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- PDB-7t1f: Crystal structure of GDP-bound T50I mutant of human KRAS4B -

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Basic information

Entry
Database: PDB / ID: 7t1f
TitleCrystal structure of GDP-bound T50I mutant of human KRAS4B
ComponentsIsoform 2B of GTPase KRas
KeywordsONCOPROTEIN / KRAS / RAS / T50I / KRAS4B / K-RAS
Function / homologysmall monomeric GTPase / Ca2+ pathway / GUANOSINE-5'-DIPHOSPHATE / Isoform 2B of GTPase KRas
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, Y. / Zhang, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: JCI Insight / Year: 2023
Title: Structural and functional analyses of a germline KRAS T50I mutation provide insights into Raf activation.
Authors: Chen, P.Y. / Huang, B.J. / Harris, M. / Boone, C. / Wang, W. / Carias, H. / Mesiona, B. / Mavrici, D. / Kohler, A.C. / Bollag, G. / Zhang, C. / Zhang, Y. / Shannon, K.
History
DepositionDec 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
B: Isoform 2B of GTPase KRas
C: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,44910
Polymers58,0233
Non-polymers1,4277
Water3,297183
1
A: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8083
Polymers19,3411
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8083
Polymers19,3411
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8334
Polymers19,3411
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.110, 70.110, 337.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))
21(chain B and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))
31(chain C and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))A1 - 59
121(chain A and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))A68 - 117
131(chain A and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))A119 - 169
211(chain B and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))B1 - 59
221(chain B and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))B68 - 117
231(chain B and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))B119 - 169
311(chain C and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))C1 - 59
321(chain C and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))C68 - 117
331(chain C and (resid 1 through 59 or resid 68 through 117 or resid 119 through 169))C119 - 169

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Components

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


Mass: 19340.865 Da / Num. of mol.: 3 / Mutation: T50I
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
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M calcium chloride and 20% PEG3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11584 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11584 Å / Relative weight: 1
ReflectionResolution: 2.2→49.289 Å / Num. obs: 26221 / % possible obs: 100 % / Redundancy: 29.2 % / Rrim(I) all: 0.174 / Net I/σ(I): 20
Reflection shell
Resolution (Å)Num. unique obsRrim(I) allDiffraction-ID
2.2-2.2618941.3341
2.26-2.3218121.1641
2.32-2.3917831.051
2.39-2.4617270.91

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LDJ

4ldj


Resolution: 2.2→49.289 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1747 6.66 %
Rwork0.2106 24474 -
obs0.2132 26221 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.77 Å2 / Biso mean: 38.0422 Å2 / Biso min: 10.12 Å2
Refinement stepCycle: final / Resolution: 2.2→49.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3886 0 88 183 4157
Biso mean--28.03 37.27 -
Num. residues----487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054102
X-RAY DIFFRACTIONf_angle_d0.8615549
X-RAY DIFFRACTIONf_chiral_restr0.053622
X-RAY DIFFRACTIONf_plane_restr0.005707
X-RAY DIFFRACTIONf_dihedral_angle_d14.4592484
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2344X-RAY DIFFRACTION12.407TORSIONAL
12B2344X-RAY DIFFRACTION12.407TORSIONAL
13C2344X-RAY DIFFRACTION12.407TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.26470.31461410.25641982
2.2647-2.33780.31681420.24011984
2.3378-2.42140.27981410.24171973
2.4214-2.51830.31311410.24381984
2.5183-2.63290.28021430.22891987
2.6329-2.77180.27351430.23692011
2.7718-2.94540.28941430.22092013
2.9454-3.17280.23111450.22242026
3.1728-3.4920.23391460.19782041
3.492-3.99710.23941470.18932060
3.9971-5.03510.18971510.16822126
5.0351-49.280.24951640.2222287
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)
16.2355-0.6311-0.37543.0913-0.14143.44870.03710.0274-0.10510.0932-0.00150.21140.1333-0.1605-0.00840.16520.0052-0.01330.15360.01020.14473.40427.80716.118
26.0579-1.85310.01555.9696-0.34542.5595-0.03120.5221-0.4589-0.35180.03060.22040.3358-0.0233-0.01410.2075-0.0311-0.00310.2395-0.03270.19770.78713.842-13.126
34.25461.0120.34465.0206-0.43142.91390.14780.2006-0.3533-0.0358-0.0125-0.42550.06910.2943-0.15850.22510.0192-0.0390.2169-0.00510.19741.10252.266-13.385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:169 )A1 - 169
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:169 )B1 - 169
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:168 )C1 - 168

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