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- PDB-9h75: NMR solution structure of the GEFH1 C1 domain -

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Basic information

Entry
Database: PDB / ID: 9h75
TitleNMR solution structure of the GEFH1 C1 domain
ComponentsRho guanine nucleotide exchange factor 2
KeywordsPROTEIN BINDING / STRUCTURE FROM CYANA 3.98.4
Function / homology
Function and homology information


asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / cellular response to muramyl dipeptide / positive regulation of neuron migration / negative regulation of microtubule depolymerization / regulation of Rho protein signal transduction / negative regulation of necroptotic process / cellular hyperosmotic response / regulation of small GTPase mediated signal transduction / positive regulation of peptidyl-tyrosine phosphorylation ...asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / cellular response to muramyl dipeptide / positive regulation of neuron migration / negative regulation of microtubule depolymerization / regulation of Rho protein signal transduction / negative regulation of necroptotic process / cellular hyperosmotic response / regulation of small GTPase mediated signal transduction / positive regulation of peptidyl-tyrosine phosphorylation / RHOB GTPase cycle / NRAGE signals death through JNK / RHOA GTPase cycle / bicellular tight junction / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of neuron differentiation / guanyl-nucleotide exchange factor activity / actin filament organization / intracellular protein transport / positive regulation of NF-kappaB transcription factor activity / positive regulation of interleukin-6 production / small GTPase binding / ruffle membrane / spindle / cell morphogenesis / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / G alpha (12/13) signalling events / regulation of cell population proliferation / cytoplasmic vesicle / microtubule binding / vesicle / microtubule / cytoskeleton / innate immune response / focal adhesion / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
ARHGEF2, PH domain / : / ARHGEF1-like, PH domain / PH 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. / Zinc finger phorbol-ester/DAG-type signature. ...ARHGEF2, PH domain / : / ARHGEF1-like, PH domain / PH 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. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsChoi, S.R. / Gossert, A.D. / Steinmetz, M.O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: To Be Published
Title: NMR solution structure of the GEFH1 C1 domain
Authors: Choi, S.R. / Gossert, A.D. / Steinmetz, M.O.
History
DepositionOct 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3823
Polymers8,2511
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein Rho guanine nucleotide exchange factor 2 / Guanine nucleotide exchange factor H1 / GEF-H1 / Microtubule-regulated Rho-GEF / Proliferating cell ...Guanine nucleotide exchange factor H1 / GEF-H1 / Microtubule-regulated Rho-GEF / Proliferating cell nucleolar antigen p40


Mass: 8250.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF2, KIAA0651, LFP40 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92974
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D CBCA(CO)NH
131isotropic23D (H)CCH-TOCSY
141isotropic13D 1H-13C NOESY
151isotropic13D 1H-15N NOESY
161isotropic12D 1H-13C HSQC
171isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-13C; U-15N] GEFH1 28-100, 150 mM NaCl, 25 mM NaPi, 10 % v/v [U-2H] D2O, 90 % v/v H2O, 90% H2O/10% D2O
Label: u-13C,15N GEFH1-C1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMGEFH1 28-100[U-13C; U-15N]1
150 mMNaClnatural abundance1
25 mMNaPinatural abundance1
10 % v/vD2O[U-2H]1
90 % v/vH2Onatural abundance1
Sample conditionsIonic strength: 175 mM / Label: Conditions_1 / pH: 7.2 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO7001
Bruker AVANCE III HDBrukerAVANCE III HD6002

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 3
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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