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- PDB-9bg1: Tri-complex of Compound-3, KRAS G12V, and CypA -

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Basic information

Entry
Database: PDB / ID: 9bg1
TitleTri-complex of Compound-3, KRAS G12V, and CypA
Components
  • GTPase KRas
  • Peptidyl-prolyl cis-trans isomerase A
KeywordsSIGNALING PROTEIN/INHIBITOR / inhibitor / complex / small GTPase / cancer / tricomplex / SIGNALING PROTEIN-INHIBITOR complex / SIGNALING PROTEIN
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / negative regulation of viral life cycle / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / negative regulation of viral life cycle / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Basigin interactions / forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Rac protein signal transduction / Early Phase of HIV Life Cycle / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Integration of provirus / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / RAS signaling downstream of NF1 loss-of-function variants / protein peptidyl-prolyl isomerization / RUNX3 regulates p14-ARF / Calcineurin activates NFAT / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / Binding and entry of HIV virion / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / positive regulation of viral genome replication / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / : / positive regulation of glial cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / homeostasis of number of cells within a tissue / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / neutrophil chemotaxis / Signaling by FGFR1 in disease / activation of protein kinase B activity / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / small monomeric GTPase / VEGFR2 mediated cell proliferation / negative regulation of protein phosphorylation / peptidylprolyl isomerase / positive regulation of protein secretion / peptidyl-prolyl cis-trans isomerase activity / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / negative regulation of protein kinase activity
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / 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
: / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsTomlinson, A.C.A. / Saldajeno-Concar, M. / Knox, J.E. / Yano, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Tri-complex of Compound-3, KRAS G12V, and CypA
Authors: Jiang, J. / Jiang, L. / Maldonato, B.J. / Wang, Y. / Holderfield, M. / Aronchik, I. / Winters, I.P. / Salman, Z. / Blaj, C. / Menard, M. / Brodbeck, J. / Chen, Z. / Wei, X. / Rosen, M.J. / ...Authors: Jiang, J. / Jiang, L. / Maldonato, B.J. / Wang, Y. / Holderfield, M. / Aronchik, I. / Winters, I.P. / Salman, Z. / Blaj, C. / Menard, M. / Brodbeck, J. / Chen, Z. / Wei, X. / Rosen, M.J. / Gindin, Y. / Lee, B.J. / Evans, J.W. / Chang, S. / Wang, Z. / Seamon, K.J. / Parsons, D. / Cregg, J. / Marquez, A. / Tomlinson, A.C.A. / Yano, J.K. / Knox, J.E. / Quintana, E. / Aguirre, A.J. / Arbour, K.C. / Reed, A. / Gustafson, W.C. / Gill, A.L. / Koltun, E.S. / Wildes, D. / Smith, J.A.M. / Wang, Z. / Singh, M.
History
DepositionApr 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
D: Peptidyl-prolyl cis-trans isomerase A
B: GTPase KRas
C: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,71410
Polymers75,0494
Non-polymers2,6656
Water17,060947
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A: GTPase KRas
D: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 38.9 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)38,8575
Polymers37,5242
Non-polymers1,3323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase KRas
C: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 38.9 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)38,8575
Polymers37,5242
Non-polymers1,3323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.996, 104.704, 66.256
Angle α, β, γ (deg.)90.000, 90.860, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ABDC

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


Mass: 19400.916 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) / References: UniProt: P01116, small monomeric GTPase
#2: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


Mass: 18123.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase

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Non-polymers , 4 types, 953 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-A1AOH / (2R)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name)


Mass: 785.994 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H55N7O6S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 947 / 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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 28% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19499 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 1.51→55.97 Å / Num. obs: 100049 / % possible obs: 97.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.1 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.055 / Net I/σ(I): 6.7
Reflection shellResolution: 1.51→1.55 Å / Rmerge(I) obs: 0.892 / Num. unique obs: 7353 / CC1/2: 0.591 / Rpim(I) all: 0.575 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→55.97 Å / SU ML: 0.2169 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5225
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2264 5012 5.02 %
Rwork0.1874 94861 -
obs0.1893 99873 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.34 Å2
Refinement stepCycle: LAST / Resolution: 1.51→55.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5223 0 178 947 6348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01235608
X-RAY DIFFRACTIONf_angle_d1.28777592
X-RAY DIFFRACTIONf_chiral_restr0.0747808
X-RAY DIFFRACTIONf_plane_restr0.0121988
X-RAY DIFFRACTIONf_dihedral_angle_d14.32152100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.530.40411620.37823010X-RAY DIFFRACTION94.29
1.53-1.550.26481730.29723164X-RAY DIFFRACTION96.92
1.55-1.560.30551760.26013135X-RAY DIFFRACTION97.7
1.56-1.580.29531970.24713098X-RAY DIFFRACTION97.6
1.58-1.60.29141290.23813240X-RAY DIFFRACTION97.68
1.6-1.630.29931770.24133142X-RAY DIFFRACTION98.22
1.63-1.650.27581780.23373163X-RAY DIFFRACTION97.75
1.65-1.670.30651400.24153163X-RAY DIFFRACTION97.87
1.67-1.70.29551570.22933159X-RAY DIFFRACTION96.93
1.7-1.730.28711320.22763165X-RAY DIFFRACTION96.54
1.73-1.760.25851630.21773012X-RAY DIFFRACTION94.27
1.76-1.790.24122030.1973091X-RAY DIFFRACTION95.92
1.79-1.820.27041600.18973177X-RAY DIFFRACTION98.49
1.82-1.860.2371560.19473179X-RAY DIFFRACTION98.41
1.86-1.90.22711630.20443209X-RAY DIFFRACTION98.57
1.9-1.950.30341680.2373163X-RAY DIFFRACTION97.8
1.95-20.25741620.20823180X-RAY DIFFRACTION97.61
2-2.050.2451700.19243164X-RAY DIFFRACTION98.49
2.05-2.110.25491620.20993181X-RAY DIFFRACTION98.04
2.11-2.180.21991620.18223216X-RAY DIFFRACTION98.37
2.18-2.260.22621890.19283121X-RAY DIFFRACTION97.04
2.26-2.350.23741610.18053099X-RAY DIFFRACTION96.51
2.35-2.450.23291660.18053123X-RAY DIFFRACTION95.36
2.45-2.580.24831840.17953195X-RAY DIFFRACTION99.18
2.58-2.740.21781550.18583231X-RAY DIFFRACTION99.12
2.74-2.960.22321900.1783207X-RAY DIFFRACTION99.07
2.96-3.250.18191740.17083206X-RAY DIFFRACTION98.71
3.25-3.720.2051540.15193249X-RAY DIFFRACTION99.18
3.72-4.690.17371770.14943101X-RAY DIFFRACTION95.46
4.69-55.970.17571720.16463318X-RAY DIFFRACTION99.83
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)
11.37256947479-0.1314958378560.5802521934721.607773363820.5659554707342.031378417340.06275766659890.0266515318472-0.0946676037793-0.03344858326510.0165112558647-0.01825960395830.1205244456650.0671180863537-0.07531189030850.08062155796510.000777906988252-0.01483865008770.09094344838130.009880436240940.099907107280328.624578956114.1946411645-28.283181169
21.4902528053-0.0830986330625-0.7217718242561.43999123199-0.01332530345292.482771285280.0474649151079-0.0375477624430.13735708661-0.06443055351940.0088935659215-0.0137579774807-0.1647461459250.0277910703478-0.05328313598870.07401894392220.0003569376667240.005298022500070.081138586219-0.001136228107060.1013331841286.4139663181537.5724717918-34.0394258602
31.404098361950.92518942991-1.010408049571.65972583504-0.1252741891021.412971136090.170118612583-0.188492616710.126276027190.312134141498-0.04527424412480.181025024366-0.1179347638980.0239159927506-0.1083538075770.151244761957-0.00189628257070.03513504250550.1399712159820.002963521483160.11766566555428.206515304732.0428844583-0.836067319235
41.358617098610.02085499210980.4905852695271.66995130997-0.4441492038192.106699601210.019765689820.103317673569-0.0608758336373-0.03622623685430.01499890075440.0693994993560.0339661969338-0.00266677867524-0.03250102897460.0581557221993-0.00299787883649-0.005179477293550.0824116358627-0.001449863027510.09719284048785.84082516118.267769763394.62656895793
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 0 through 167)AA0 - 1671 - 168
22(chain 'D' and resid 3 through 201)DD - E3 - 2011
33(chain 'B' and resid 0 through 167)BF0 - 1671 - 168
44(chain 'C' and resid 0 through 201)CI - J0 - 2011

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