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- PDB-2esw: Atomic structure of the N-terminal SH3 domain of mouse beta PIX,p... -

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Basic information

Entry
Database: PDB / ID: 2esw
TitleAtomic structure of the N-terminal SH3 domain of mouse beta PIX,p21-activated kinase (PAK)-interacting exchange factor
ComponentsRho guanine nucleotide exchange factor 7
KeywordsSIGNALING PROTEIN / BETA BARREL / SH3 DOMAIN
Function / homology
Function and homology information


presynaptic actin cytoskeleton organization / RHOV GTPase cycle / negative regulation of microtubule nucleation / Ephrin signaling / RHOQ GTPase cycle / RHOU GTPase cycle / RHOA GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / RAC1 GTPase cycle ...presynaptic actin cytoskeleton organization / RHOV GTPase cycle / negative regulation of microtubule nucleation / Ephrin signaling / RHOQ GTPase cycle / RHOU GTPase cycle / RHOA GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / RAC1 GTPase cycle / G alpha (12/13) signalling events / storage vacuole / astrocyte cell migration / positive regulation of growth hormone secretion / postsynaptic actin cytoskeleton organization / gamma-tubulin binding / lamellipodium assembly / small GTPase-mediated signal transduction / mitotic spindle pole / Golgi organization / Rho protein signal transduction / GABA-ergic synapse / hematopoietic progenitor cell differentiation / ruffle / guanyl-nucleotide exchange factor activity / positive regulation of GTPase activity / lamellipodium / cell cortex / growth cone / postsynapse / neuron projection / positive regulation of apoptotic process / focal adhesion / centrosome / neuronal cell body / protein kinase binding / protein-containing complex / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Unstructured region one on RhoGEF 6 and 7 / Rho guanine nucleotide exchange factor 6/7, coiled-coil domain / betaPIX coiled coil / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / 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 6/7, coiled-coil domain / betaPIX coiled coil / Rho guanine nucleotide exchange factor 7, SH3 domain / RhoGEF 6/7, PH domain / Unstructured region two on RhoGEF 6 and 7 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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. / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
: / Rho guanine nucleotide exchange factor 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.01 Å
AuthorsRao, Z.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Crystal structure of the N-terminal SH3 domain of mouse betaPIX, p21-activated kinase-interacting exchange factor
Authors: Li, X. / Liu, X. / Sun, F. / Gao, J. / Zhou, H. / Gao, G.F. / Bartlam, M. / Rao, Z.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 7
B: Rho guanine nucleotide exchange factor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,25511
Polymers13,9452
Non-polymers1,3109
Water2,000111
1
A: Rho guanine nucleotide exchange factor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6456
Polymers6,9731
Non-polymers6735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rho guanine nucleotide exchange factor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6105
Polymers6,9731
Non-polymers6374
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-136 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.287, 88.287, 40.558
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Rho guanine nucleotide exchange factor 7 / PAK-interacting exchange factor beta / Beta-Pix / p85SPR


Mass: 6972.619 Da / Num. of mol.: 2 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ES28
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.27 Å3/Da / Density % sol: 62.4 % / Description: The file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Hepes Na, 1.45M Lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 22511
Reflection shellResolution: 2.01→2.08 Å / % possible all: 98.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.01→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The file contains Friedel pairs
RfactorNum. reflectionSelection details
Rfree0.254 1087 random
Rwork0.232 --
all0.256 --
obs0.254 22511 -
Refinement stepCycle: LAST / Resolution: 2.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 9 111 1083
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2056
X-RAY DIFFRACTIONc_bond_d0.007

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