[English] 日本語
Yorodumi
- PDB-7cso: Structure of Ephexin4 DH-PH-SH3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cso
TitleStructure of Ephexin4 DH-PH-SH3
ComponentsRho guanine nucleotide exchange factor 16
KeywordsSIGNALING PROTEIN / Ephexin4 / GEF / Autoinhibition
Function / homology
Function and homology information


CDC42 GTPase cycle / RHOG GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / 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 ...CDC42 GTPase cycle / RHOG GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / 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 / small GTPase binding / cytoplasm
Similarity search - Function
ARHGEF16/ARHGEF26, SH3 domain / Variant SH3 domain / RhoGEF domain / Dbl homology (DH) domain superfamily / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. ...ARHGEF16/ARHGEF26, SH3 domain / Variant SH3 domain / RhoGEF domain / Dbl homology (DH) domain superfamily / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 16
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsZhang, M. / Lin, L. / Wang, C. / Zhu, J.
CitationJournal: 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
DepositionAug 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)211,51117
Polymers210,2634
Non-polymers1,24913
Water11,043613
1
A: Rho guanine nucleotide exchange factor 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8544
Polymers52,5661
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22580 Å2
MethodPISA
2
B: Rho guanine nucleotide exchange factor 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8544
Polymers52,5661
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23000 Å2
MethodPISA
3
C: Rho guanine nucleotide exchange factor 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8544
Polymers52,5661
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22970 Å2
MethodPISA
4
D: Rho guanine nucleotide exchange factor 16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9505
Polymers52,5661
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-15 kcal/mol
Surface area22870 Å2
MethodPISA
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 number151
Space group name H-MP3112

-
Components

#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) (unknown) / Strain (production host): BL21(DE3) / References: UniProt: Q3U5C8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70.44 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2.39→48.42 Å / Num. obs: 267055 / % possible obs: 99.8 % / Redundancy: 6.973 % / Biso Wilson estimate: 51.304 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.179 / Rrim(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 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.39-2.547.0470.7692.130170443372428120.8220.8398.7
2.54-2.717.0330.523.1128494040513405120.9090.561100
2.71-2.936.8570.3314.4825925937808378080.9490.358100
2.93-3.217.1540.2336.5524912934825348250.970.252100
3.21-3.586.7780.1788.8521322031457314570.9750.192100
3.58-4.137.1070.15711.2819756727799277980.9790.169100
4.13-5.056.8950.14212.3316186023479234760.9790.154100
5.05-7.116.8980.14512.3112543418186181850.980.157100
7.11-48.426.7750.13813.436898810215101820.9850.14999.7

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
CRANK2phasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2041 6640 4.87 %
Rwork0.1757 129728 -
obs0.1771 136368 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.74 Å2 / Biso mean: 53.6759 Å2 / Biso min: 22.32 Å2
Refinement stepCycle: final / Resolution: 2.39→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13980 0 65 613 14658
Biso mean--74.15 51.27 -
Num. residues----1736
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.420.24282240.22164087431195
2.42-2.450.27712210.214243584579100
2.45-2.480.2612120.214842814493100
2.48-2.510.25571940.212543144508100
2.51-2.540.29051950.210643254520100
2.54-2.580.22092180.199143464564100
2.58-2.610.23911990.19342994498100
2.61-2.650.23712090.197443184527100
2.65-2.690.23522260.200843074533100
2.7-2.740.24972670.199742574524100
2.74-2.790.25622190.207143444563100
2.79-2.840.25412060.211143194525100
2.84-2.890.25152480.218943034551100
2.89-2.950.29542130.213943174530100
2.95-3.010.23082180.208343124530100
3.01-3.080.2231710.204543394510100
3.08-3.160.21572050.193943444549100
3.16-3.250.22972490.191242904539100
3.25-3.340.2322280.189443064534100
3.34-3.450.23362400.1943454585100
3.45-3.570.20492200.179442984518100
3.57-3.720.19692170.164343464563100
3.72-3.890.17872380.150943074545100
3.89-4.090.16242050.147543474552100
4.09-4.350.17042510.140943474598100
4.35-4.680.17752660.139243054571100
4.68-5.150.16892440.139443524596100
5.15-5.90.21512360.180843504586100
5.9-7.430.19211740.191644544628100
7.43-48.420.14842270.160445114738100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.16911.1001-0.77122.7932-0.97352.182-0.0466-0.2591-0.21470.1378-0.12770.09680.0514-0.05960.18510.25050.08380.02030.3620.00480.278826.9893-22.611779.6912
22.75910.81020.32061.57250.2250.6137-0.0390.5155-0.05570.11290.0619-0.0350.05350.1691-0.03270.32130.07750.01220.39220.0460.304755.1792-25.923868.9198
33.0632-0.7307-0.59872.157-0.93792.8048-0.017-0.06520.23280.18230.015-0.2399-0.08040.10920.01530.26890.0345-0.04510.31750.01140.276264.7382-27.194275.3376
44.88771.7064-1.18964.1207-0.17121.9329-0.2056-0.3393-0.53840.50070.14480.19060.16870.01150.07710.47680.14110.09340.56140.14270.381747.8714-35.553886.3307
52.17970.2813-0.14372.92121.2452.5092-0.02480.2499-0.3354-0.1181-0.14540.1659-0.0725-0.08250.17260.23150.07730.0110.3608-0.00520.295339.9572-26.450242.4344
61.8398-0.9771-0.48991.60680.24631.1787-0.06230.2502-0.33730.1483-0.15830.37760.0813-0.2780.22160.23410.0524-0.00550.4073-0.02470.378122.5447-18.374250.1801
70.22821.3597-0.96286.671-4.59434.1816-0.04540.07650.11540.22820.18440.058-0.150.008-0.14160.28910.0863-0.01990.30410.0170.395218.078412.049451.8994
83.3755-0.16640.96752.06420.23113.1731-0.1483-0.02480.6168-0.05290.09530.0278-0.1947-0.16790.12230.3340.076-0.02760.3050.02440.3779.33468.417948.5696
93.3846-0.85620.12185.10680.31522.83490.28070.6187-0.5488-0.6106-0.3092-0.04780.31630.06680.04290.59670.1714-0.030.6127-0.06140.437417.7247-14.025536.2002
102.62921.88741.79933.1321.79182.9218-0.0827-0.36330.35340.2128-0.13420.0526-0.1202-0.09550.21370.30320.1031-0.02460.3818-0.01760.342348.7244-18.71959.212
112.49631.00890.86413.37220.71261.9331-0.0692-0.00560.170.19220.02960.0374-0.0375-0.06880.05530.26450.09260.03880.30720.02480.222143.4608-21.561.568
122.0061-0.0819-0.27081.2922-0.24541.0308-0.25030.06630.34850.10820.13470.1317-0.2199-0.25690.13230.32660.15180.03740.41080.06010.403929.1492-11.4893-3.5227
136.98132.6551-5.21341.0276-1.94164.4988-0.11950.5830.01350.0795-0.0440.0150.162-0.28550.14790.34690.05660.15010.6120.04460.64680.9369-23.245-3.7282
142.5020.7282-0.95852.2076-0.0472.72910.27620.65720.60190.06220.06860.5692-0.3867-0.7627-0.45930.36960.13420.14490.80440.13340.8684-1.4602-13.9174-4.2349
154.78011.49371.18381.95240.75582.014-0.0849-0.10870.4540.37860.07970.4331-0.10340.0074-0.050.43270.130.16830.5551-0.00780.5716.5884-10.87076.5339
167.7293.85810.93917.02561.81612.8926-0.1454-0.90851.25970.5348-0.15270.6315-0.2394-0.10140.21070.5490.20690.0810.5916-0.07790.628326.8182-2.922512.0776
170.4764-0.43750.37282.2353-1.44762.2819-0.04350.0310.1187-0.1179-0.0398-0.12320.0540.03310.09150.23350.0226-0.00160.34710.01280.28238.3799-14.735-30.4503
182.9512-0.0919-0.51272.93780.38192.7498-0.2545-0.0071-0.40960.11080.1436-0.01910.17070.13870.07990.26590.04640.03720.284-0.01720.291260.1185-48.8695-19.7348
192.4736-1.08230.49264.3779-2.07751.676-0.01270.61990.3129-0.21-0.0696-0.2968-0.1602-0.01520.11370.42530.03590.06910.5760.0330.30358.3506-30.0525-35.1082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 264 through 448 )A264 - 448
2X-RAY DIFFRACTION2chain 'A' and (resid 449 through 535 )A449 - 535
3X-RAY DIFFRACTION3chain 'A' and (resid 536 through 658 )A536 - 658
4X-RAY DIFFRACTION4chain 'A' and (resid 659 through 709 )A659 - 709
5X-RAY DIFFRACTION5chain 'B' and (resid 264 through 425 )B264 - 425
6X-RAY DIFFRACTION6chain 'B' and (resid 426 through 513 )B426 - 513
7X-RAY DIFFRACTION7chain 'B' and (resid 514 through 549 )B514 - 549
8X-RAY DIFFRACTION8chain 'B' and (resid 550 through 619 )B550 - 619
9X-RAY DIFFRACTION9chain 'B' and (resid 620 through 709 )B620 - 709
10X-RAY DIFFRACTION10chain 'C' and (resid 264 through 335 )C264 - 335
11X-RAY DIFFRACTION11chain 'C' and (resid 336 through 425 )C336 - 425
12X-RAY DIFFRACTION12chain 'C' and (resid 426 through 513 )C426 - 513
13X-RAY DIFFRACTION13chain 'C' and (resid 514 through 549 )C514 - 549
14X-RAY DIFFRACTION14chain 'C' and (resid 550 through 599 )C550 - 599
15X-RAY DIFFRACTION15chain 'C' and (resid 600 through 679 )C600 - 679
16X-RAY DIFFRACTION16chain 'C' and (resid 680 through 711 )C680 - 711
17X-RAY DIFFRACTION17chain 'D' and (resid 264 through 488 )D264 - 488
18X-RAY DIFFRACTION18chain 'D' and (resid 489 through 599 )D489 - 599
19X-RAY DIFFRACTION19chain 'D' and (resid 600 through 709 )D600 - 709

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more