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- PDB-5vbe: Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras... -

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Basic information

Entry
Database: PDB / ID: 5vbe
TitleCrystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C GDP
ComponentsGTPase HRas
Keywordshydrolase/hydrolase inhibitor / GTPase / Inhibitor / GDP / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan ...phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / SHC-mediated cascade:FGFR2 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR2 signaling / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / Tie2 Signaling / FRS-mediated FGFR1 signaling / GRB2 events in EGFR signaling / FLT3 Signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / EPHB-mediated forward signaling / Signaling by FGFR1 in disease / myelination / GRB2 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / positive regulation of epithelial cell proliferation / positive regulation of GTPase activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / small monomeric GTPase / VEGFR2 mediated cell proliferation / regulation of actin cytoskeleton organization / animal organ morphogenesis / FCERI mediated MAPK activation / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / positive regulation of MAP kinase activity / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / G protein activity / Regulation of RAS by GAPs / positive regulation of type II interferon production / endocytosis / RAS processing / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / chemotaxis / GDP binding / cellular senescence / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / MAPK cascade / DAP12 signaling / insulin receptor signaling pathway
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / 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 nucleotide triphosphate hydrolases / Rossmann fold ...Small GTPase, Ras-type / small GTPase Ras family profile. / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-92V / GUANOSINE-5'-DIPHOSPHATE / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsGentile, D.R. / Jenkins, M.L. / Moss, S.M. / Burke, J.E. / Shokat, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01CA190409-01 United States
SU2C Lung Cancer Dream Team United States
CitationJournal: Cell Chem Biol / Year: 2017
Title: Ras Binder Induces a Modified Switch-II Pocket in GTP and GDP States.
Authors: Gentile, D.R. / Rathinaswamy, M.K. / Jenkins, M.L. / Moss, S.M. / Siempelkamp, B.D. / Renslo, A.R. / Burke, J.E. / Shokat, K.M.
History
DepositionMar 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0774
Polymers19,2511
Non-polymers8273
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.648, 92.648, 120.532
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 19250.594 Da / Num. of mol.: 1 / Mutation: M72C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01112
#2: 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
#3: Chemical ChemComp-92V / 1-(4-methoxyphenyl)-N-(3-sulfanylpropyl)-5-(trifluoromethyl)-1H-pyrazole-4-carboxamide


Mass: 359.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16F3N3O2S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.64 Å3/Da / Density % sol: 53.43 % / Description: Hexagonal gems
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 22% PEG8000 .1M Tris HCl (pH 7.7) .1 M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 27936 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 17.44 Å2 / Rmerge(I) obs: 0.074 / Χ2: 0.921 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.57-1.69.90.8370.629197.3
1.6-1.6310.40.7080.609199.3
1.63-1.6610.70.6980.6491100
1.66-1.6910.90.6090.6311100
1.69-1.73110.4890.6541100
1.73-1.77110.4420.6721100
1.77-1.81110.3540.6791100
1.81-1.86110.3040.721100
1.86-1.92110.2340.7791100
1.92-1.98110.190.8531100
1.98-2.0511.10.1430.8621100
2.05-2.1311.10.1250.9341100
2.13-2.23110.1080.9721100
2.23-2.3511.10.0981.1191100
2.35-2.49110.0941.3291100
2.49-2.6810.90.0841.4931100
2.68-2.9510.90.071.3761100
2.95-3.3810.60.051.2851100
3.38-4.2610.80.0341.0851100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LYJ

4lyj


Resolution: 1.57→46.324 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.84
RfactorNum. reflection% reflection
Rfree0.201 1499 5.37 %
Rwork0.1768 --
obs0.1782 27930 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 189.41 Å2 / Biso mean: 35.286 Å2 / Biso min: 10.11 Å2
Refinement stepCycle: final / Resolution: 1.57→46.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 80 103 1467
Biso mean--44.69 32.13 -
Num. residues----163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191406
X-RAY DIFFRACTIONf_angle_d1.0971899
X-RAY DIFFRACTIONf_chiral_restr0.058210
X-RAY DIFFRACTIONf_plane_restr0.006245
X-RAY DIFFRACTIONf_dihedral_angle_d15.697848
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5695-1.62020.25361030.24232323242697
1.6202-1.67810.2283990.222224342533100
1.6781-1.74530.21721340.20823762510100
1.7453-1.82470.23161500.202423702520100
1.8247-1.92090.25641550.208523772532100
1.9209-2.04130.2311520.186823882540100
2.0413-2.19890.2371200.181524182538100
2.1989-2.42020.19911530.174323862539100
2.4202-2.77030.22041240.175724322556100
2.7703-3.49020.19051650.170824062571100
3.4902-46.34420.16141440.153325212665100
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)
17.223-4.18123.8575.2323-2.58044.7582-0.1578-0.4579-0.06970.29850.20280.7041-0.1282-0.4760.03420.1351-0.00880.05290.1389-0.03330.226-24.586815.7754-24.5545
26.71740.09831.65555.2426-2.4963.8571-0.1199-0.18540.73350.11270.04630.0558-0.4025-0.17950.10180.18140.02160.00640.1279-0.04840.1662-11.651921.8727-25.2125
38.3340.2902-2.90878.2769-4.32953.20120.1858-0.6085-0.10360.59270.0241-0.5413-0.13930.7739-0.31820.33350.0291-0.05450.2402-0.07470.2752-6.161319.2589-17.0297
45.9016-6.19565.47727.3294-6.28895.3468-0.3954-0.58210.09260.34250.34490.0013-0.2885-0.60940.06490.1805-0.04020.02540.19780.00360.1497-24.117523.0238-25.0435
56.1951-3.60344.02834.8385-3.70317.0001-0.1308-0.5294-0.11430.35460.30850.4323-0.1692-0.2127-0.05980.213-0.00120.03790.1451-0.03540.22-23.291918.9393-22.8377
68.96111.53545.68513.4295-3.14249.02541.1094-1.06940.62632.0888-0.27220.0498-1.15380.3522-0.83380.8824-0.19240.21320.6155-0.03780.7754-21.69938.8711-14.5902
77.392-1.1011-1.28733.66050.29111.0973-0.0893-0.3124-0.16140.30150.06160.26880.0673-0.05430.02850.1149-0.01190.02520.1370.00910.0878-14.10916.1646-27.462
84.65075.47044.19329.36765.43753.86620.14010.0318-0.57280.61560.00510.21550.2456-0.1975-0.11210.1961-0.00770.03670.21710.08880.2992-18.4106-0.1877-24.7251
98.13731.654-1.29896.686-0.83817.55710.1131-0.5785-0.38330.268-0.49920.39030.6643-0.68060.20470.2362-0.07210.09050.2060.04570.3268-26.9731-0.3601-24.5217
107.30880.9559-3.20962.8129-0.60722.7111-0.00780.3752-0.0142-0.06490.0637-0.00260.0250.0371-0.04610.12720.0126-0.01980.10250.01990.115-11.629610.7339-33.209
114.95722.44270.35074.1293-0.52780.9537-0.07390.525-0.1253-0.1960.1110.16450.10850.036-0.04130.1359-0.007-0.00750.1819-0.01560.1184-12.55364.5622-38.7842
124.98411.67850.91014.4434-0.30361.8597-0.18140.26220.2633-0.14190.25710.4911-0.055-0.1651-0.05890.12270.00190.00140.1230.04620.2017-19.918317.6664-34.2502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:12)A1 - 12
2X-RAY DIFFRACTION2(chain A and resid 13:28)A13 - 28
3X-RAY DIFFRACTION3(chain A and resid 29:35)A29 - 35
4X-RAY DIFFRACTION4(chain A and resid 36:49)A36 - 49
5X-RAY DIFFRACTION5(chain A and resid 50:59)A50 - 59
6X-RAY DIFFRACTION6(chain A and resid 60:72)A60 - 72
7X-RAY DIFFRACTION7(chain A and resid 73:94)A73 - 94
8X-RAY DIFFRACTION8(chain A and resid 95:99)A95 - 99
9X-RAY DIFFRACTION9(chain A and resid 100:107)A100 - 107
10X-RAY DIFFRACTION10(chain A and resid 108:123)A108 - 123
11X-RAY DIFFRACTION11(chain A and resid 124:143)A124 - 143
12X-RAY DIFFRACTION12(chain A and resid 144:166)A144 - 166

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