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- PDB-2mio: Solution NMR Structure of SH3 Domain 1 of Rho GTPase-activating P... -

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Basic information

Entry
Database: PDB / ID: 2mio
TitleSolution NMR Structure of SH3 Domain 1 of Rho GTPase-activating Protein 10 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR9129A
ComponentsRho GTPase-activating protein 10
KeywordsStructural genomics / Unknown function / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


Regulation of PAK-2p34 activity by PS-GAP/RHG10 / : / regulation of small GTPase mediated signal transduction / cytoskeleton organization / GTPase activator activity / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / plasma membrane / cytosol
Similarity search - Function
GRAF2, SH3 domain / Rho GTPase-activating protein 10 / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Variant SH3 domain / Rho GTPase activation protein / SH3 Domains ...GRAF2, SH3 domain / Rho GTPase-activating protein 10 / AH/BAR domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Variant SH3 domain / Rho GTPase activation protein / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Rho GTPase-activating protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsXu, X. / Eletsky, A. / Pulavarti, S.V.S.R.K. / Wang, H. / Janjua, H. / Xiao, R. / Everett, J.K. / Sukumaran, D.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of SH3 Domain 1 of Rho GTPase-activating Protein 10 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) Target HR9129A
Authors: Xu, X. / Eletsky, A. / Pulavarti, S.V.S.R.K. / Wang, H. / O'Connell, P.T. / Janjua, H. / Xiao, R. / Everett, J.K. / Sukumaran, D. / Montelione, G.T. / Szyperski, T.
History
DepositionDec 16, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho GTPase-activating protein 10


Theoretical massNumber of molelcules
Total (without water)8,0441
Polymers8,0441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Rho GTPase-activating protein 10 / GTPase regulator associated with focal adhesion kinase 2 / Graf-related protein 2 / Rho-type GTPase- ...GTPase regulator associated with focal adhesion kinase 2 / Graf-related protein 2 / Rho-type GTPase-activating protein 10


Mass: 8044.095 Da / Num. of mol.: 1 / Fragment: SH3 domain 1 residues 728-786
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGAP10, GRAF2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: A1A4S6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C CT HSQC aliphatic
1323D HNCO
1423D CBCA(CO)NH
1523D HN(CA)CB
1622D 1H-13C CT HSQC aromatic
1723D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1822D 1H-13C HSQC aliphatic
1922D 1H-13C HSQC aromatic
11023D HBHA(CO)NH
11123D(H)CCH-TOCSY ali
11223D (H)CCH-COSY ali
1132GFT-43D (H)CCH-COSY aromatic
11423D HN(CA)CO
1152gNfHSQC His
11612D 1H-15N HSQC
11712D 1H-13C ct-HSQC methyl(28ms)
11812D 1H-13C CT HSQC-methyl (42ms)
11912D 1H-13C CT HSQC-methyl (56ms)
12012D J-modulation 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.72 mM U-100% 13C-U-100%15N labeled protein, 90% H2O/10% D2O90% H2O/10% D2O
20.72 mM 10% 13C U-100% 15N labeled protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
VnmrJVariancollection
TALOSNShen, Cornilescu, Delaglio and Baxgeometry optimization
PSVSBhattacharya, Montelionestructure validation
PSVSBhattacharya, Montelioneprocessing
PSVSGuntertstructure validation
PSVSGuntertprocessing
PSVSBhattacharya, Montelionestructure validation
PSVSBhattacharya, Montelioneprocessing
PSVSGuntertstructure validation
PSVSGuntertprocessing
CSIDavid Wishart,Leigh Willard,Tim Jellard,Brian Sykesdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by running CYANA and ASDP in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOSN. Consensus peak assignments ...Details: Structure determination was performed by running CYANA and ASDP in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOSN. Consensus peak assignments were selected and used in iterative refinement with CYANA. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field NMR.
NMR constraintsNOE constraints total: 860 / NOE intraresidue total count: 236 / NOE long range total count: 332 / NOE medium range total count: 69 / NOE sequential total count: 223 / Protein chi angle constraints total count: 26 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 26 / Protein psi angle constraints total count: 26
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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