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- PDB-2l3g: Solution NMR Structure of CH domain of Rho guanine nucleotide exc... -

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Basic information

Entry
Database: PDB / ID: 2l3g
TitleSolution NMR Structure of CH domain of Rho guanine nucleotide exchange factor 7 from Homo sapiens, Northeast Structural Genomics Consortium Target HR4495E
ComponentsRho guanine nucleotide exchange factor 7
KeywordsSIGNALING PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / calponin-homology domain / Protein Structure Initiative
Function / homology
Function and homology information


negative regulation of microtubule nucleation / positive regulation of lamellipodium morphogenesis / gamma-tubulin binding / focal adhesion assembly / positive regulation of fibroblast migration / Ephrin signaling / lamellipodium assembly / RHOV GTPase cycle / Activation of RAC1 downstream of NMDARs / NRAGE signals death through JNK ...negative regulation of microtubule nucleation / positive regulation of lamellipodium morphogenesis / gamma-tubulin binding / focal adhesion assembly / positive regulation of fibroblast migration / Ephrin signaling / lamellipodium assembly / RHOV GTPase cycle / Activation of RAC1 downstream of NMDARs / NRAGE signals death through JNK / RHOJ GTPase cycle / mitotic spindle pole / RHOQ GTPase cycle / Golgi organization / CDC42 GTPase cycle / RHOU GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / ephrin receptor signaling pathway / positive regulation of substrate adhesion-dependent cell spreading / ruffle / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / positive regulation of GTPase activity / EGFR downregulation / G alpha (12/13) signalling events / lamellipodium / nervous system development / cell cortex / postsynapse / neuron projection / positive regulation of apoptotic process / focal adhesion / centrosome / neuronal cell body / protein kinase binding / signal transduction / protein-containing complex / cytoplasm / cytosol
Similarity search - Function
Unstructured region one on RhoGEF 6 and 7 / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Calponin homology domain ...Unstructured region one on RhoGEF 6 and 7 / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Calponin homology domain / Calponin homology (CH) 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. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Xiao, R. / Janjua, H. / Acton, T.B. / Ciccosanti, A. / Shastry, R. / Everett, J. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target HR4495E
Authors: Liu, G. / Xiao, R. / Janjua, H. / Ciccosanti, C. / Shastry, R. / Acton, T.B. / Everett, J. / Montelione, G.T.
History
DepositionSep 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 7


Theoretical massNumber of molelcules
Total (without water)14,0701
Polymers14,0701
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Rho guanine nucleotide exchange factor 7 / PAK-interacting exchange factor beta / Beta-Pix / COOL-1 / p85


Mass: 14070.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ARHGEF7, COOL1, KIAA0142, P85SPR, PAK3BP, PIXB, Nbla10314
Production host: Escherichia coli (E. coli) / References: UniProt: Q14155
Sequence detailsRESIDUES 85-105 ARE NOT PRESENT IN THIS ISOFORM 3.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Rho guanine nucleotide exchange factor 7's Alternative name(s)PAK-interacting exchange factor beta Beta-Pix COOL-1 p85) CH domain: calponin-homology domain.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.87 mM [U-100% 13C; U-100% 15N] HR4495E, 95% H2O/5% D2O95% H2O/5% D2O
20.85 mM [U-5% 13C; U-100% 15N] HR4495E, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.87 mMHR4495E-1[U-100% 13C; U-100% 15N]1
0.85 mMHR4495E-2[U-5% 13C; U-100% 15N]2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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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,refinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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