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- PDB-6ob2: Crystal structure of wild-type KRAS (GMPPNP-bound) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6ob2
TitleCrystal structure of wild-type KRAS (GMPPNP-bound) in complex with GAP-related domain (GRD) of neurofibromin (NF1)
Components
  • GTPase KRas
  • Neurofibromin
KeywordsGTP Binding/Lipid Binding / KRAS / RAS / KRAS4b / NF1 / GAP / Neurofibromin / GTP Binding-Lipid Binding complex
Function / homology
Function and homology information


positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / observational learning / negative regulation of Schwann cell migration / Schwann cell migration / amygdala development / vascular associated smooth muscle cell migration / Schwann cell proliferation / negative regulation of mast cell proliferation ...positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / observational learning / negative regulation of Schwann cell migration / Schwann cell migration / amygdala development / vascular associated smooth muscle cell migration / Schwann cell proliferation / negative regulation of mast cell proliferation / mast cell apoptotic process / gamma-aminobutyric acid secretion, neurotransmission / vascular associated smooth muscle cell proliferation / negative regulation of Schwann cell proliferation / glutamate secretion, neurotransmission / negative regulation of leukocyte migration / mast cell proliferation / forebrain morphogenesis / regulation of cell-matrix adhesion / hair follicle maturation / regulation of blood vessel endothelial cell migration / camera-type eye morphogenesis / cell communication / smooth muscle tissue development / negative regulation of neurotransmitter secretion / negative regulation of oligodendrocyte differentiation / sympathetic nervous system development / myeloid leukocyte migration / peripheral nervous system development / phosphatidylcholine binding / myelination in peripheral nervous system / negative regulation of Ras protein signal transduction / metanephros development / phosphatidylethanolamine binding / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / collagen fibril organization / regulation of long-term synaptic potentiation / regulation of postsynapse organization / endothelial cell proliferation / regulation of bone resorption / artery morphogenesis / neural tube development / adrenal gland development / response to mineralocorticoid / negative regulation of neuroblast proliferation / GMP binding / forebrain astrocyte development / LRR domain binding / negative regulation of protein import into nucleus / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / spinal cord development / negative regulation of astrocyte differentiation / negative regulation of vascular associated smooth muscle cell migration / pigmentation / response to gravity / epithelial tube branching involved in lung morphogenesis / negative regulation of endothelial cell proliferation / negative regulation of osteoclast differentiation / type I pneumocyte differentiation / Rac protein signal transduction / oligodendrocyte differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / myoblast proliferation / RAS signaling downstream of NF1 loss-of-function variants / skeletal muscle cell differentiation / RUNX3 regulates p14-ARF / negative regulation of cell-matrix adhesion / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway via death domain receptors / SOS-mediated signalling / positive regulation of GTPase activity / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / neuroblast proliferation / SHC1 events in ERBB4 signaling / regulation of angiogenesis / cardiac muscle cell proliferation / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / regulation of ERK1 and ERK2 cascade / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / negative regulation of fibroblast proliferation / MET activates RAS signaling / skeletal muscle tissue development / negative regulation of stem cell proliferation / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Erythropoietin activates RAS
Similarity search - Function
: / PH domain-like / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins (rasGAP) domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins (rasGAP) domain profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Divergent CRAL/TRIO domain ...: / PH domain-like / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins (rasGAP) domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins (rasGAP) domain profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase activation protein / 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 / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / IMIDAZOLE / GTPase KRas / Neurofibromin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.845 Å
AuthorsTran, T.H. / Dharmaiah, S. / Simanshu, D.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: KRAS G13D sensitivity to neurofibromin-mediated GTP hydrolysis.
Authors: Rabara, D. / Tran, T.H. / Dharmaiah, S. / Stephens, R.M. / McCormick, F. / Simanshu, D.K. / Holderfield, M.
History
DepositionMar 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
B: Neurofibromin
C: GTPase KRas
D: Neurofibromin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,52312
Polymers97,1414
Non-polymers1,3828
Water75742
1
A: GTPase KRas
B: Neurofibromin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4068
Polymers48,5712
Non-polymers8356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-24 kcal/mol
Surface area18030 Å2
MethodPISA
2
C: GTPase KRas
D: Neurofibromin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1174
Polymers48,5712
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-23 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.728, 99.736, 155.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name N or name...
21chain C
12(chain B and (resid 1219 through 1265 or (resid 1266...
22(chain D and (resid 1219 through 1254 or (resid 1255...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETMETMET(chain A and ((resid 1 and (name N or name...AA12
121METMETGOLGOL(chain A and ((resid 1 and (name N or name...AA - E1 - 2012
131METMETGOLGOL(chain A and ((resid 1 and (name N or name...AA - E1 - 2012
141METMETGOLGOL(chain A and ((resid 1 and (name N or name...AA - E1 - 2012
151METMETGOLGOL(chain A and ((resid 1 and (name N or name...AA - E1 - 2012
211METMETLYSLYSchain CCC1 - 1652 - 166
112GLYGLYVALVAL(chain B and (resid 1219 through 1265 or (resid 1266...BB1219 - 126512 - 58
122GLUGLUSERSER(chain B and (resid 1219 through 1265 or (resid 1266...BB1266 - 127059 - 63
132GLYGLYHOHHOH(chain B and (resid 1219 through 1265 or (resid 1266...BB - N1219 - 160112
142GLYGLYHOHHOH(chain B and (resid 1219 through 1265 or (resid 1266...BB - N1219 - 160112
152GLYGLYHOHHOH(chain B and (resid 1219 through 1265 or (resid 1266...BB - N1219 - 160112
162GLYGLYHOHHOH(chain B and (resid 1219 through 1265 or (resid 1266...BB - N1219 - 160112
212GLYGLYTYRTYR(chain D and (resid 1219 through 1254 or (resid 1255...DD1219 - 125412 - 47
222GLNGLNGLNGLN(chain D and (resid 1219 through 1254 or (resid 1255...DD125548
232GLYGLYSERSER(chain D and (resid 1219 through 1254 or (resid 1255...DD1219 - 146312 - 256
242GLYGLYSERSER(chain D and (resid 1219 through 1254 or (resid 1255...DD1219 - 146312 - 256
252GLYGLYSERSER(chain D and (resid 1219 through 1254 or (resid 1255...DD1219 - 146312 - 256
262GLYGLYSERSER(chain D and (resid 1219 through 1254 or (resid 1255...DD1219 - 146312 - 256

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 19328.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01116
#2: Protein Neurofibromin / Neurofibromatosis-related protein NF-1


Mass: 29241.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NF1 / Production host: unidentified baculovirus / References: UniProt: P21359

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Non-polymers , 6 types, 50 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.0 and 19% PAA-co-maleic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.845→45.996 Å / Num. obs: 30699 / % possible obs: 98.1 % / Redundancy: 6.42 % / Biso Wilson estimate: 73.851 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.098 / Χ2: 1.088 / Net I/σ(I): 13.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.845-3.026.1990.824247200.6640.89995.2
3.02-3.226.7090.4553.846240.8840.49299
3.22-3.486.6340.246.9843350.9710.2699.3
3.48-3.816.5470.13412.4139990.990.14599.2
3.81-4.266.4640.08917.8936200.9950.09699.4
4.26-4.916.2760.06423.7832510.9980.06999.1
4.91-66.2190.06224.2727480.9970.06798.5
6-8.416.2160.04829.0921520.9980.05297.3
8.41-45.9966.0760.03438.2412500.9990.03794

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NF1

1nf1


Resolution: 2.845→45.996 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.36
RfactorNum. reflection% reflection
Rfree0.2471 2000 6.52 %
Rwork0.1993 --
obs0.2023 30689 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.65 Å2 / Biso mean: 81.4405 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.845→45.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6287 0 84 42 6413
Biso mean--78.2 65.25 -
Num. residues----820
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A978X-RAY DIFFRACTION7.271TORSIONAL
12C978X-RAY DIFFRACTION7.271TORSIONAL
21B1458X-RAY DIFFRACTION7.271TORSIONAL
22D1458X-RAY DIFFRACTION7.271TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.845-2.91650.35531280.31921849197790
2.9165-2.99530.33381430.29842041218499
2.9953-3.08340.32761430.278120402183100
3.0834-3.18290.3311420.26532046218899
3.1829-3.29670.30471410.25372024216599
3.2967-3.42860.32891430.25752057220099
3.4286-3.58460.28931420.21772031217399
3.5846-3.77350.26321430.20142066220999
3.7735-4.00980.25691440.19132063220799
4.0098-4.31920.23271470.174520872234100
4.3192-4.75340.19581440.15832070221499
4.7534-5.44030.20751450.17212084222999
5.4403-6.85060.25551460.20562091223798
6.8506-46.00220.19841490.17122140228995
Refinement TLS params.Method: refined / Origin x: 17.0607 Å / Origin y: -12.4144 Å / Origin z: -19.4248 Å
111213212223313233
T0.3958 Å20.0704 Å20.0187 Å2-0.5162 Å20.0005 Å2--0.3742 Å2
L1.0453 °20.5156 °20.0458 °2-1.611 °20.0445 °2--1.3326 °2
S0.0077 Å °0.2562 Å °0.0887 Å °-0.057 Å °0.0283 Å °-0.2979 Å °-0.1117 Å °0.3295 Å °-0.0328 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 201
2X-RAY DIFFRACTION1allB1219 - 1601
3X-RAY DIFFRACTION1allC1 - 165
4X-RAY DIFFRACTION1allD1219 - 1463
5X-RAY DIFFRACTION1allS1 - 42
6X-RAY DIFFRACTION1allL1 - 9

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