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- PDB-2uzi: Crystal structure of HRAS(G12V) - anti-RAS Fv complex -

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Basic information

Entry
Database: PDB / ID: 2uzi
TitleCrystal structure of HRAS(G12V) - anti-RAS Fv complex
Components
  • ANTI-RAS FV HEAVY CHAIN
  • ANTI-RAS FV LIGHT CHAIN
  • GTPASE HRASHRAS
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / SIGNAL TRANSDUCTION / IMMUNOGLOBULIN DOMAIN / MEMBRANE / ANTIBODY / ONCOGENE / PALMITATE / INTRABODY / DISEASE MUTATION / NUCLEOTIDE-BINDING / PROTO-ONCOGENE / CANCER THERAPY / GOLGI APPARATUS / PRENYLATION / METHYLATION / LIPOPROTEIN / GTP- BINDING / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


GTPase complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of ruffle assembly / regulation of MAP kinase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / negative regulation of GTPase activity / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of ruffle assembly / regulation of MAP kinase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / negative regulation of GTPase activity / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of actin cytoskeleton reorganization / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / Signaling by PDGFRA extracellular domain mutants / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by FGFR4 in disease / positive regulation of phospholipase C activity / SHC-mediated cascade:FGFR2 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR4 / Signaling by FLT3 ITD and TKD mutants / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Tie2 Signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / EPHB-mediated forward signaling / FRS-mediated FGFR1 signaling / G protein activity / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in EGFR signaling / p38MAPK events / Signaling by FLT3 fusion proteins / FLT3 Signaling / EGFR Transactivation by Gastrin / small monomeric GTPase / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / intrinsic apoptotic signaling pathway / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / NCAM signaling for neurite out-growth / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / RAF activation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / animal organ morphogenesis / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / Regulation of RAS by GAPs / GDP binding / RAS processing / Negative regulation of MAPK pathway / fibroblast proliferation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytosis / positive regulation of GTPase activity / chemotaxis / Signaling by BRAF and RAF1 fusions / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of type II interferon production / MAPK cascade / positive regulation of MAP kinase activity / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / regulation of cell population proliferation / T cell receptor signaling pathway
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like / P-loop containing nucleoside triphosphate hydrolase ...Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like / P-loop containing nucleoside triphosphate hydrolase / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTPase HRas
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTanaka, T. / williams, R.L. / Rabbitts, T.H.
CitationJournal: Embo J. / Year: 2007
Title: Tumour Prevention by a Single Antibody Domain Targeting the Interaction of Signal Transduction Proteins with Ras.
Authors: Tanaka, T. / Williams, R.L. / Rabbitts, T.H.
History
DepositionApr 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: ANTI-RAS FV HEAVY CHAIN
L: ANTI-RAS FV LIGHT CHAIN
R: GTPASE HRAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,70110
Polymers42,8263
Non-polymers8757
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.528, 84.632, 62.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11R-2096-

HOH

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Components

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Protein , 1 types, 1 molecules R

#3: Protein GTPASE HRAS / HRAS / H-RAS ONCOPROTEIN / TRANSFORMING PROTEIN P21 / P21RAS / H-RAS-1 / C-H-RAS / HA-RAS


Mass: 18917.271 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-166 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRK172 / Production host: ESCHERICHIA COLI BL21(DE3) (unknown) / Variant (production host): C41 / References: UniProt: P01112

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Antibody , 2 types, 2 molecules HL

#1: Antibody ANTI-RAS FV HEAVY CHAIN


Mass: 12688.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRK-HISTEV-VH-RAS-VL / Production host: ESCHERICHIA COLI BL21(DE3) (unknown) / Variant (production host): C41
#2: Antibody ANTI-RAS FV LIGHT CHAIN


Mass: 11220.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRK-HISTEV-VH-RAS-VL / Production host: ESCHERICHIA COLI BL21(DE3) (unknown) / Variant (production host): C41

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Non-polymers , 4 types, 296 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN R, GLY 12 TO VAL

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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: 2.15 Å3/Da / Density % sol: 38.2 %
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM 17-18 % PEG3350, 400 MM ZINC ACETATE, 100 MM SODIUM CACODYLATE, PH 5.8, 0.03 % DICHLOROMETHANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→50.32 Å / Num. obs: 27214 / % possible obs: 98.2 % / Observed criterion σ(I): 3.7 / Redundancy: 3.38 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.42
Reflection shellResolution: 2→2.02 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.67 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
TRUNCATEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AGP, 1A2Y
Resolution: 2→41.89 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.894 / SU B: 4.749 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1369 5 %RANDOM
Rwork0.194 ---
obs0.198 25816 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.27 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3003 0 38 289 3330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223094
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.9634193
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8855381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86523.873142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38815521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4351522
X-RAY DIFFRACTIONr_chiral_restr0.1420.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022329
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.21498
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22064
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4190.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1831.51964
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79623061
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8731326
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1544.51132
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 114
Rwork0.208 1824

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