdf.gz	2.9 MB	Display
Data in XML	6gvc_validation.xml.gz	80.3 KB	Display
Data in CIF	6gvc_validation.cif.gz	107.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gv/6gvc ftp://data.pdbj.org/pub/pdb/validation_reports/gv/6gvc	HTTPS FTP

-
Related structure data

Related structure data	2v52S S: Starting model for refinement
Similar structure data	4jf1-d 4jev-d 4jew-d 3dup-d 4pkq-d 5cer-4 1ais-d 3k28-2 2pb2-d 2a2l-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) 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

Related structure data

2v52S

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#19 - Jul 2001 Actin similarity (10) #18 - Jun 2001 Myosin similarity (9) #245 - May 2020 Spliceosomes similarity (5) #148 - Apr 2012 Ras Protein similarity (2) #241 - Jan 2020 Twenty Years of Molecules similarity (3)

Deposited unit

B: Actin, alpha skeletal muscle

A: Actin, alpha skeletal muscle

C: Actin, alpha skeletal muscle

D: Actin, alpha skeletal muscle

R: Rho GTPase-activating protein 12

Q: Rho GTPase-activating protein 12

S: Rho GTPase-activating protein 12

T: Rho GTPase-activating protein 12

hetero molecules

279 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Actin, alpha skeletal muscle

R: Rho GTPase-activating protein 12

hetero molecules

defined by author&software
Evidence: gel filtration
69.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Actin, alpha skeletal muscle

S: Rho GTPase-activating protein 12

hetero molecules

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

3

C: Actin, alpha skeletal muscle

T: Rho GTPase-activating protein 12

hetero molecules

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

4

D: Actin, alpha skeletal muscle

Q: Rho GTPase-activating protein 12

hetero molecules

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

Unit cell

Length a, b, c (Å)	101.650, 130.240, 109.300
Angle α, β, γ (deg.)	90.00, 111.17, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
Protein , 2 types, 8 molecules BACDRQST

#1: Protein	Actin, alpha skeletal muscle / Alpha-actin-1 Mass: 42096.953 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein	Rho GTPase-activating protein 12 / Rho-type GTPase-activating protein 12 Mass: 26669.887 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arhgap12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8C0D4

-
Non-polymers , 5 types, 202 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-LAB / LATRUNCULIN B Mass: 395.513 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₂₀H₂₉NO₅S / Comment: toxin*YM
#5: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.85 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 0.2M Sodium Thiocyanate 0.1 M Bis Tris Propane pH6.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 7, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.6→54.132 Å / Num. obs: 81113 / % possible obs: 99.43 % / Redundancy: 6.2 % / B_iso Wilson estimate: 47.76 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.17 / R_pim(I) all: 0.06 / R_rim(I) all: 0.18 / Net I/av σ(I): 10.8 / Net I/σ(I): 10.8
Reflection shell	Resolution: 2.6→2.69 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.77 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 7746 / CC_1/2: 0.62 / R_pim(I) all: 0.48 / R_rim(I) all: 0.91 / % possible all: 95.83

-
Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2v52

2v52

Resolution: 2.6→54.132 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.34

	R_factor	Num. reflection	% reflection
R_free	0.2508	4063	5.01 %
R_work	0.2067	-	-
obs	0.209	81098	99.44 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.6→54.132 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17871	0	268	182	18321

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	18551
X-RAY DIFFRACTION	f_angle_d	0.615	25194
X-RAY DIFFRACTION	f_dihedral_angle_d	11.793	12828
X-RAY DIFFRACTION	f_chiral_restr	0.043	2878
X-RAY DIFFRACTION	f_plane_restr	0.004	3213

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 (%)
2.6002-2.6308	0.3908	137	0.3283	2297	X-RAY DIFFRACTION	89
2.6308-2.6629	0.3465	127	0.3155	2704	X-RAY DIFFRACTION	100
2.6629-2.6966	0.3375	137	0.301	2620	X-RAY DIFFRACTION	99
2.6966-2.732	0.3375	150	0.2902	2634	X-RAY DIFFRACTION	100
2.732-2.7695	0.3486	139	0.2858	2687	X-RAY DIFFRACTION	100
2.7695-2.809	0.3451	134	0.2868	2662	X-RAY DIFFRACTION	100
2.809-2.851	0.346	130	0.2767	2652	X-RAY DIFFRACTION	100
2.851-2.8955	0.3089	135	0.2769	2683	X-RAY DIFFRACTION	100
2.8955-2.943	0.303	123	0.2675	2639	X-RAY DIFFRACTION	100
2.943-2.9937	0.3209	116	0.2586	2706	X-RAY DIFFRACTION	100
2.9937-3.0481	0.3153	133	0.2543	2636	X-RAY DIFFRACTION	100
3.0481-3.1068	0.288	156	0.2508	2666	X-RAY DIFFRACTION	100
3.1068-3.1702	0.3224	133	0.2517	2661	X-RAY DIFFRACTION	100
3.1702-3.2391	0.307	156	0.2548	2640	X-RAY DIFFRACTION	100
3.2391-3.3144	0.271	148	0.2405	2662	X-RAY DIFFRACTION	100
3.3144-3.3973	0.2669	162	0.223	2649	X-RAY DIFFRACTION	100
3.3973-3.4892	0.2611	135	0.2108	2648	X-RAY DIFFRACTION	100
3.4892-3.5918	0.2743	152	0.2036	2658	X-RAY DIFFRACTION	100
3.5918-3.7077	0.212	147	0.1869	2657	X-RAY DIFFRACTION	100
3.7077-3.8402	0.2489	124	0.1869	2700	X-RAY DIFFRACTION	100
3.8402-3.9939	0.2297	153	0.1764	2644	X-RAY DIFFRACTION	100
3.9939-4.1756	0.2163	146	0.1723	2680	X-RAY DIFFRACTION	100
4.1756-4.3957	0.1854	154	0.1598	2663	X-RAY DIFFRACTION	100
4.3957-4.6709	0.1769	133	0.1461	2684	X-RAY DIFFRACTION	100
4.6709-5.0313	0.2045	130	0.1653	2699	X-RAY DIFFRACTION	100
5.0313-5.5372	0.2526	158	0.1866	2667	X-RAY DIFFRACTION	100
5.5372-6.3374	0.2386	137	0.1979	2690	X-RAY DIFFRACTION	100
6.3374-7.9803	0.2412	122	0.1988	2723	X-RAY DIFFRACTION	100
7.9803-54.1434	0.2075	156	0.1801	2724	X-RAY DIFFRACTION	99

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	0.5113	-0.2337	-0.0711	0.1486	0.0291	0.0141	-0.1131	-0.0356	0.2781	-0.1824	-0.1821	-0.1518	0.0782	-0.3916	-0.0304	0.3676	-0.0643	-0.0061	0.6302	0.103	0.2837	-12.4181	-21.5619	43.4373
2	0.388	0.173	-0.6298	0.1209	-0.2391	1.0715	-0.289	0.0606	0.5189	-0.3903	-0.2823	0.1946	0.1824	-0.1407	-0.2053	0.5084	0.1962	-0.0981	0.7062	0.1399	0.5479	-12.0351	-4.1033	40.5477
3	0.6078	-0.4735	-0.5205	0.4024	0.5364	0.9871	0.2558	-0.0984	0.1659	0.0972	0.1694	0.0566	-0.5677	-0.6533	0.6003	0.2842	0.2097	-0.0325	0.4762	0.2063	0.3214	-11.0496	-7.6769	47.0228
4	-0.0003	-0.017	-0.05	0.0039	0.1013	0.5492	0.0551	0.1648	0.0496	-0.0301	0.0801	0.0343	-0.0177	-0.4289	0.2162	0.275	0.0128	-0.035	0.4647	0.0852	0.3105	-5.0715	-21.8317	52.3813
5	0.0234	0.0328	0.0265	0.4242	0.3503	0.2829	0.025	0.0831	0.0556	0.1803	0.0539	-0.2629	-0.2955	-0.1022	0.0001	0.34	-0.0042	0.0098	0.2943	0.0377	0.3056	9.76	-15.5088	41.1971
6	0.308	0.5079	-0.0375	0.8726	-0.0993	0.4468	0.0254	0.2536	0.0264	-0.8166	0.336	-0.1639	-0.1458	-0.1394	0.2488	0.4594	-0.0518	0.0727	0.4399	0.1049	0.3312	8.3591	-10.9401	23.3625
7	0.3897	0.1221	-0.1067	0.2918	0.2415	0.3193	-0.1977	-0.0512	0.2775	-0.2188	0.0833	-0.5561	0.1969	-0.0082	0.0151	0.255	0.005	0.0076	0.2151	0.0175	0.3201	15.9197	-16.6838	34.9081
8	0.0842	0.0646	0.0865	0.0419	0.0551	0.0815	-0.1824	0.1024	0.0061	0.0748	0.184	-0.5882	0.1586	-0.2666	-0.0017	0.3915	-0.0144	-0.0519	0.3373	-0.0176	0.349	11.0267	-30.669	43.2714
9	0.1121	0.1139	-0.0813	0.1127	-0.0799	0.0562	-0.3497	0.1623	0.2345	-0.4639	0.2371	-0.3562	0.4642	-0.105	-0.0055	0.4371	0.0038	0.074	0.4184	-0.0465	0.4118	14.6505	-31.69	36.4133
10	0.2114	0.1576	-0.29	0.2285	-0.25	0.386	-0.0748	0.1962	0.0413	0.1279	-0.0967	-0.0142	-0.0621	-0.4669	-0.1376	0.2323	-0.0628	-0.0598	0.4484	0.1046	0.3182	-10.674	-26.644	55.6823
11	0.3236	-0.0659	-0.2485	0.5442	-0.0466	0.4273	-0.2552	-0.0454	-0.137	-0.0506	0.3412	-0.0724	0.5707	0.6286	0.2503	0.1271	0.5819	-0.0848	0.3915	0.0271	0.2459	-20.2458	14.2587	24.4424
12	0.2788	0.2043	0.0053	0.2213	-0.0097	0.0471	-0.2297	-0.0544	-0.0711	-0.1337	0.2497	0.3086	0.0244	0.1412	0.0006	0.3418	0.0613	-0.001	0.3625	-0.0052	0.3791	-28.7073	13.7681	6.8538
13	0.1863	-0.1194	-0.1743	1.1641	0.4348	0.2389	-0.2371	0.0579	0.0951	-0.4669	0.3853	-0.2281	0.0276	0.2033	0.1371	0.2821	0.0093	0.0192	0.3153	-0.0596	0.1833	-18.9521	9.8072	-5.0046
14	0.3594	-0.037	-0.4795	1.2739	0.1958	0.6076	-0.0417	0.03	0.0842	-0.1277	0.253	-0.0172	-0.0867	0.2736	0.1605	0.1619	0.1084	0.0002	0.3088	0.0092	0.2377	-28.2857	27.084	15.3998
15	0.1339	-0.1111	-0.0443	0.0899	0.0233	0.0743	-0.1381	0.189	0.2341	-0.2192	0.162	-0.4529	0.058	0.2754	0.0302	0.2984	-0.1286	0.0104	0.4385	-0.0714	0.668	0.9885	-10.7682	-28.0728
16	0.2045	-0.1391	-0.0776	0.2818	0.0838	0.2126	0.0722	0.1553	0.1002	-0.1583	-0.1109	-0.3518	-0.0598	-0.1178	0.0004	0.3462	-0.0646	0.1109	0.4174	-0.0523	0.6003	-1.5691	-16.2367	-32.1627
17	0.0573	-0.1285	0.0747	0.3519	-0.3268	0.2688	0.035	0.0282	-0.0272	-0.1383	0.082	-0.2369	-0.0954	0.0101	0	0.2446	0.0074	0.0284	0.3403	-0.0734	0.3735	-12.8087	-18.4783	-25.0854
18	0.6992	-0.0132	0.2077	0.2337	0.0829	0.1101	-0.1772	0.2592	-0.2015	-0.2632	0.0861	-0.1736	-0.246	-0.1505	-0.0278	0.5703	-0.1086	0.0335	0.3709	0.0236	0.2815	-19.1977	-3.2104	-32.4291
19	0.278	0.0888	0.2438	0.0299	0.0777	0.2121	-0.1792	0.3179	0.5774	-0.4434	0.1479	0.255	-0.2646	0.1063	-0.0446	0.6419	-0.2129	0.1098	0.5332	0.1262	0.4915	-5.5812	8.9231	-36.0638
20	0.9998	0.1751	-0.1488	1.2071	0.6179	1.0211	0.1075	0.1038	0.0305	-0.0428	0.0137	0.0303	-0.5053	-0.213	0.1206	0.4176	0.0395	0.0649	0.2901	-0.011	0.2867	-21.8155	3.2288	-24.6562
21	0.0582	0.0607	-0.0216	0.0788	-0.048	0.0471	-0.1729	0.0413	0.0395	0.1008	0.2726	-0.2321	0.0412	0.007	0.0001	0.3226	0.0178	0.0283	0.3474	-0.0584	0.5308	-9.4894	-31.4439	-21.1046
22	0.1625	-0.1503	0.0621	0.2001	0.0313	0.1429	0.0711	0.2346	0.0949	-0.5595	0.3013	0.312	-0.1664	0.1464	0.1508	0.395	-0.148	-0.1118	0.4155	0.0253	0.4379	10.8052	9.9729	-1.13
23	0.0226	-0.0191	0.0036	0.0162	-0.0023	-0.0013	-0.3805	0.2007	-0.389	-0.3526	0.3656	-0.0863	-0.0174	0.3119	-0.0016	0.668	-0.1472	-0.1053	0.501	-0.0415	0.5043	20.2265	8.1603	-11.6963
24	0.3874	-0.2568	-0.2346	0.1851	0.0302	0.5067	-0.0621	0.0693	0.0057	-0.197	-0.01	0.0613	0.2333	0.1023	-0.0351	0.3392	-0.0742	-0.0639	0.2711	0.0494	0.2979	16.6876	17.2404	2.3016
25	0.6495	0.1408	0.5147	0.0939	0.0603	0.4455	-0.4811	-0.0302	-0.1093	-0.2756	0.184	0.344	0.0524	0.5356	-0.416	0.5013	-0.0381	0.2066	0.2828	-0.0531	0.3467	29.3782	1.1977	5.6572
26	0.2211	-0.1463	-0.2005	0.3534	-0.1984	0.629	-0.2825	0.0797	-0.2696	-0.3067	-0.0422	0.0491	0.9316	-0.5276	-0.0478	0.7822	-0.0395	0.2081	0.3762	-0.0447	0.5649	23.545	-15.5842	1.0377
27	0.1802	0.2048	0.2396	0.836	-0.1505	0.5916	-0.1763	0.052	-0.082	0.1328	0.0503	-0.0018	0.362	0.1543	-0.0049	0.3957	-0.0139	0.0608	0.3001	-0.0016	0.3362	26.5427	-0.7007	15.3487
28	0.0458	-0.0187	0.0141	0.2734	0.2461	0.2286	0.1592	-0.112	0.119	0.0631	0.0454	0.303	-0.1071	0.2463	-0.0001	0.3382	-0.0122	-0.0912	0.3503	0.0254	0.4036	14.1756	29.496	8.0852
29	0.0972	0.106	-0.0328	0.1687	-0.0816	0.0571	-0.1042	-0.1042	0.0583	0.2468	-0.0091	0.0442	0.0144	-0.0665	0	0.3926	-0.0546	-0.023	0.4412	0.0401	0.3354	2.6565	-34.3276	58.0845
30	0.3132	-0.142	-0.1841	0.1119	0.2345	0.5394	0.0723	0.1787	0.1272	-0.1275	0.0286	-0.3226	-0.2494	0.0832	0.0369	0.2436	0.0126	-0.0391	0.1686	-0.0102	0.2443	14.0077	-7.9789	65.1187
31	0.1473	0.0018	0.1215	0.5209	0.2647	0.2291	0.0311	-0.103	0.0646	-0.0927	0.151	0.3287	0.1886	-0.2279	0	0.406	0.0259	-0.0039	0.362	0.0059	0.4196	8.0111	-10.1036	70.5209
32	0.0025	-0.0002	-0.026	0.1035	0.0209	0.0594	0.0021	-0.3486	0.2873	0.3323	0.1785	-0.0806	-0.0765	0.3959	0	0.5403	0.0404	0.0534	0.4702	-0.083	0.4241	11.2252	-6.5669	83.8212
33	0.1148	-0.0547	0.2472	0.0443	-0.1888	0.8923	0.0422	0.0197	0.2241	-0.0419	0.2519	-0.1641	-0.6226	-0.4307	0.2543	0.396	0.1213	0.0656	0.3473	-0.0957	0.4887	2.9159	-1.4706	74.9591
34	0.6441	0.2533	-0.0932	0.9699	-0.5252	0.2903	0.2773	0.2585	0.182	0.3121	0.2453	0.2097	-0.3372	0.3392	0.381	0.3713	0.0205	0.158	0.4632	-0.1641	0.4389	4.8796	-2.8783	84.315
35	0.0642	0.1416	-0.1219	0.3346	-0.2252	0.2057	0.041	0.1483	-0.0949	0.0011	0.1281	0.275	-0.4607	-0.1333	0.0125	0.3362	0.0519	-0.0152	0.3611	0.0548	0.4837	7.4111	12.9739	21.3586
36	0.0643	-0.0739	-0.0521	0.0756	0.049	0.0285	0.0549	0.1152	-0.1107	-0.0756	-0.132	-0.0256	-0.2391	0.249	0.0001	0.3465	-0.0511	-0.0603	0.4744	-0.0345	0.5751	30.9699	24.1112	19.026
37	0.1107	0.1298	0.029	0.35	-0.1883	0.2301	-0.0519	-0.0394	-0.1528	-0.1236	-0.0741	-0.0797	0.3075	-0.0733	0	0.3135	0.0187	0.0564	0.3383	0.0515	0.3408	46.9907	23.018	-0.3895
38	0.0449	0.0314	-0.0309	0.02	-0.014	0.0237	-0.1011	-0.3907	-0.1662	-0.024	-0.217	0.4623	0.1264	0.1159	0.0006	0.3667	0.0239	0.0661	0.3276	0.0355	0.4097	36.4875	14.8819	2.9032
39	0.0394	0.0327	0.0249	0.0471	0.0271	0.0175	-0.0911	-0.1479	0.1916	-0.5466	0.0708	-0.4079	0.0444	-0.1496	0.0008	0.5341	0.0411	0.0998	0.3011	0.0372	0.4605	45.1567	10.5564	0.8813
40	0.0796	-0.1403	-0.2657	0.6559	0.412	0.8508	-0.0073	0.2686	0.3148	0.0423	-0.2711	0.5625	-0.0542	-0.3759	-0.1721	0.2666	0.0566	-0.0858	0.3495	0.0344	0.512	39.4063	35.3854	0.3708
41	0.1195	-0.0965	0.0323	0.1254	-0.0844	0.0799	-0.1868	-0.0533	0.1292	0.0373	-0.0278	-0.0959	-0.6222	0.1448	-0.0251	0.5107	-0.1226	-0.1538	0.3923	0.2018	0.5958	48.7615	47.4628	1.1236
42	0.0775	-0.0012	0.0421	0.0326	0.0434	0.078	-0.0554	0.0305	0.2882	-0.0945	-0.3171	-0.2374	-0.1422	0.2383	-0.0918	0.428	-0.0546	-0.031	0.4135	0.1931	0.4317	50.8865	32.818	-1.9934
43	0.0719	0.1416	-0.1017	0.3964	-0.1874	0.1089	-0.0984	-0.0955	-0.1154	-0.2606	-0.0596	0.22	-0.1072	0.1839	0.0016	0.3852	0.0134	-0.0998	0.6131	0.0796	0.4898	40.7753	33.7732	-9.1521
44	0.1222	-0.0066	-0.0107	0.079	0.1406	0.2432	0.0364	0.053	0.2527	-0.7283	-0.2262	-0.3663	-0.3383	-0.3454	-0.0378	0.4561	0.0685	-0.1137	0.4065	0.1392	0.6571	46.0596	41.7799	-6.8056
45	0.034	-0.0107	-0.0776	0.2139	-0.0059	0.1829	-0.018	-0.3176	0.2374	0.3194	-0.0735	0.3218	0.1	0.1432	-0.006	0.3529	0.1157	0.021	0.4207	-0.0448	0.4711	-34.2629	32.7759	23.9753
46	0.4291	0.2283	-0.3815	0.1173	-0.2009	0.3243	0.1172	0.2087	-0.0417	-0.1285	-0.1919	-0.2085	0.4388	-0.1676	-0.0011	0.6515	0.0143	-0.0071	0.3385	0.0521	0.4963	-50.6631	4.5777	23.0054
47	0.1525	-0.0859	-0.0793	0.0846	0.0748	0.0689	0.2569	0.3642	0.0844	-0.1381	-0.1522	0.1486	0.5152	0.6693	0.0001	0.5017	0.1029	0.0613	0.3136	0.0465	0.423	-42.1497	7.4217	14.4459
48	0.4275	0.3858	-0.1563	0.4804	-0.434	0.7617	0.0383	-0.1958	-0.052	0.138	-0.0363	-0.0463	0.3351	-0.231	-0.0615	0.5878	0.0063	-0.0023	0.2934	0.0859	0.32	-51.9901	5.007	37.7828
49	0.1845	-0.2626	-0.0815	0.4422	-0.0175	0.1998	-0.1106	0.0438	-0.044	0.0174	0.2238	-0.0354	-0.0135	-0.0714	0.0003	0.4532	-0.0525	-0.0639	0.4618	-0.0409	0.4945	-21.0073	-19.7914	-14.6201
50	0.3306	-0.0371	-0.0011	0.3145	0.3213	0.3136	0.118	-0.1524	-0.0007	-0.285	-0.1282	-0.0523	-0.0086	0.2282	-0	0.427	0.0532	0.0288	0.3811	-0.0098	0.3896	-28.2848	-24.7051	-48.8382
51	0.2518	0.2107	0.2272	0.1766	0.1927	0.1974	0.0541	-0.1056	0.1054	-0.0514	-0.1268	-0.2475	-0.0781	-0.1701	-0.0001	0.3196	-0.0269	0.0023	0.3269	-0.0585	0.3072	-23.9443	-18.0757	-43.99
52	0.5102	0.1036	0.0414	0.4568	-0.0151	0.4933	-0.0466	0.2214	-0.6052	-0.2041	-0.0965	-0.1754	0.2827	0.3023	-0.0229	0.4475	0.0865	0.0163	0.4074	-0.0921	0.5441	-24.5881	-40.9228	-49.6638

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 5 through 28 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 29 through 60 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 61 through 97 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 98 through 165 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 166 through 196 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 197 through 246 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 247 through 283 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 284 through 308 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 309 through 334 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 335 through 375 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 5 through 165 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 166 through 196 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 197 through 273 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 274 through 375 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 5 through 60 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 61 through 112 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 113 through 165 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 166 through 196 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 197 through 216 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 217 through 348 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 349 through 375 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 6 through 38 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 39 through 78 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 79 through 165 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 166 through 196 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 197 through 246 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 247 through 347 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 348 through 375 )
29	X-RAY DIFFRACTION	29	chain 'R' and (resid 568 through 602 )
30	X-RAY DIFFRACTION	30	chain 'R' and (resid 603 through 653 )
31	X-RAY DIFFRACTION	31	chain 'R' and (resid 654 through 702 )
32	X-RAY DIFFRACTION	32	chain 'R' and (resid 703 through 737 )
33	X-RAY DIFFRACTION	33	chain 'R' and (resid 738 through 770 )
34	X-RAY DIFFRACTION	34	chain 'R' and (resid 771 through 790 )
35	X-RAY DIFFRACTION	35	chain 'Q' and (resid 561 through 581 )
36	X-RAY DIFFRACTION	36	chain 'Q' and (resid 582 through 602 )
37	X-RAY DIFFRACTION	37	chain 'Q' and (resid 603 through 641 )
38	X-RAY DIFFRACTION	38	chain 'Q' and (resid 642 through 653 )
39	X-RAY DIFFRACTION	39	chain 'Q' and (resid 654 through 667 )
40	X-RAY DIFFRACTION	40	chain 'Q' and (resid 668 through 702 )
41	X-RAY DIFFRACTION	41	chain 'Q' and (resid 703 through 718 )
42	X-RAY DIFFRACTION	42	chain 'Q' and (resid 719 through 737 )
43	X-RAY DIFFRACTION	43	chain 'Q' and (resid 738 through 770 )
44	X-RAY DIFFRACTION	44	chain 'Q' and (resid 771 through 790 )
45	X-RAY DIFFRACTION	45	chain 'S' and (resid 567 through 602 )
46	X-RAY DIFFRACTION	46	chain 'S' and (resid 603 through 641 )
47	X-RAY DIFFRACTION	47	chain 'S' and (resid 642 through 667 )
48	X-RAY DIFFRACTION	48	chain 'S' and (resid 668 through 790 )
49	X-RAY DIFFRACTION	49	chain 'T' and (resid 561 through 602 )
50	X-RAY DIFFRACTION	50	chain 'T' and (resid 603 through 641 )
51	X-RAY DIFFRACTION	51	chain 'T' and (resid 642 through 681 )
52	X-RAY DIFFRACTION	52	chain 'T' and (resid 682 through 790 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 2 types, 8 molecules BACDRQST

-
Non-polymers , 5 types, 202 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 2 types, 8 molecules BACDRQST

-Non-polymers , 5 types, 202 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 2 types, 8 molecules BACDRQST

-
Non-polymers , 5 types, 202 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
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