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- PDB-6d4g: N-GTPase domain of p190RhoGAP-A -

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Basic information

Entry
Database: PDB / ID: 6d4g
TitleN-GTPase domain of p190RhoGAP-A
ComponentsRho GTPase-activating protein 35
KeywordsHYDROLASE / GTPase / pseudoGTPase / GTP / p190RhoGAP
Function / homology
Function and homology information


Sema4D mediated inhibition of cell attachment and migration / RHOJ GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHOB GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RND3 GTPase cycle / : ...Sema4D mediated inhibition of cell attachment and migration / RHOJ GTPase cycle / RND2 GTPase cycle / RND1 GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHOB GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RND3 GTPase cycle / : / RHOG GTPase cycle / RAC2 GTPase cycle / : / RHOQ GTPase cycle / RAC1 GTPase cycle / neuron projection guidance / central nervous system neuron axonogenesis / RHOA GTPase cycle / establishment or maintenance of actin cytoskeleton polarity / regulation of actin polymerization or depolymerization / cellular response to extracellular stimulus / positive regulation of cilium assembly / mammary gland development / camera-type eye development / negative regulation of vascular permeability / axonal fasciculation / GTPase activating protein binding / wound healing, spreading of cells / negative regulation of Rho protein signal transduction / regulation of cell size / regulation of axonogenesis / Rho protein signal transduction / forebrain development / GTPase activator activity / ciliary basal body / neural tube closure / axon guidance / regulation of actin cytoskeleton organization / phospholipid binding / positive regulation of neuron projection development / positive regulation of GTPase activity / cell migration / actin cytoskeleton / regulation of cell shape / GTPase activity / protein-containing complex binding / GTP binding / DNA binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / FF domain / FF domain ...Rho GTPase-activating protein, pG1 and pG2 domain / p190RhoGAP, pG1 and pG2 domains / Rho GTPase-activating protein, FF domain / Rho GTPase-activating protein, pG2 domain / Rho GTPase-activating protein, pG1 domain / p190-A and -B Rho GAPs FF domain / pG1 pseudoGTPase domain profile. / pG2 pseudoGTPase domain profile. / FF domain / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Small GTPase / Ras family / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Rho GTPase-activating protein 35
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsStiegler, A.L. / Boggon, T.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114621 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102262 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS085078 United States
CitationJournal: Structure / Year: 2018
Title: The N-Terminal GTPase Domain of p190RhoGAP Proteins Is a PseudoGTPase.
Authors: Stiegler, A.L. / Boggon, T.J.
History
DepositionApr 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho GTPase-activating protein 35
B: Rho GTPase-activating protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3476
Polymers61,2522
Non-polymers1,0954
Water905
1
A: Rho GTPase-activating protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1743
Polymers30,6261
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rho GTPase-activating protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1743
Polymers30,6261
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.690, 69.270, 154.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rho GTPase-activating protein 35 / GAP-associated protein p190 / Glucocorticoid receptor DNA-binding factor 1


Mass: 30626.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgap35, Grlf1, P190A, p190ARHOGAP / Production host: Escherichia coli (E. coli) / References: UniProt: P81128
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% (w/v) PEG 8000, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→42.032 Å / Num. obs: 12101 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 51.596 % / Biso Wilson estimate: 92.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.179 / Rrim(I) all: 0.181 / Χ2: 1.098 / Net I/σ(I): 20.41 / Num. measured all: 624368 / Scaling rejects: 967
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.954.5013.5291.8711920.6913.561100
2.9-3.0253.292.2462.7512270.8432.268100
3.02-3.1554.221.4124.7611300.9231.425100
3.15-3.3253.1860.9277.0212040.9680.93699.9
3.32-3.5350.3320.56211.412010.9840.568100
3.53-3.848.8830.33817.6111760.9920.34299.3
3.8-4.1854.4430.2127.8611930.9980.212100
4.18-4.7951.6230.14437.4812430.9990.145100
4.79-6.0350.5470.13740.3212280.9990.139100
6.03-42.03245.590.08548.8513070.9990.08698.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.39 Å42.03 Å
Translation4.39 Å42.03 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
PHASER2.7.16phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C5H

3c5h


Resolution: 2.8→42.032 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.54
RfactorNum. reflection% reflection
Rfree0.2901 605 5 %
Rwork0.2499 --
obs0.252 12097 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 266.1 Å2 / Biso mean: 129.2882 Å2 / Biso min: 46.74 Å2
Refinement stepCycle: final / Resolution: 2.8→42.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 66 5 3379
Biso mean--88.52 69.23 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083434
X-RAY DIFFRACTIONf_angle_d0.6634618
X-RAY DIFFRACTIONf_chiral_restr0.043518
X-RAY DIFFRACTIONf_plane_restr0.003581
X-RAY DIFFRACTIONf_dihedral_angle_d14.7042055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8001-3.08180.34441490.277628152964
3.0818-3.52750.32931480.278928222970
3.5275-4.44350.27861500.245928613011
4.4435-42.03720.27991580.241829943152
Refinement TLS params.

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

IDL11 (°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)
15.4438-3.79234.00175.42530.21436.24650.56940.6856-0.4308-0.4397-1.0488-0.60420.46950.72650.53510.57430.02810.0710.6340.05520.74257.24315.9937152.1933
26.19571.41983.99693.9137-1.43949.48550.2930.48640.0237-0.3851-0.5373-2.780.94942.76960.61291.09610.3762-0.0740.81470.09011.257118.71941.9601161.3196
38.90490.43314.1186.5696-0.92022.12661.00681.2186-1.78150.30180.061-1.70421.64111.4768-0.38281.45990.5937-0.16310.8048-0.17441.391713.9357-5.411153.1376
43.301-1.67682.3516.5004-1.38975.9392-0.51211.43120.4135-1.11570.2132-0.29442.87061.3977-0.20311.13130.2655-0.05391.142-0.02810.75948.1462.5108141.4187
58.4909-3.60110.58573.07842.69485.45133.4381.2456-2.7124-1.2411-0.5084-0.24692.13732.04360.99621.9431.1252-0.37170.6161-0.87321.291812.3919-9.0872150.9312
64.2696-3.73468.21172.0143-5.70381.95990.80162.1298-2.0963-0.0745-2.8325-2.61141.21964.1057-0.21951.77220.69010.18181.1035-0.44231.533623.9513-8.0081150.4981
76.0741-2.4984-0.02726.40782.55536.04820.48580.1102-0.3158-1.5243-0.4070.41231.71620.0463-0.2660.96360.0167-0.14080.68820.07551.12045.47723.4128156.3597
89.57971.0261.42454.1823-1.35035.29790.22170.3108-0.08610.3734-0.15110.32910.9968-0.8791-0.24410.7705-0.07640.03870.59780.09450.5806-1.1877.0198157.8122
94.66140.54922.49117.6229-1.89087.64510.235-1.10140.56270.8280.15090.7070.2343-1.2042-0.42130.6727-0.01850.04270.9950.01620.68810.717610.727165.9757
107.97586.7864.82596.14484.54844.61920.651-1.7098-0.17792.1650.05450.80843.1604-0.46310.22111.6417-0.13560.28240.79430.32941.30071.7754-5.4815169.0131
117.292-2.7919-3.13393.5926-0.94463.6283-0.8045-0.0971-0.9202-0.36512.1994-0.7340.19921.4537-1.57221.5343-0.43040.15961.0382-0.19570.9152-10.8553-3.3483132.4585
128.63643.83710.95988.17040.16745.6091-0.92372.61110.8271-0.95430.3923-0.8091-0.90661.94760.60131.3479-0.2936-0.05071.85120.41540.9964-3.24086.7835126.5046
132.2099-3.61683.08927.6244-5.6474.12420.77470.0162-0.60960.0564-0.14550.15560.417-0.7264-0.42720.7873-0.3223-0.18521.01150.14880.779-12.17566.9143135.1086
143.91222.21424.20787.25154.09634.89231.39771.04610.7920.2598-1.4417-0.9876-1.157-0.15520.34441.6697-0.2478-0.38422.28970.41271.7381-5.601412.613122.1717
156.39983.43292.23624.94445.46496.4391-0.27021.6406-0.6859-0.16290.9084-0.41290.06640.2484-0.00061.2968-0.2285-0.06861.85450.36461.0054-7.69671.2599123.4351
165.65744.7128-2.61016.8625-2.29897.64190.6954-0.96090.16-2.2121-0.89912.64482.3491-1.9479-0.50611.8435-0.3641-0.52921.7277-0.16271.3462-21.255-4.756124.3259
172.0198-3.1824-2.60432.69140.63717.6785-1.33873.9327-4.10750.15782.72362.81633.22310.383-2.52111.4759-0.1913-0.50552.5242-0.73871.855-10.9747-8.6364118.7715
184.65282.8665-3.27637.8379-7.34036.9714-0.61462.1002-3.0839-3.4198-1.32990.6591-2.430.18391.14032.8617-0.0404-0.99931.7118-0.30231.9677-16.9056-17.6377120.9976
193.0552-4.25362.48325.8778-2.79055.26520.6441.7913-2.48050.50170.58020.3160.86331.7893-1.05031.62330.1902-0.15031.8861-1.25271.1427-7.0576-10.8847116.4919
207.1449-6.82556.9898.9043-5.12628.85852.60891.697-2.3121-1.4551-2.75662.11155.1344-1.48630.2572.953-0.27890.07783.108-0.66421.0905-8.2459-3.2606108.7709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 34 )A14 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 53 )A35 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 96 )A54 - 96
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 120 )A97 - 120
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 135 )A121 - 135
6X-RAY DIFFRACTION6chain 'A' and (resid 136 through 150 )A136 - 150
7X-RAY DIFFRACTION7chain 'A' and (resid 151 through 173 )A151 - 173
8X-RAY DIFFRACTION8chain 'A' and (resid 174 through 206 )A174 - 206
9X-RAY DIFFRACTION9chain 'A' and (resid 207 through 235 )A207 - 235
10X-RAY DIFFRACTION10chain 'A' and (resid 236 through 252 )A236 - 252
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 34 )B18 - 34
12X-RAY DIFFRACTION12chain 'B' and (resid 35 through 96 )B35 - 96
13X-RAY DIFFRACTION13chain 'B' and (resid 97 through 120 )B97 - 120
14X-RAY DIFFRACTION14chain 'B' and (resid 121 through 135 )B121 - 135
15X-RAY DIFFRACTION15chain 'B' and (resid 136 through 173 )B136 - 173
16X-RAY DIFFRACTION16chain 'B' and (resid 174 through 191 )B174 - 191
17X-RAY DIFFRACTION17chain 'B' and (resid 192 through 206 )B192 - 206
18X-RAY DIFFRACTION18chain 'B' and (resid 207 through 218 )B207 - 218
19X-RAY DIFFRACTION19chain 'B' and (resid 219 through 235 )B219 - 235
20X-RAY DIFFRACTION20chain 'B' and (resid 236 through 247 )B236 - 247

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