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- PDB-7rp2: Crystal structure of Kas G12C in complex with 2H11 CLAMP -

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Basic information

Entry
Database: PDB / ID: 7rp2
TitleCrystal structure of Kas G12C in complex with 2H11 CLAMP
Components
  • (immunoglobulin IgG ...) x 2
  • GTPase KRas
KeywordsHydrolase/Immune System / GTPase / antibody / conformation-specific / Hydrolase-Immune System complex
Function / homology
Function and homology information


forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / 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 / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / 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:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / striated muscle cell differentiation / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / 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 / Signaling by CSF1 (M-CSF) in myeloid cells / MAPK cascade / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / Ras protein signal transduction / negative regulation of neuron apoptotic process / mitochondrial outer membrane / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CACODYLATE ION / GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOh, A. / Tam, C. / Wang, W.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat.Biotechnol. / Year: 2022
Title: Conformation-locking antibodies for the discovery and characterization of KRAS inhibitors.
Authors: Davies, C.W. / Oh, A.J. / Mroue, R. / Steffek, M. / Bruning, J.M. / Xiao, Y. / Feng, S. / Jayakar, S. / Chan, E. / Arumugam, V. / Uribe, S.C. / Drummond, J. / Frommlet, A. / Lu, C. / Franke, ...Authors: Davies, C.W. / Oh, A.J. / Mroue, R. / Steffek, M. / Bruning, J.M. / Xiao, Y. / Feng, S. / Jayakar, S. / Chan, E. / Arumugam, V. / Uribe, S.C. / Drummond, J. / Frommlet, A. / Lu, C. / Franke, Y. / Merchant, M. / Koeppen, H. / Quinn, J.G. / Malhotra, S. / Do, S. / Gazzard, L. / Purkey, H.E. / Rudolph, J. / Mulvihill, M.M. / Koerber, J.T. / Wang, W. / Evangelista, M.
History
DepositionAug 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
H: immunoglobulin IgG heavy chain
I: immunoglobulin IgG light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0059
Polymers66,0653
Non-polymers9416
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.918, 68.796, 101.002
Angle α, β, γ (deg.)90.000, 114.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-424-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19352.785 Da / Num. of mol.: 1 / Mutation: G12C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116

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Antibody , 2 types, 2 molecules HI

#2: Antibody immunoglobulin IgG heavy chain


Mass: 23833.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody immunoglobulin IgG light chain


Mass: 22878.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 110 molecules

#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.6 Å3/Da / Density % sol: 65.82 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.5, 40% 2-methyl 2,4-pentanediol (MPD), 7% PEG 8000, 0.5% ethyl acetate, 10 mM spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9999999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999999 Å / Relative weight: 1
ReflectionResolution: 2.2→48.49 Å / Num. obs: 92744 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 51.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.326.90.9694805169210.8160.3961.0481.8100
6.96-48.496.30.042989015580.9990.0180.04530.598.4

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
PHENIX1.12-2829_finalrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DSU, 3R1G

4dsu

3r1g


Resolution: 2.2→48.49 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.05 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2249 4587 4.95 %
Rwork0.2076 88157 -
obs0.2084 92744 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.81 Å2 / Biso mean: 79.7097 Å2 / Biso min: 40.07 Å2
Refinement stepCycle: final / Resolution: 2.2→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 48 104 4788
Biso mean--129.83 60.16 -
Num. residues----610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044802
X-RAY DIFFRACTIONf_angle_d0.9916533
X-RAY DIFFRACTIONf_chiral_restr0.071734
X-RAY DIFFRACTIONf_plane_restr0.008827
X-RAY DIFFRACTIONf_dihedral_angle_d15.2242862
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2250.39461850.4304293299
2.225-2.25120.38571640.4159287699
2.2512-2.27860.45111650.40832980100
2.2786-2.30750.42511620.41212948100
2.3075-2.33780.4031730.36072926100
2.3378-2.36990.34211510.3623298599
2.3699-2.40370.32641330.3547294399
2.4037-2.43960.30751420.34172949100
2.4396-2.47770.36531460.33993005100
2.4777-2.51830.3271460.32122870100
2.5183-2.56180.38641440.29792971100
2.5618-2.60840.3611650.30512999100
2.6084-2.65850.27991540.29492996100
2.6585-2.71280.2831600.28782878100
2.7128-2.77180.26931570.27083007100
2.7718-2.83620.24481590.25562920100
2.8362-2.90710.23641600.24342932100
2.9071-2.98570.26651540.24152998100
2.9857-3.07360.24661800.24292887100
3.0736-3.17280.21831630.22294899
3.1728-3.28610.25141550.2166293899
3.2861-3.41770.21221250.2177294099
3.4177-3.57320.25051340.2108294899
3.5732-3.76150.19961360.2034290198
3.7615-3.99710.20471320.1798294098
3.9971-4.30550.18451270.169290498
4.3055-4.73850.16251350.1425296799
4.7385-5.42330.17991770.1504285599
5.4233-6.82980.19111580.1893292597
6.8298-48.490.15161450.1311288998
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72340.10320.38710.7028-0.27610.8267-0.0739-0.67520.1291-0.04040.0729-0.20.15470.394100.86010.0865-0.00961.43540.01020.5565-4.01939.04847.031
21.7574-0.12140.31381.09320.06540.92620.1108-0.3854-0.27280.04260.09720.0266-0.0933-0.02760.01540.44340.01940.01410.54170.10180.5863-5.17132.00314.246
31.55751.164-0.0053.35340.64180.39390.0794-0.00650.0413-0.0904-0.2088-0.0773-0.0268-0.083800.50260.03380.00980.44280.07710.5088-35.62125.615-1.779
40.0514-0.0460.05630.0365-0.0510.05580.0915-0.31680.0769-0.6487-0.19060.33620.09710.09620.00011.887-0.1526-0.02792.4271-0.042.491-5.77231.18915.824
50.38590.4798-0.02280.1250.1756-0.0066-0.0128-0.256-0.06720.00170.03930.0561-0.090.04780.00350.56950.0209-0.0170.55580.06340.3897-16.27932.6885.769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:169 )A0 - 169
2X-RAY DIFFRACTION2( CHAIN I AND RESID 2:110 ) OR ( CHAIN H AND RESID 1:110 )I2 - 110
3X-RAY DIFFRACTION2( CHAIN I AND RESID 2:110 ) OR ( CHAIN H AND RESID 1:110 )H1 - 110
4X-RAY DIFFRACTION3( CHAIN I AND RESID 111:213 ) OR ( CHAIN H AND RESID 111:214 )I111 - 213
5X-RAY DIFFRACTION3( CHAIN I AND RESID 111:213 ) OR ( CHAIN H AND RESID 111:214 )H111 - 214
6X-RAY DIFFRACTION4( CHAIN H AND RESID 301:302 ) OR ( CHAIN I AND RESID 301:302 )H301 - 302
7X-RAY DIFFRACTION4( CHAIN H AND RESID 301:302 ) OR ( CHAIN I AND RESID 301:302 )I301 - 302
8X-RAY DIFFRACTION5( CHAIN A AND RESID 301:307 ) OR ( CHAIN H AND RESID 401:458 ) OR ( CHAIN I AND RESID 401:439 )A301 - 307
9X-RAY DIFFRACTION5( CHAIN A AND RESID 301:307 ) OR ( CHAIN H AND RESID 401:458 ) OR ( CHAIN I AND RESID 401:439 )H401 - 458
10X-RAY DIFFRACTION5( CHAIN A AND RESID 301:307 ) OR ( CHAIN H AND RESID 401:458 ) OR ( CHAIN I AND RESID 401:439 )I401 - 439

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