PDB-6aj4: Crystal structure of the DHR-2 domain of DOCK7 in complex with Cdc42

ID or keywords:

Entry

Database: PDB / ID: 6aj4

Title

Crystal structure of the DHR-2 domain of DOCK7 in complex with Cdc42

Components

Cell division control protein 42 homolog
Dedicator of cytokinesis protein 7

Keywords

SIGNALING PROTEIN / DOCK / GEF / DHR-2 /

GTPase / Rho / Rac /

Cdc42

Function / homology

Function and homology information

establishment of neuroblast polarity / interkinetic nuclear migration / GBD domain binding / submandibular salivary gland formation / actin filament branching /

Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process /

Cdc42 protein signal transduction ...establishment of neuroblast polarity / interkinetic nuclear migration / GBD domain binding / submandibular salivary gland formation / actin filament branching /

Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process /

Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / neuron fate determination / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 /

cardiac conduction system development / GTP-dependent protein binding /

regulation of filopodium assembly / basal part of cell / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport /

cell junction assembly /

filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / embryonic heart tube development /

thioesterase binding /

regulation of stress fiber assembly / activation of GTPase activity / positive regulation of vascular associated smooth muscle cell migration / RHO GTPases activate KTN1 /

regulation of lamellipodium assembly / nuclear migration / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / negative regulation of cold-induced thermogenesis / adherens junction organization /

sprouting angiogenesis /

Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / regulation of mitotic nuclear division / establishment or maintenance of cell polarity /

phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction /

heart contraction /

Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle /

regulation of neurogenesis / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / negative regulation of protein-containing complex assembly / phagocytic vesicle / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation /

axonogenesis / guanyl-nucleotide exchange factor activity /

small monomeric GTPase / G protein activity /

filopodium / positive regulation of DNA replication /

secretory granule / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / EGFR downregulation / positive regulation of JNK cascade / MAPK6/MAPK4 signaling
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.256 Å

Authors

Kukimoto-Niino, M. / Shirouzu, M.

Funding support

Japan, 1items

Citation

Journal: Structure / Year: 2019
Title: Structural Basis for the Dual Substrate Specificity of DOCK7 Guanine Nucleotide Exchange Factor.
Authors: Kukimoto-Niino, M. / Tsuda, K. / Ihara, K. / Mishima-Tsumagari, C. / Honda, K. / Ohsawa, N. / Shirouzu, M.

History

Deposition	Aug 27, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2	May 22, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.3	Nov 22, 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

-
Download

PDBx/mmCIF format	6aj4.cif.gz	752.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6aj4.ent.gz	632.6 KB	Display	PDB format
PDBx/mmJSON format	6aj4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aj/6aj4 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/6aj4	HTTPS FTP

-
Related structure data

Related structure data	6ajlC 3vhlS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6ajl-1 6ajl-2 6ajl-3 6ajl-4 6axq-d 7auc-d 6hlm-2 6hlj-1 6q9c-1 6hli-1 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

6ajlC

3vhlS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#245 - May 2020 Spliceosomes similarity (15) #148 - Apr 2012 Ras Protein similarity (5) #35 - Nov 2002 Ferritin and Transferrin similarity (7) #43 - Jul 2003 Src Tyrosine Kinase similarity (6) #60 - Dec 2004 Ubiquitin similarity (4) #44 - Aug 2003 Calmodulin similarity (2) #64 - Apr 2005 Kinesin similarity (1) #196 - Apr 2016 Lead Poisoning similarity (3) #28 - Apr 2002 Anthrax Toxin similarity (2) #195 - Mar 2016 RAF Protein Kinases similarity (2) #128 - Aug 2010 Interferons similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #239 - Nov 2019 Phospholipase A2 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#245 - May 2020
Spliceosomes
similarity (15)
#148 - Apr 2012
Ras Protein
similarity (5)
#35 - Nov 2002
Ferritin and Transferrin
similarity (7)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (6)
#60 - Dec 2004
Ubiquitin
similarity (4)
#44 - Aug 2003
Calmodulin
similarity (2)
#64 - Apr 2005
Kinesin
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (3)
#28 - Apr 2002
Anthrax Toxin
similarity (2)
#195 - Mar 2016
RAF Protein Kinases
similarity (2)
#128 - Aug 2010
Interferons
similarity (1)
#94 - Oct 2007
Superoxide Dismutase
similarity (1)
#205 - Jan 2017
Nuclear Pore Complex
similarity (1)
#163 - Jul 2013
HIV Capsid
similarity (1)
#239 - Nov 2019
Phospholipase A2
similarity (1)

Deposited unit

A: Dedicator of cytokinesis protein 7

B: Cell division control protein 42 homolog

C: Dedicator of cytokinesis protein 7

D: Cell division control protein 42 homolog

E: Dedicator of cytokinesis protein 7

F: Cell division control protein 42 homolog

G: Dedicator of cytokinesis protein 7

H: Cell division control protein 42 homolog

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

1

A: Dedicator of cytokinesis protein 7

B: Cell division control protein 42 homolog

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

2

C: Dedicator of cytokinesis protein 7

D: Cell division control protein 42 homolog

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

3

E: Dedicator of cytokinesis protein 7

F: Cell division control protein 42 homolog

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

4

G: Dedicator of cytokinesis protein 7

H: Cell division control protein 42 homolog

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

Unit cell

Length a, b, c (Å)	196.460, 105.560, 118.140
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Dedicator of cytokinesis protein 7 Mass: 33877.574 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: DOCK7, KIAA1771 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q96N67
#2: Protein	Cell division control protein 42 homolog / G25K GTP-binding protein Mass: 21461.537 Da / Num. of mol.: 4 / Mutation: C188S Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P60953

#1: Protein

Dedicator of cytokinesis protein 7

Mass: 33877.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.)

Homo sapiens (human) / Gene: DOCK7, KIAA1771 / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: Q96N67

#2: Protein

Cell division control protein 42 homolog / G25K GTP-binding protein

Mass: 21461.537 Da / Num. of mol.: 4 / Mutation: C188S
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.)

Homo sapiens (human) / Gene: CDC42 / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: P60953

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.55 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350 and tri-potassium citrate monohydrate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 16, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.256→50 Å / Num. obs: 73997 / % possible obs: 99.4 % / Redundancy: 3.9 % / CC_1/2: 0.996 / R_rim(I) all: 0.12 / Net I/σ(I): 11.9
Reflection shell	Resolution: 3.26→3.45 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 11796 / CC_1/2: 0.639 / R_rim(I) all: 0.96 / % possible all: 97.8

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3VHL

3vhl

Resolution: 3.256→46.802 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0.95 / Phase error: 27.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2588	3777	5.11 %
R_work	0.1837	-	-
obs	0.1876	73981	99.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.256→46.802 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14684	0	0	0	14684

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	15020
X-RAY DIFFRACTION	f_angle_d	1.289	20320
X-RAY DIFFRACTION	f_dihedral_angle_d	5.155	9152
X-RAY DIFFRACTION	f_chiral_restr	0.061	2248
X-RAY DIFFRACTION	f_plane_restr	0.008	2624

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 (%)
3.256-3.2972	0.353	127	0.3212	2446	X-RAY DIFFRACTION	91
3.2972-3.3406	0.3776	138	0.3025	2556	X-RAY DIFFRACTION	100
3.3406-3.3863	0.3224	145	0.2906	2653	X-RAY DIFFRACTION	100
3.3863-3.4347	0.3651	140	0.2809	2596	X-RAY DIFFRACTION	100
3.4347-3.4859	0.4361	141	0.276	2589	X-RAY DIFFRACTION	99
3.4859-3.5404	0.3294	137	0.2603	2582	X-RAY DIFFRACTION	99
3.5404-3.5984	0.3118	140	0.2345	2629	X-RAY DIFFRACTION	99
3.5984-3.6604	0.3108	134	0.2242	2576	X-RAY DIFFRACTION	99
3.6604-3.727	0.3087	142	0.2215	2575	X-RAY DIFFRACTION	100
3.727-3.7986	0.3107	141	0.1995	2630	X-RAY DIFFRACTION	100
3.7986-3.8761	0.2753	143	0.2029	2615	X-RAY DIFFRACTION	100
3.8761-3.9604	0.2753	141	0.2027	2581	X-RAY DIFFRACTION	100
3.9604-4.0524	0.2855	144	0.1922	2632	X-RAY DIFFRACTION	100
4.0524-4.1537	0.2891	141	0.1888	2596	X-RAY DIFFRACTION	100
4.1537-4.266	0.3107	139	0.1731	2607	X-RAY DIFFRACTION	100
4.266-4.3914	0.2364	141	0.1577	2667	X-RAY DIFFRACTION	100
4.3914-4.533	0.2045	138	0.1535	2564	X-RAY DIFFRACTION	100
4.533-4.6949	0.1908	144	0.1484	2586	X-RAY DIFFRACTION	100
4.6949-4.8827	0.2425	141	0.1499	2627	X-RAY DIFFRACTION	100
4.8827-5.1046	0.2312	138	0.1507	2614	X-RAY DIFFRACTION	100
5.1046-5.3734	0.2389	139	0.1499	2625	X-RAY DIFFRACTION	100
5.3734-5.7095	0.2621	137	0.1603	2599	X-RAY DIFFRACTION	100
5.7095-6.1495	0.2179	143	0.1654	2623	X-RAY DIFFRACTION	100
6.1495-6.7667	0.2826	143	0.1873	2603	X-RAY DIFFRACTION	100
6.7667-7.742	0.2468	140	0.1802	2606	X-RAY DIFFRACTION	100
7.742-9.7396	0.1834	140	0.1288	2617	X-RAY DIFFRACTION	100
9.7396-46.8069	0.2194	140	0.1794	2610	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	4.0502	1.871	-3.2437	6.0853	2.3644	6.4901	-0.1401	0.9221	-0.4635	-0.938	0.2168	-0.084	0.1072	0.9605	-0.0247	0.5812	0.0247	0.0033	0.9096	-0.0676	0.4568	7.8346	7.5708	-0.506
2	7.1338	-0.8232	-4.5657	6.4592	5.7116	7.7471	-0.116	1.2326	-0.1912	-2.2679	0.8508	0.0343	-1.4621	2.0557	-0.5725	1.2056	-0.4821	0.123	1.4763	-0.2721	0.686	18.2754	14.8679	-7.318
3	4.9191	0.9716	1.233	4.6361	2.306	3.5741	-0.3292	0.7523	0.1622	-0.8295	0.272	0.1004	-1.2063	-0.268	0.0388	0.8074	0.1	0.0503	0.6794	0.0805	0.4043	-0.087	19.5775	5.7498
4	3.432	-0.742	0.3624	5.6559	-0.3488	4.8686	-0.0826	-0.6712	0.5194	0.1349	0.3365	-0.0224	-0.6919	0.0819	-0.2045	0.5759	-0.0701	0.0556	0.5992	-0.1536	0.4931	7.0898	28.4425	30.4674
5	6.0016	1.0604	-0.4861	7.5691	-1.2627	9.5628	-0.0104	0.4709	-0.3418	-0.0142	-0.1135	-0.2502	-0.721	1.1645	0.1579	0.5576	0.0193	0.0214	0.8211	-0.1558	0.4757	19.1981	12.9221	22.8827
6	3.3104	-1.3981	0.7875	7.5119	2.0454	4.1619	0.3172	0.4409	-0.2923	-0.1879	-0.2182	-0.108	-0.3294	0.4403	-0.1139	0.5733	-0.1269	0.0136	0.8324	-0.1249	0.612	12.4281	14.6435	17.0521
7	3.2887	0.0351	0.6933	6.0461	0.7897	4.8685	0.1607	-0.5198	0.3027	0.4274	-0.0236	-0.8998	-0.0767	0.7889	-0.1176	0.4418	-0.0258	-0.0581	0.9643	-0.2053	0.6672	27.2419	12.2836	29.2014
8	3.3851	3.404	-0.4353	7.0701	-1.3783	0.3055	-0.6969	2.5066	0.4858	-3.6823	0.2087	-1.3168	-0.8182	2.5817	0.4643	1.5317	-0.2079	0.5924	1.5714	0.1979	1.0516	37.3422	14.9536	6.7446
9	6.2893	3.0651	-2.0415	6.3223	2.4752	6.4821	-1.0996	0.4672	-0.7969	-1.6217	0.6351	-0.6864	1.0831	0.9715	0.5508	0.5465	-0.0912	0.2129	1.2469	-0.0604	1.0649	39.3884	4.7773	17.5538
10	3.5156	-1.1775	-4.0571	9.8933	-1.0366	5.3596	0.5724	-0.282	0.7177	-1.246	-0.4433	-0.9732	0.7041	0.7014	-0.0163	0.595	0.0171	0.1694	0.5922	-0.1264	0.5724	26.6936	5.2529	16.339
11	5.1613	1.9229	-5.1607	5.3442	-1.7738	5.2025	-1.1488	0.7391	-0.98	-0.3229	-0.4368	-0.6142	1.0204	-0.8096	1.1791	0.623	0.0138	-0.006	0.6936	-0.0982	0.5786	18.5058	1.2519	21.7495
12	4.3044	0.3957	1.7607	3.6283	1.5532	4.0119	-0.2038	-0.6498	0.5107	0.9145	0.331	-0.5454	-0.1132	0.7685	0.0035	0.6582	0.0397	-0.0041	0.9789	-0.2418	0.6804	13.689	-6.0242	91.0116
13	5.2136	-0.6616	-0.0502	3.9358	-0.0879	2.5119	-0.103	-0.4197	0.0663	0.3854	0.2259	0.0392	0.682	-0.0292	-0.1131	0.654	-0.0628	-0.0374	0.4822	0.0022	0.3982	5.9904	-18.6109	82.5451
14	6.8595	-4.6353	5.1442	5.0461	-6.5646	8.7143	-0.4316	-0.4713	0.249	0.1745	0.882	0.2467	-0.1983	-1.1804	-0.3061	0.5015	-0.0369	-0.0027	0.5089	-0.01	0.4823	11.3129	-23.4075	65.366
15	2.7589	-0.1854	0.1453	7.2951	-2.0904	4.7003	-0.0807	0.4965	-0.2877	-0.8657	0.1769	-0.538	0.8025	0.3946	-0.0722	0.696	-0.011	0.1015	0.6751	-0.1268	0.51	16.2962	-25.0245	56.3559
16	0.7349	-1.0239	2.3503	7.6042	0.816	9.6938	0.0603	-0.0349	-0.1831	0.4203	-0.0049	-0.1571	0.63	0.679	-0.1318	0.4387	-0.143	0.0999	0.4806	-0.1058	0.6998	22.0783	-6.5036	65.8099
17	0.5747	-0.6539	-1.7476	6.1976	0.2182	7.329	0.1842	-0.4261	0.5107	0.2642	0.0299	-0.3865	0.1576	0.8602	-0.3406	0.3463	-0.0048	0.0436	0.6043	-0.0667	0.6934	20.4569	-9.6694	65.7152
18	1.2069	-0.3861	-1.5797	3.7311	-1.1361	2.7531	-0.0959	0.4789	0.0703	-0.3339	0.2883	-1.0676	-0.3622	0.9877	-0.2229	0.5676	-0.1181	0.1518	0.859	-0.1332	0.9245	32.3896	-2.1429	59.3
19	8.4661	-0.2266	-4.8722	5.6367	0.8107	3.1664	-0.6312	-1.6341	-0.27	1.2222	0.3645	-1.8712	-0.1632	0.5408	0.0255	0.6526	0.0367	-0.1675	0.663	-0.1421	0.9857	37.0884	-0.1204	74.0241
20	8.4448	-2.0742	9.8931	2.6723	-0.7448	2.0015	-2.245	0.6887	2.595	-0.3121	0.1408	-1.5187	-2.7482	0.3949	1.4672	0.994	-0.2713	0.1403	0.7715	-0.252	1.6335	35.9319	10.6845	67.3508
21	4.1095	0.3091	-0.7373	3.899	4.8796	6.3976	0.6384	-0.0451	-0.3454	0.3677	-0.4353	-0.0857	0.3625	0.0877	-0.2546	0.5472	-0.0109	-0.1207	0.374	0.0435	0.7698	22.5024	3.6635	69.8451
22	7.2246	-1.8521	2.2692	7.8139	-3.9061	6.543	0.7854	-0.8351	-1.0114	0.9626	-0.11	-0.7945	1.5068	0.7485	-0.4355	1.5027	0.2297	-0.4277	0.7634	-0.0964	0.784	27.317	-34.065	35.1834
23	6.7833	-1.4067	1.973	3.6133	-2.6019	7.048	0.1018	-0.7304	-1.0401	0.9841	0.3858	0.2821	0.5486	-0.3731	-0.4504	0.916	0.0405	-0.1203	0.607	0.0239	0.6483	16.9625	-31.2308	26.888
24	5.2081	-1.0117	1.0102	5.199	4.5419	6.3123	0.6635	-0.0811	-1.0249	0.6744	0.3235	0.0406	1.8884	0.4484	-0.3205	1.3172	0.1882	-0.2512	0.4618	-0.0291	0.7143	17.0329	-36.3897	22.1552
25	5.5048	3.1271	0.9125	6.5869	1.3372	1.3504	0.0584	1.6551	-0.0496	-0.6078	0.1572	-0.0868	0.4141	0.6136	-0.1864	0.7821	0.3844	-0.0567	1.4169	-0.0247	0.5582	22.8059	-22.0079	-0.7305
26	4.3545	0.6588	0.3792	3.1508	1.1141	1.7637	0.053	0.8387	-0.3083	0.2254	0.102	-0.5274	0.0582	0.074	-0.1099	0.7657	0.3601	-0.0913	1.2442	-0.1702	0.6625	41.7779	-23.0221	11.298
27	8.591	-5.7997	-0.0443	4.0138	0.7253	4.3356	1.6498	0.0899	-3.3777	-0.3121	-0.1102	0.8505	2.7522	-0.1858	-1.0625	1.5034	0.2638	-0.7466	1.1663	-0.4617	2.0248	50.831	-43.6585	19.6308
28	3.0259	-1.7508	-0.1398	4.857	-1.5519	0.8165	0.4013	0.1991	-0.2941	0.3062	-0.0476	-0.8352	0.3506	-0.1308	-0.32	0.8755	0.3518	-0.3458	1.1529	-0.2013	0.8651	49.5683	-25.5284	21.2529
29	5.3164	1.2282	-0.6774	7.6628	-2.8393	7.1574	-0.1122	0.9287	0.2085	-0.8832	-0.265	-0.8528	-0.4863	0.0974	0.3316	0.8253	-0.0192	0.1051	0.4433	-0.0132	0.4853	15.0784	39.0659	53.4551
30	6.8913	6.1915	-6.1574	5.7814	-5.3451	5.7354	1.277	1.4751	0.1953	-0.5289	-0.054	0.4984	-2.6042	-1.0628	-1.3805	1.4529	0.0374	0.095	0.8237	0.1315	0.9264	15.1682	53.2377	56.5184
31	3.3963	0.7766	-0.8429	3.7531	0.5527	6.4702	0.169	0.0527	0.139	-0.2119	0.1073	-0.0463	-0.5244	-0.7441	-0.1709	0.6406	0.116	0.0136	0.4251	-0.0154	0.4716	4.7047	34.5472	64.6148
32	7.1309	-2.2759	-1.2657	3.4264	-1.4108	5.9121	0.0362	-1.245	-0.33	0.7983	-0.1563	-0.4052	-0.5672	0.1582	0.1265	0.7987	-0.2788	-0.1756	0.624	0.1058	0.614	13.9731	28.0433	89.3303
33	3.588	-1.4941	0.2231	1.5281	-0.1006	2.3664	0.2007	-0.3582	0.4124	0.3284	-0.4444	-1.0903	-0.4777	0.5405	0.1554	0.7195	-0.2819	-0.2258	0.6941	0.2165	0.9805	32.1082	35.1503	78.0632
34	3.5301	-1.9376	1.1338	7.9612	3.7878	3.669	-0.0014	1.3652	1.3488	-3.6879	-1.7736	0.6528	-2.8032	1.0444	1.8579	1.2813	0.0776	-0.0418	1.1911	0.2944	1.5012	32.6192	54.0112	67.2465
35	2.4005	2.9785	1.7697	3.8379	2.9162	4.9658	-0.7422	0.3641	1.4321	-0.7788	0.0749	1.4542	-3.0882	0.4944	0.2141	1.9193	-0.4915	-0.2593	1.0914	0.6972	1.8605	39.3328	59.3857	72.8604
36	4.8635	3.1114	0.4619	2.591	0.8568	0.6162	0.0083	1.0882	0.4056	-0.0801	-0.7165	-1.4275	-0.4616	1.0358	0.3367	0.7103	-0.217	-0.0883	1.0905	0.5044	1.0375	38.7614	37.4061	67.5884

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1805 through 1853 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1854 through 1877 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1878 through 1960 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1961 through 2079 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 24 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 25 through 49 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 50 through 115 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 116 through 132 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 133 through 148 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 149 through 164 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 165 through 178 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1805 through 1877 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1878 through 1960 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1961 through 1980 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1981 through 2079 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 25 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 26 through 67 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 68 through 104 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 105 through 138 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 139 through 149 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 150 through 178 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 1805 through 1862 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 1863 through 1908 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 1909 through 1960 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 1961 through 2079 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 1 through 115 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 116 through 132 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 133 through 178 )
29	X-RAY DIFFRACTION	29	chain 'G' and (resid 1805 through 1854 )
30	X-RAY DIFFRACTION	30	chain 'G' and (resid 1855 through 1877 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 1878 through 1960 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 1961 through 2079 )
33	X-RAY DIFFRACTION	33	chain 'H' and (resid 1 through 115 )
34	X-RAY DIFFRACTION	34	chain 'H' and (resid 116 through 125 )
35	X-RAY DIFFRACTION	35	chain 'H' and (resid 126 through 138 )
36	X-RAY DIFFRACTION	36	chain 'H' and (resid 139 through 178 )

-
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

-
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

-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

-
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