PDB-7cso: Structure of Ephexin4 DH-PH-SH3

ID or keywords:

Entry

Database: PDB / ID: 7cso

Title

Structure of Ephexin4 DH-PH-SH3

Components

Rho guanine nucleotide exchange factor 16

Keywords

SIGNALING PROTEIN / Ephexin4 / GEF / Autoinhibition

Function / homology

Function and homology information

CDC42 GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / RHOG GTPase cycle / activation of GTPase activity / cell chemotaxis / guanyl-nucleotide exchange factor activity / PDZ domain binding / positive regulation of protein localization to plasma membrane / receptor tyrosine kinase binding ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.39 Å

Authors

Zhang, M. / Lin, L. / Wang, C. / Zhu, J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Double inhibition and activation mechanisms of Ephexin family RhoGEFs.
Authors: Zhang, M. / Lin, L. / Wang, C. / Zhu, J.

History

Deposition	Aug 15, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 3, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Mar 27, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7cso.cif.gz	717.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7cso.ent.gz	594.8 KB	Display	PDB format
PDBx/mmJSON format	7cso.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7cso_validation.pdf.gz	464.2 KB	Display	wwPDB validaton report
Full document	7cso_full_validation.pdf.gz	472.2 KB	Display
Data in XML	7cso_validation.xml.gz	62.7 KB	Display
Data in CIF	7cso_validation.cif.gz	89.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cs/7cso ftp://data.pdbj.org/pub/pdb/validation_reports/cs/7cso	HTTPS FTP

-
Related structure data

Related structure data	7cspC 7csrC C: citing same article (ref.)
Similar structure data	7csr-2 7csr-1 4ufk-d 5uiy-d 4yc1-d 6zpw-d 4cce-d 6zpx-d 3zr5-d 3n95-6 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

7cspC

7csrC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#148 - Apr 2012 Ras Protein similarity (6) #58 - Oct 2004 G Proteins similarity (1)

Deposited unit

A: Rho guanine nucleotide exchange factor 16

B: Rho guanine nucleotide exchange factor 16

C: Rho guanine nucleotide exchange factor 16

D: Rho guanine nucleotide exchange factor 16

hetero molecules

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

1

A: Rho guanine nucleotide exchange factor 16

hetero molecules

defined by author&software
Evidence: gel filtration
52.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Rho guanine nucleotide exchange factor 16

hetero molecules

defined by author&software
52.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Rho guanine nucleotide exchange factor 16

hetero molecules

defined by author&software
52.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Rho guanine nucleotide exchange factor 16

hetero molecules

defined by author&software
52.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	144.444, 144.444, 290.518
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	151
Space group name H-M	P3₁12

#1: Protein	Rho guanine nucleotide exchange factor 16 / Ephexin-4 Mass: 52565.652 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arhgef16 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3U5C8
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.16 Å³/Da / Density % sol: 70.44 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 800 mM Potassium phosphate dibasic, 800 mM Sodium phosphate monobasic, 100 mM HEPES, pH7.5

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.97775 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 17, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97775 Å / Relative weight: 1

Reflection

Resolution: 2.39→48.42 Å / Num. obs: 267055 / % possible obs: 99.8 % / Redundancy: 6.973 % / B_iso Wilson estimate: 51.304 Å² / CC_1/2: 0.987 / R_merge(I) obs: 0.179 / R_rim(I) all: 0.193 / Χ²: 0.796 / Net I/σ(I): 6.95 / Num. measured all: 1862101

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.39-2.54	7.047	0.769	2.1	301704	43372	42812	0.822	0.83	98.7
2.54-2.71	7.033	0.52	3.11	284940	40513	40512	0.909	0.561	100
2.71-2.93	6.857	0.331	4.48	259259	37808	37808	0.949	0.358	100
2.93-3.21	7.154	0.233	6.55	249129	34825	34825	0.97	0.252	100
3.21-3.58	6.778	0.178	8.85	213220	31457	31457	0.975	0.192	100
3.58-4.13	7.107	0.157	11.28	197567	27799	27798	0.979	0.169	100
4.13-5.05	6.895	0.142	12.33	161860	23479	23476	0.979	0.154	100
5.05-7.11	6.898	0.145	12.31	125434	18186	18185	0.98	0.157	100
7.11-48.42	6.775	0.138	13.43	68988	10215	10182	0.985	0.149	99.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.39→48.42 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2041	6640	4.87 %
R_work	0.1757	129728	-
obs	0.1771	136368	99.82 %

Solvent computation

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

Displacement parameters

B_iso max: 142.74 Å² / B_iso mean: 53.6759 Å² / B_iso min: 22.32 Å²

Refinement step

Cycle: final / Resolution: 2.39→48.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13980	0	65	613	14658
B_iso mean	-	-	74.15	51.27	-
Num. residues	-	-	-	-	1736

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.39-2.42	0.2428	224	0.2216	4087	4311	95
2.42-2.45	0.2771	221	0.2142	4358	4579	100
2.45-2.48	0.261	212	0.2148	4281	4493	100
2.48-2.51	0.2557	194	0.2125	4314	4508	100
2.51-2.54	0.2905	195	0.2106	4325	4520	100
2.54-2.58	0.2209	218	0.1991	4346	4564	100
2.58-2.61	0.2391	199	0.193	4299	4498	100
2.61-2.65	0.2371	209	0.1974	4318	4527	100
2.65-2.69	0.2352	226	0.2008	4307	4533	100
2.7-2.74	0.2497	267	0.1997	4257	4524	100
2.74-2.79	0.2562	219	0.2071	4344	4563	100
2.79-2.84	0.2541	206	0.2111	4319	4525	100
2.84-2.89	0.2515	248	0.2189	4303	4551	100
2.89-2.95	0.2954	213	0.2139	4317	4530	100
2.95-3.01	0.2308	218	0.2083	4312	4530	100
3.01-3.08	0.223	171	0.2045	4339	4510	100
3.08-3.16	0.2157	205	0.1939	4344	4549	100
3.16-3.25	0.2297	249	0.1912	4290	4539	100
3.25-3.34	0.232	228	0.1894	4306	4534	100
3.34-3.45	0.2336	240	0.19	4345	4585	100
3.45-3.57	0.2049	220	0.1794	4298	4518	100
3.57-3.72	0.1969	217	0.1643	4346	4563	100
3.72-3.89	0.1787	238	0.1509	4307	4545	100
3.89-4.09	0.1624	205	0.1475	4347	4552	100
4.09-4.35	0.1704	251	0.1409	4347	4598	100
4.35-4.68	0.1775	266	0.1392	4305	4571	100
4.68-5.15	0.1689	244	0.1394	4352	4596	100
5.15-5.9	0.2151	236	0.1808	4350	4586	100
5.9-7.43	0.1921	174	0.1916	4454	4628	100
7.43-48.42	0.1484	227	0.1604	4511	4738	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	2.1691	1.1001	-0.7712	2.7932	-0.9735	2.182	-0.0466	-0.2591	-0.2147	0.1378	-0.1277	0.0968	0.0514	-0.0596	0.1851	0.2505	0.0838	0.0203	0.362	0.0048	0.2788	26.9893	-22.6117	79.6912
2	2.7591	0.8102	0.3206	1.5725	0.225	0.6137	-0.039	0.5155	-0.0557	0.1129	0.0619	-0.035	0.0535	0.1691	-0.0327	0.3213	0.0775	0.0122	0.3922	0.046	0.3047	55.1792	-25.9238	68.9198
3	3.0632	-0.7307	-0.5987	2.157	-0.9379	2.8048	-0.017	-0.0652	0.2328	0.1823	0.015	-0.2399	-0.0804	0.1092	0.0153	0.2689	0.0345	-0.0451	0.3175	0.0114	0.2762	64.7382	-27.1942	75.3376
4	4.8877	1.7064	-1.1896	4.1207	-0.1712	1.9329	-0.2056	-0.3393	-0.5384	0.5007	0.1448	0.1906	0.1687	0.0115	0.0771	0.4768	0.1411	0.0934	0.5614	0.1427	0.3817	47.8714	-35.5538	86.3307
5	2.1797	0.2813	-0.1437	2.9212	1.245	2.5092	-0.0248	0.2499	-0.3354	-0.1181	-0.1454	0.1659	-0.0725	-0.0825	0.1726	0.2315	0.0773	0.011	0.3608	-0.0052	0.2953	39.9572	-26.4502	42.4344
6	1.8398	-0.9771	-0.4899	1.6068	0.2463	1.1787	-0.0623	0.2502	-0.3373	0.1483	-0.1583	0.3776	0.0813	-0.278	0.2216	0.2341	0.0524	-0.0055	0.4073	-0.0247	0.3781	22.5447	-18.3742	50.1801
7	0.2282	1.3597	-0.9628	6.671	-4.5943	4.1816	-0.0454	0.0765	0.1154	0.2282	0.1844	0.058	-0.15	0.008	-0.1416	0.2891	0.0863	-0.0199	0.3041	0.017	0.3952	18.0784	12.0494	51.8994
8	3.3755	-0.1664	0.9675	2.0642	0.2311	3.1731	-0.1483	-0.0248	0.6168	-0.0529	0.0953	0.0278	-0.1947	-0.1679	0.1223	0.334	0.076	-0.0276	0.305	0.0244	0.377	9.3346	8.4179	48.5696
9	3.3846	-0.8562	0.1218	5.1068	0.3152	2.8349	0.2807	0.6187	-0.5488	-0.6106	-0.3092	-0.0478	0.3163	0.0668	0.0429	0.5967	0.1714	-0.03	0.6127	-0.0614	0.4374	17.7247	-14.0255	36.2002
10	2.6292	1.8874	1.7993	3.132	1.7918	2.9218	-0.0827	-0.3633	0.3534	0.2128	-0.1342	0.0526	-0.1202	-0.0955	0.2137	0.3032	0.1031	-0.0246	0.3818	-0.0176	0.3423	48.7244	-18.7195	9.212
11	2.4963	1.0089	0.8641	3.3722	0.7126	1.9331	-0.0692	-0.0056	0.17	0.1922	0.0296	0.0374	-0.0375	-0.0688	0.0553	0.2645	0.0926	0.0388	0.3072	0.0248	0.2221	43.4608	-21.56	1.568
12	2.0061	-0.0819	-0.2708	1.2922	-0.2454	1.0308	-0.2503	0.0663	0.3485	0.1082	0.1347	0.1317	-0.2199	-0.2569	0.1323	0.3266	0.1518	0.0374	0.4108	0.0601	0.4039	29.1492	-11.4893	-3.5227
13	6.9813	2.6551	-5.2134	1.0276	-1.9416	4.4988	-0.1195	0.583	0.0135	0.0795	-0.044	0.015	0.162	-0.2855	0.1479	0.3469	0.0566	0.1501	0.612	0.0446	0.6468	0.9369	-23.245	-3.7282
14	2.502	0.7282	-0.9585	2.2076	-0.047	2.7291	0.2762	0.6572	0.6019	0.0622	0.0686	0.5692	-0.3867	-0.7627	-0.4593	0.3696	0.1342	0.1449	0.8044	0.1334	0.8684	-1.4602	-13.9174	-4.2349
15	4.7801	1.4937	1.1838	1.9524	0.7558	2.014	-0.0849	-0.1087	0.454	0.3786	0.0797	0.4331	-0.1034	0.0074	-0.05	0.4327	0.13	0.1683	0.5551	-0.0078	0.57	16.5884	-10.8707	6.5339
16	7.729	3.8581	0.9391	7.0256	1.8161	2.8926	-0.1454	-0.9085	1.2597	0.5348	-0.1527	0.6315	-0.2394	-0.1014	0.2107	0.549	0.2069	0.081	0.5916	-0.0779	0.6283	26.8182	-2.9225	12.0776
17	0.4764	-0.4375	0.3728	2.2353	-1.4476	2.2819	-0.0435	0.031	0.1187	-0.1179	-0.0398	-0.1232	0.054	0.0331	0.0915	0.2335	0.0226	-0.0016	0.3471	0.0128	0.282	38.3799	-14.735	-30.4503
18	2.9512	-0.0919	-0.5127	2.9378	0.3819	2.7498	-0.2545	-0.0071	-0.4096	0.1108	0.1436	-0.0191	0.1707	0.1387	0.0799	0.2659	0.0464	0.0372	0.284	-0.0172	0.2912	60.1185	-48.8695	-19.7348
19	2.4736	-1.0823	0.4926	4.3779	-2.0775	1.676	-0.0127	0.6199	0.3129	-0.21	-0.0696	-0.2968	-0.1602	-0.0152	0.1137	0.4253	0.0359	0.0691	0.576	0.033	0.303	58.3506	-30.0525	-35.1082

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 264 through 448 )	A	264 - 448
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 449 through 535 )	A	449 - 535
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 536 through 658 )	A	536 - 658
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 659 through 709 )	A	659 - 709
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 264 through 425 )	B	264 - 425
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 426 through 513 )	B	426 - 513
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 514 through 549 )	B	514 - 549
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 550 through 619 )	B	550 - 619
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 620 through 709 )	B	620 - 709
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 264 through 335 )	C	264 - 335
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 336 through 425 )	C	336 - 425
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 426 through 513 )	C	426 - 513
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 514 through 549 )	C	514 - 549
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 550 through 599 )	C	550 - 599
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 600 through 679 )	C	600 - 679
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 680 through 711 )	C	680 - 711
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 264 through 488 )	D	264 - 488
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 489 through 599 )	D	489 - 599
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 600 through 709 )	D	600 - 709

-
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