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- PDB-8fmj: Crystal structure of human KRAS in space group R32 -

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Basic information

Entry
Database: PDB / ID: 8fmj
TitleCrystal structure of human KRAS in space group R32
ComponentsGTPase KRas
KeywordsHYDROLASE / cancer
Function / homology
Function and homology information


response to mineralocorticoid / GMP binding / negative regulation of epithelial cell differentiation / forebrain astrocyte development / LRR domain binding / epithelial tube branching involved in lung morphogenesis / regulation of synaptic transmission, GABAergic / response to isolation stress / response to gravity / type I pneumocyte differentiation ...response to mineralocorticoid / GMP binding / negative regulation of epithelial cell differentiation / forebrain astrocyte development / LRR domain binding / epithelial tube branching involved in lung morphogenesis / regulation of synaptic transmission, GABAergic / response to isolation stress / response to gravity / type I pneumocyte differentiation / skeletal muscle cell differentiation / myoblast proliferation / Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / cardiac muscle cell proliferation / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of glial cell proliferation / 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 / homeostasis of number of cells within a tissue / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / positive regulation of Rac protein signal transduction / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / striated muscle cell differentiation / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / protein-membrane adaptor activity / Signaling by FGFR2 in disease / Signaling by FLT3 fusion proteins / GRB2 events in EGFR signaling / 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 / GRB2 events in ERBB2 signaling / Downstream signal transduction / response to glucocorticoid / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / liver development / Constitutive Signaling by Overexpressed ERBB2 / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / female pregnancy / Signaling by ERBB2 TMD/JMD mutants / Signaling by SCF-KIT / RAF activation / Constitutive Signaling by EGFRvIII / visual learning / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / cytokine-mediated signaling pathway / cytoplasmic side of plasma membrane / gene expression / Signaling by RAF1 mutants / Signaling by CSF1 (M-CSF) in myeloid cells / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Negative regulation of MAPK pathway / RAS processing / Regulation of RAS by GAPs / MAPK cascade / positive regulation of cellular senescence / Signaling by BRAF and RAF1 fusions / neuron apoptotic process / GDP binding
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain 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
GUANOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsBrenner, R. / Landgraf, A. / Gonzalez-Gutierrez, G. / Bum-Erdene, K. / Meroueh, S.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA264471 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA197928 United States
CitationJournal: Biochemistry / Year: 2023
Title: Crystal Packing Reveals a Potential Autoinhibited KRAS Dimer Interface and a Strategy for Small-Molecule Inhibition of RAS Signaling.
Authors: Brenner, R.J. / Landgraf, A.D. / Bum-Erdene, K. / Gonzalez-Gutierrez, G. / Meroueh, S.O.
History
DepositionDec 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0626
Polymers20,2741
Non-polymers7885
Water3,603200
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)92.516, 92.516, 117.775
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-203-

TRS

21A-203-

TRS

31A-340-

HOH

41A-361-

HOH

51A-400-

HOH

61A-438-

HOH

71A-471-

HOH

81A-486-

HOH

91A-500-

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: 20273.811 Da / Num. of mol.: 1 / Mutation: C118S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01116, small monomeric GTPase

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Non-polymers , 6 types, 205 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris 0.1 M pH 7.8 - 8.0 NaAc 0.2 M PEG3350 30-34% / PH range: 7.8 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.33→47.45 Å / Num. obs: 43647 / % possible obs: 98 % / Redundancy: 9.8 % / Biso Wilson estimate: 12.96 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.034 / Rrim(I) all: 0.107 / Rsym value: 0.101 / Net I/σ(I): 12.4
Reflection shellResolution: 1.33→1.35 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2229 / CC1/2: 0.686 / Rpim(I) all: 0.549 / Rrim(I) all: 1.606 / Rsym value: 1.507 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→47.45 Å / SU ML: 0.1002 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.0726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1665 2199 5.04 %
Rwork0.1421 41444 -
obs0.1432 43643 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.62 Å2
Refinement stepCycle: LAST / Resolution: 1.33→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 22 200 1615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841571
X-RAY DIFFRACTIONf_angle_d1.13192137
X-RAY DIFFRACTIONf_chiral_restr0.0765227
X-RAY DIFFRACTIONf_plane_restr0.0092282
X-RAY DIFFRACTIONf_dihedral_angle_d12.3168238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.360.24861250.25582669X-RAY DIFFRACTION100
1.36-1.390.24771580.23392564X-RAY DIFFRACTION99.96
1.39-1.430.21931740.21362584X-RAY DIFFRACTION100
1.43-1.460.20731600.20352605X-RAY DIFFRACTION100
1.46-1.510.19661440.19342626X-RAY DIFFRACTION100
1.51-1.560.18831330.18122609X-RAY DIFFRACTION100
1.56-1.610.22271360.16432653X-RAY DIFFRACTION100
1.61-1.680.15691410.14722607X-RAY DIFFRACTION99.96
1.68-1.750.14281430.13962631X-RAY DIFFRACTION99.96
1.75-1.850.18521340.13932647X-RAY DIFFRACTION100
1.85-1.960.1721080.13812661X-RAY DIFFRACTION100
1.96-2.110.14951150.12142096X-RAY DIFFRACTION79.36
2.11-2.330.16861040.1182402X-RAY DIFFRACTION89.92
2.33-2.660.12821670.12132639X-RAY DIFFRACTION100
2.66-3.350.14691240.12932703X-RAY DIFFRACTION100
3.35-47.450.16641330.13172748X-RAY DIFFRACTION98.56
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)
11.52396953809-0.7897659909570.9438915114292.38387607714-0.7100212385921.409090030240.1538659286740.2141451724660.243937920953-0.226656276956-0.162622970538-0.238035159822-0.008239585702250.105465052837-0.02069059171040.09201255078290.002905049488290.04219839820620.1364812655030.02367704878340.11440133675525.1905081048-7.3321194148823.6214667394
26.505059838877.163296904826.384940327338.424689624378.062294228618.958632313840.02881948657040.5076270917340.185636687884-0.5688713126190.00319799510963-0.165745715917-0.4681382697160.14288059350.01790567482750.237161212740.02574908192770.08031987219010.2544070650830.1161567039890.28793099685622.47900883463.4602798546618.9589297143
33.57682081038-1.617548863893.130821013850.835203092695-1.375093395374.552769403590.02565862932950.3358063863090.08071842651330.0155223455715-0.074244367215-0.00915770548517-0.1029100080720.3146122956520.09149487749030.124561485627-0.00906606098840.01257334606890.1573834641990.01946370753950.13054436430332.2072740613-10.609804873924.3053662134
43.383445896680.7792790408970.5668513927074.507281733030.5602040104846.663600751860.1655021186670.680537566386-0.0251790546369-0.881704983788-0.02228186195320.2237850944240.107711043661-0.167725599848-0.1584983774050.260453307850.0118557670719-0.0276806161110.293200298303-0.03077851301390.1420920765318.193168045-14.893104274413.5601554105
52.60006588979-2.28466308268-1.00798955563.557603311071.124160422920.9924345733520.04757017476320.150884478475-0.186246432449-0.118913654891-0.1217220396960.223449640470.0605393302715-0.07474144108440.06274631121510.101481981246-0.00100469528521-0.007942780785870.0894037090093-0.003964875705380.08799469589210.5742429486-11.914785270425.8605008175
61.76252136013-1.53785838552-0.2553892493924.787450212942.29901020372.11343799504-0.02390155216310.0457148176277-0.1522786036270.223720227451-0.006235772335340.182856348840.302056722243-0.003399249033250.02878477219420.108811308204-0.002843432157570.005377881172630.1032646585180.0021452159840.10704923135715.7811418087-17.159981704430.2210735981
72.21160494107-0.341983821696-0.1496647821542.5144752623-0.3609388699640.6797964129720.000516136785936-0.07736238452180.1591020914720.07710535148850.0358852606111-0.0236492736575-0.0631060396922-0.00159190228101-0.0341844449970.10269811210.00341642645309-0.007670662851720.10272469797-0.01224104274610.098601301711113.4733543121-3.3150925748535.8965386094
83.47455931333-2.443326199040.04059429794542.270154281340.1201185157542.98081006644-0.0331743113992-0.0464889996083-0.04611563091890.005287472704650.103846237189-0.1902772337770.08005064978610.122667735113-0.07478642114650.08764013262580.007503544592460.001756881835690.101400539037-0.001648394710960.090895966349526.8616621953-15.070052105733.0310720275
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 25 )0 - 251 - 26
22chain 'A' and (resid 26 through 37 )26 - 3727 - 38
33chain 'A' and (resid 38 through 57 )38 - 5739 - 58
44chain 'A' and (resid 58 through 74 )58 - 7459 - 75
55chain 'A' and (resid 75 through 104 )75 - 10476 - 105
66chain 'A' and (resid 105 through 116 )105 - 116106 - 117
77chain 'A' and (resid 117 through 151 )117 - 151118 - 152
88chain 'A' and (resid 152 through 169 )152 - 169153 - 170

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