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- PDB-1wq1: RAS-RASGAP COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1wq1
TitleRAS-RASGAP COMPLEX
Components
  • H-RAS
  • P120GAP
KeywordsCOMPLEX (GTP-BINDING/GTPASE ACTIVATION) / RAS / GAP / SIGNAL TRANSDUCTION / GROWTH REGULATION / GTP HYDROLYSIS / TRANSITION STATE / COMPLEX (GTP-BINDING-GTPASE ACTIVATION) / COMPLEX (GTP-BINDING-GTPASE ACTIVATION) complex
Function / homology
Function and homology information


regulation of RNA metabolic process / regulation of actin filament polymerization / potassium channel inhibitor activity / phospholipase C activator activity / negative regulation of cell adhesion / GTPase complex / oncogene-induced cell senescence / blood vessel morphogenesis / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly ...regulation of RNA metabolic process / regulation of actin filament polymerization / potassium channel inhibitor activity / phospholipase C activator activity / negative regulation of cell adhesion / GTPase complex / oncogene-induced cell senescence / blood vessel morphogenesis / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / mitotic cytokinesis / RAS signaling downstream of NF1 loss-of-function variants / negative regulation of cell-matrix adhesion / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / positive regulation of protein targeting to membrane / SHC1 events in ERBB4 signaling / adipose tissue development / ephrin receptor signaling pathway / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / vasculogenesis / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / p38MAPK events / Signaling by FGFR3 in disease / ruffle / protein-membrane adaptor activity / Tie2 Signaling / Signaling by FGFR2 in disease / phosphotyrosine residue binding / myelination / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / intrinsic apoptotic signaling pathway / Downstream signal transduction / GRB2 events in ERBB2 signaling / Insulin receptor signalling cascade / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / GTPase activator activity / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / animal organ morphogenesis / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / small monomeric GTPase / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / FCERI mediated MAPK activation / RAF activation / Signaling by ERBB2 TMD/JMD mutants / cellular response to gamma radiation / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / regulation of long-term neuronal synaptic plasticity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of type II interferon production / endocytosis / positive regulation of fibroblast proliferation / chemotaxis / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants
Similarity search - Function
GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Ras GTPase-activating protein 1, N-terminal SH2 domain / RasGAP, SH3 domain / Ras GTPase-activating protein 1, C-terminal SH2 domain / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins (rasGAP) domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins (rasGAP) domain profile. ...GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Ras GTPase-activating protein 1, N-terminal SH2 domain / RasGAP, SH3 domain / Ras GTPase-activating protein 1, C-terminal SH2 domain / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins (rasGAP) domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins (rasGAP) domain profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Rho GTPase activation protein / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Rho (Ras homology) subfamily of Ras-like small GTPases / SH2 domain / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Src homology 2 (SH2) domain profile. / Rab subfamily of small GTPases / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / PH-like domain superfamily / 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
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / GTPase HRas / Ras GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsScheffzek, K. / Ahmadian, M.R. / Kabsch, W. / Wiesmueller, L. / Lautwein, A. / Schmitz, F. / Wittinghofer, A.
Citation
Journal: Science / Year: 1997
Title: The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants.
Authors: Scheffzek, K. / Ahmadian, M.R. / Kabsch, W. / Wiesmuller, L. / Lautwein, A. / Schmitz, F. / Wittinghofer, A.
#1: Journal: FEBS Lett. / Year: 1997
Title: The Interaction of Ras with Gtpase-Activating Proteins
Authors: Wittinghofer, A. / Scheffzek, K. / Ahmadian, M.R.
#2: Journal: Science / Year: 1996
Title: Formation of a Transition-State Analog of the Ras Gtpase Reaction by Ras-Gdp, Tetrafluoroaluminate, and Gtpase-Activating Proteins
Authors: Mittal, R. / Ahmadian, M.R. / Goody, R.S. / Wittinghofer, A.
#3: Journal: Nature / Year: 1996
Title: Crystal Structure of the Gtpase-Activating Domain of Human P120Gap and Implications for the Interaction with Ras
Authors: Scheffzek, K. / Lautwein, A. / Kabsch, W. / Ahmadian, M.R. / Wittinghofer, A.
#4: Journal: Embo J. / Year: 1990
Title: Refined Crystal Structure of the Triphosphate Conformation of H-Ras P21 at 1.35 A Resolution: Implications for the Mechanism of GTP Hydrolysis
Authors: Pai, E.F. / Krengel, U. / Petsko, G.A. / Goody, R.S. / Kabsch, W. / Wittinghofer, A.
#5: Journal: Science / Year: 1987
Title: A Cytoplasmic Protein Stimulates Normal N-Ras P21 Gtpase, But Does not Affect Oncogenic Mutants
Authors: Trahey, M. / Mccormick, F.
#6: Journal: Cell(Cambridge,Mass.) / Year: 1986
Title: Biological and Biochemical Properties of Human Rash Genes Mutated at Codon 61
Authors: Der, C.J. / Finkel, T. / Cooper, G.M.
#7: Journal: Nature / Year: 1984
Title: Biological Properties of Human C-Ha-Ras1 Genes Mutated at Codon 12
Authors: Seeburg, P.H. / Colby, W.W. / Capon, D.J. / Goeddel, D.V. / Levinson, A.D.
History
DepositionJul 3, 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 9, 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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: H-RAS
G: P120GAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6505
Polymers57,0982
Non-polymers5513
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-25 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.900, 41.100, 89.000
Angle α, β, γ (deg.)90.00, 108.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules RG

#1: Protein H-RAS / P21RAS / RAS / HARVEY-RAS


Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1 - 166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H-RAS-1 / Organ: PLACENTA / Plasmid: PTRCGAP-334 / Gene (production host): GENE FRAGMENT OF P120GAP POSI / Production host: Escherichia coli (E. coli) / Strain (production host): CK 600 K / References: UniProt: P01112
#2: Protein P120GAP / GAP-334 / GAPETTE


Mass: 38223.277 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 714 - 1047
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOSOL / Gene: GENE FRAGMENT OF P120GAP POSI / Organ: PLACENTA / Plasmid: PTRCGAP-334
Gene (production host): GENE FRAGMENT OF P120GAP, POSITION 2258 - 3259
Production host: Escherichia coli (E. coli) / Strain (production host): DG103 / References: UniProt: P20936

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Non-polymers , 4 types, 38 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 45 %
Crystal growpH: 8 / Details: SEE REF. DESCRIBING THE STRUCTURE, pH 8.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 mMHEPES1drop
32 mM1dropAlCl3
420 mM1dropNaF
515-20 %PEG33501reservoir
6100 mMHEPES1reservoir
720 mMammonium sulfate1reservoir
820 mM1reservoirNaF

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 14, 1997 / Details: FRANKS DOUBLE MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 15811 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 41.9 Å2 / Rsym value: 0.06 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.35 / % possible all: 64
Reflection
*PLUS
Num. measured all: 35339 / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
XDS(W. KABSCH)data scaling
XSCALE(W. KABSCH)data scaling
X-PLOR3.8model building
X-PLOR3.8refinement
XDS(W.KABSCH)data reduction
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RAS:GPPNP (PDB ENTRY 5P21), GAP-334 (PDB ENTRY 1WER)

5p21

1wer


Resolution: 2.5→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.319 1352 10 %RANDOM
Rwork0.233 ---
obs0.233 13522 77.3 %-
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.34 Å
Luzzati d res low-30 Å
Luzzati sigma a0.48 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 33 35 3923
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.36
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.691.5
X-RAY DIFFRACTIONx_mcangle_it4.42
X-RAY DIFFRACTIONx_scbond_it4.42
X-RAY DIFFRACTIONx_scangle_it6.932.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.414 78 9.3 %
Rwork0.311 764 -
obs--39 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.36

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