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- PDB-1am4: COMPLEX BETWEEN CDC42HS.GMPPNP AND P50 RHOGAP (H. SAPIENS) -

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Basic information

Entry
Database: PDB / ID: 1am4
TitleCOMPLEX BETWEEN CDC42HS.GMPPNP AND P50 RHOGAP (H. SAPIENS)
Components
  • CDC42HS
  • P50-RHOGAP
KeywordsCOMPLEX (GTPASE-ACTIVATING/GTP-BINDING) / COMPLEX (GTPASE-ACTIVATING-GTP-BINDING) / GTPASE ACTIVATION / COMPLEX (GTPASE-ACTIVATING-GTP-BINDING) complex
Function / homology
Function and homology information


negative regulation of endocytic recycling / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding ...negative regulation of endocytic recycling / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / GTP-dependent protein binding / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / RHOD GTPase cycle / embryonic heart tube development / RHOF GTPase cycle / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / RND2 GTPase cycle / endosomal transport / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOB GTPase cycle / RHOV GTPase cycle / nuclear migration / small GTPase-mediated signal transduction / Myogenesis / positive regulation of cytokinesis / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / RHOC GTPase cycle / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / Rho protein signal transduction / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / ruffle / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of substrate adhesion-dependent cell spreading / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / actin filament organization / EGFR downregulation / transferrin transport / small monomeric GTPase / integrin-mediated signaling pathway / MAPK6/MAPK4 signaling / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / filopodium / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / cellular response to type II interferon / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis / G beta:gamma signalling through CDC42 / mitotic spindle
Similarity search - Function
: / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Cdc42 / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase-activating protein domain ...: / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Cdc42 / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Small GTPase Rho / Small GTPase Rho domain profile. / Rho GTPase activation protein / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Cell division control protein 42 homolog / Rho GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRittinger, K. / Walker, P. / Gamblin, S.J. / Smerdon, S.J.
CitationJournal: Nature / Year: 1997
Title: Crystal structure of a small G protein in complex with the GTPase-activating protein rhoGAP.
Authors: Rittinger, K. / Walker, P.A. / Eccleston, J.F. / Nurmahomed, K. / Owen, D. / Laue, E. / Gamblin, S.J. / Smerdon, S.J.
History
DepositionJun 22, 1997Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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.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.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P50-RHOGAP
D: CDC42HS
B: P50-RHOGAP
E: CDC42HS
C: P50-RHOGAP
F: CDC42HS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,78412
Polymers127,1456
Non-polymers1,6406
Water5,441302
1
A: P50-RHOGAP
D: CDC42HS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9284
Polymers42,3822
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: P50-RHOGAP
F: CDC42HS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9284
Polymers42,3822
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-20 kcal/mol
Surface area17200 Å2
MethodPISA
3
B: P50-RHOGAP
E: CDC42HS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9284
Polymers42,3822
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.110, 78.120, 78.100
Angle α, β, γ (deg.)90.01, 90.00, 90.05
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-9.7E-5, 1, 0.000273), (-2.4E-5, 0.000273, -1), (-1, -9.7E-5, 2.4E-5)32.64486, 6.7725, 39.41171
2given(-0.00055, 2.1E-5, -1), (1, -6.1E-5, -0.00055), (-6.1E-5, -1, -2.1E-5)39.37717, 45.48096, 6.77439

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Components

#1: Protein P50-RHOGAP


Mass: 22741.998 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q07960
#2: Protein CDC42HS


Mass: 19639.521 Da / Num. of mol.: 3 / Mutation: M501P
Source method: isolated from a genetically manipulated source
Details: HETERODIMER / Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P60953
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.75 Å3/Da / Density % sol: 55 %
Crystal growpH: 5.9 / Details: pH 5.9
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG40001reservoir
2100 mMsodium cacodylate1reservoir
310 mM1reservoirMgCl2
43 mMdithiothreitol1reservoir
53 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 49357 / % possible obs: 97.6 % / Redundancy: 5 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 26
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 5 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 246060
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameClassification
AMoREphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1RGP, 1MH1

1rgp

1mh1


Resolution: 2.7→12 Å / Cross valid method: THROUGHOUT
Rfactor% reflectionSelection details
Rfree0.28 5 %RANDOM
Rwork0.23 --
obs-96 %-
Displacement parametersBiso mean: 18 Å2
Refinement stepCycle: LAST / Resolution: 2.7→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8907 0 0 297 9204
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_deg / Dev ideal: 2.7

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