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- PDB-7rp3: Crystal structure of GNE-1952 alkylated KRAS G12C in complex with... -

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Basic information

Entry
Database: PDB / ID: 7rp3
TitleCrystal structure of GNE-1952 alkylated KRAS G12C in complex with 2H11 CLAMP
Components
  • (immunoglobulin IgG ...) x 2
  • Isoform 2B of GTPase KRas
KeywordsHydrolase/Immune System / GTPase / inhibitor / conformation-specific antibody / Hydrolase-Immune System complex
Function / homology
Function and homology information


small monomeric GTPase / Ca2+ pathway
Similarity search - Function
P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Chem-MKZ / Isoform 2B of GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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
Revision 1.3Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
H: immunoglobulin IgG heavy chain
I: immunoglobulin IgG light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,68314
Polymers66,1303
Non-polymers1,55311
Water5,224290
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)59.236, 74.330, 77.880
Angle α, β, γ (deg.)90.000, 104.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 19417.861 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: P01116-2, small monomeric GTPase

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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 , 7 types, 301 molecules

#4: Chemical ChemComp-MKZ / 1-[4-[6-chloranyl-7-(5-methyl-1~{H}-indazol-4-yl)quinazolin-4-yl]piperazin-1-yl]propan-1-one


Mass: 434.921 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23ClN6O / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.10% n-Octyl-B-D-glucoside, 0.1 M sodium citrate pH 5.5, 22% PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→45.36 Å / Num. obs: 83629 / % possible obs: 98.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 34.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Net I/σ(I): 15.5
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
2-2.113.50.4262257063670.8860.2670.5042.998.8
6.32-45.363.40.024488214160.9990.0150.02939.897.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data 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→33.577 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.86 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 4015 4.8 %
Rwork0.1907 79614 -
obs0.1928 83629 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.08 Å2 / Biso mean: 51.3508 Å2 / Biso min: 21.69 Å2
Refinement stepCycle: final / Resolution: 2→33.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4511 0 101 290 4902
Biso mean--53.41 49.36 -
Num. residues----592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084726
X-RAY DIFFRACTIONf_angle_d0.9526425
X-RAY DIFFRACTIONf_chiral_restr0.053712
X-RAY DIFFRACTIONf_plane_restr0.01811
X-RAY DIFFRACTIONf_dihedral_angle_d17.0372786
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02360.34491280.302281198
2.0236-2.04820.31151330.28277798
2.0482-2.07420.28521150.2818280898
2.0742-2.10140.29211250.2638279997
2.1014-2.13020.32721740.2576270397
2.1302-2.16070.30121280.2407276696
2.1607-2.19290.25931390.2463277897
2.1929-2.22720.31281390.2414269696
2.2272-2.26370.27221190.2379277596
2.2637-2.30270.29251440.2248265494
2.3027-2.34450.28431100.2403260892
2.3445-2.38960.28881350.2346252988
2.3896-2.43840.30711190.2247273795
2.4384-2.49140.23891770.211277999
2.4914-2.54930.30571400.2116274898
2.5493-2.61310.26311250.2124282499
2.6131-2.68370.28451620.2206284099
2.6837-2.76260.25531640.2068275698
2.7626-2.85170.24221250.2063280799
2.8517-2.95360.23391360.2034282998
2.9536-3.07180.23421270.2053274997
3.0718-3.21150.25411570.2062265495
3.2115-3.38070.31171230.1998264492
3.3807-3.59220.25281290.1866259691
3.5922-3.86920.18321500.1666283899
3.8692-4.25790.19781540.1458280499
4.2579-4.87240.15871370.1331282599
4.8724-6.13270.19031510.1547275197
6.1327-33.5770.20411500.1747272996
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)
12.4101-1.167-0.72283.10741.19872.65780.07030.00510.3889-0.24310.1108-0.1178-0.48550.00740.00110.38390.01490.02470.28380.01650.3711-23.63118.82-12.677
21.3955-0.4534-0.34081.66350.3281.1666-0.0092-0.06570.0410.07610.0366-0.20390.12590.07970.00070.26290.0509-0.01220.32460.02790.2699-10.717-11.69-17.119
33.0247-1.30581.66811.2089-0.79361.6360.46470.5084-0.1308-0.6254-0.5047-0.27311.0050.49820.00010.70240.32480.13830.61310.15110.53699.22-34.639-29.156
40.5357-0.2347-0.22830.7335-0.05030.25360.0173-0.00630.0157-0.0735-0.0173-0.1373-0.00840.04210.00010.36140.0348-0.00490.38430.01580.3657-11.913-9.6-19.03
50.0406-0.0023-0.14820.0174-0.02170.1135-0.09220.2128-0.2525-0.26290.04140.2202-0.1451-0.1130.00040.7623-0.0486-0.02970.64390.02690.6542-16.524-4.595-27.55
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:167 OR RESID 307:325 ) )A1 - 167
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1:167 OR RESID 307:325 ) )A307 - 325
3X-RAY DIFFRACTION2( CHAIN I AND RESID 2:110 ) OR ( CHAIN H AND RESID 1:110 )I2 - 110
4X-RAY DIFFRACTION2( CHAIN I AND RESID 2:110 ) OR ( CHAIN H AND RESID 1:110 )H1 - 110
5X-RAY DIFFRACTION3( CHAIN I AND RESID 111:210 ) OR ( CHAIN H AND RESID 111:213 )I111 - 210
6X-RAY DIFFRACTION3( CHAIN I AND RESID 111:210 ) OR ( CHAIN H AND RESID 111:213 )H111 - 213
7X-RAY DIFFRACTION4( CHAIN H AND RESID 401:494 ) OR ( CHAIN I AND RESID 401:524 )H401 - 494
8X-RAY DIFFRACTION4( CHAIN H AND RESID 401:494 ) OR ( CHAIN I AND RESID 401:524 )I401 - 524
9X-RAY DIFFRACTION5( CHAIN A AND RESID 204:206 ) OR ( CHAIN H AND RESID 302:302 ) OR ( CHAIN I AND RESID 301:303 )A204 - 206
10X-RAY DIFFRACTION5( CHAIN A AND RESID 204:206 ) OR ( CHAIN H AND RESID 302:302 ) OR ( CHAIN I AND RESID 301:303 )H302
11X-RAY DIFFRACTION5( CHAIN A AND RESID 204:206 ) OR ( CHAIN H AND RESID 302:302 ) OR ( CHAIN I AND RESID 301:303 )I301 - 303

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