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

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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 / NRAGE signals death through JNK / RHOG GTPase cycle / G alpha (12/13) signalling events / activation of GTPase activity / positive regulation of protein localization to plasma membrane / cell chemotaxis / guanyl-nucleotide exchange factor activity / PDZ domain binding / receptor tyrosine kinase binding ...CDC42 GTPase cycle / NRAGE signals death through JNK / RHOG GTPase cycle / G alpha (12/13) signalling events / activation of GTPase activity / positive regulation of protein localization to plasma membrane / cell chemotaxis / guanyl-nucleotide exchange factor activity / PDZ domain binding / receptor tyrosine kinase binding / small GTPase binding / cytoplasm
Similarity search - Function
: / : / ARHGEF16/ARHGEF26, SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain / PH domain profile. ...: / : / ARHGEF16/ARHGEF26, SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / 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 / SH3 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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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) (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 interestN

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Experimental details

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Experiment

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

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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

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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

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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

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