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- PDB-7l0f: Monobody 12VC3 Bound to HRAS(WT) -

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Basic information

Entry
Database: PDB / ID: 7l0f
TitleMonobody 12VC3 Bound to HRAS(WT)
Components
  • GTPase HRas
  • Monobody 12VC3
KeywordsSIGNALING PROTEIN / RAS GTPase
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 / 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 / SHC-mediated cascade:FGFR2 / 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 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / myelination / GRB2 events in ERBB2 signaling / 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 / intrinsic apoptotic signaling pathway / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / positive regulation of GTPase activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of epithelial cell proliferation / 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 / positive regulation of type II interferon production / Regulation of RAS by GAPs / 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 / cellular senescence / positive regulation of fibroblast proliferation / GDP binding / MAPK cascade / Signaling by BRAF and RAF1 fusions / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsTeng, K.W. / Hattori, T. / Tsai, S. / Koide, S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA194864 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA212608 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F32 CA225131 United States
American Cancer SocietyPF-18-180-01-TBE United States
CitationJournal: Nat Commun / Year: 2021
Title: Selective and noncovalent targeting of RAS mutants for inhibition and degradation.
Authors: Teng, K.W. / Tsai, S.T. / Hattori, T. / Fedele, C. / Koide, A. / Yang, C. / Hou, X. / Zhang, Y. / Neel, B.G. / O'Bryan, J.P. / Koide, S.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: GTPase HRas
F: Monobody 12VC3
A: GTPase HRas
B: Monobody 12VC3
G: GTPase HRas
H: Monobody 12VC3
L: GTPase HRas
M: Monobody 12VC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,07016
Polymers116,8158
Non-polymers2,2548
Water11,548641
1
E: GTPase HRas
F: Monobody 12VC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7674
Polymers29,2042
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-28 kcal/mol
Surface area11660 Å2
MethodPISA
2
A: GTPase HRas
B: Monobody 12VC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7674
Polymers29,2042
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-28 kcal/mol
Surface area11770 Å2
MethodPISA
3
G: GTPase HRas
H: Monobody 12VC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7674
Polymers29,2042
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-27 kcal/mol
Surface area11900 Å2
MethodPISA
4
L: GTPase HRas
M: Monobody 12VC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7674
Polymers29,2042
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-27 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.012, 64.816, 127.124
Angle α, β, γ (deg.)90.000, 102.370, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21A
12E
22G
13E
23L
14F
24B
15F
25H
16F
26M
17A
27G
18A
28L
19B
29H
110B
210M
111G
211L
112H
212M

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010E1 - 166
2010A1 - 166
1020E1 - 166
2020G1 - 166
1030E1 - 166
2030L1 - 166
1040F3 - 94
2040B3 - 94
1050F3 - 94
2050H3 - 94
1060F3 - 95
2060M3 - 95
1070A1 - 166
2070G1 - 166
1080A1 - 166
2080L1 - 166
1090B2 - 95
2090H2 - 95
10100B3 - 94
20100M3 - 94
10110G1 - 166
20110L1 - 166
10120H3 - 94
20120M3 - 94

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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


Mass: 18962.268 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112, small monomeric GTPase
#2: Antibody
Monobody 12VC3


Mass: 10241.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.225 M Potassium sodium tartrate tetrahydrate, 15% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 77326 / % possible obs: 96 % / Redundancy: 5 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.056 / Rrim(I) all: 0.128 / Χ2: 0.954 / Net I/σ(I): 7.9 / Num. measured all: 388685
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.014.90.76738390.770.370.8540.58295.3
2.01-2.0550.61938290.8380.2970.6890.63796.9
2.05-2.0950.55239120.8770.2640.6140.67396.4
2.09-2.135.10.49438550.8940.2360.5480.7696.8
2.13-2.185.10.44238690.9070.2110.4910.8597.4
2.18-2.2350.37638970.9290.180.4180.90796.1
2.23-2.294.90.32336680.9370.1560.3590.96492.3
2.29-2.355.10.27337430.9570.1310.3040.98692.9
2.35-2.425.20.23639230.9650.1120.2621.09497.8
2.42-2.495.20.21239560.9680.1010.2351.09697.8
2.49-2.5850.17338680.9770.0840.1931.07397.6
2.58-2.6950.1539070.9780.0730.1681.13796.8
2.69-2.8150.13636350.9820.0660.1521.08290.8
2.81-2.965.10.11439550.9880.0550.1271.01997.8
2.96-3.145.20.10739230.9870.0520.1190.96298.1
3.14-3.395.10.09139470.9910.0440.1011.07597.5
3.39-3.734.80.08337670.9920.0410.0931.05893.2
3.73-4.265.10.07339800.9940.0350.0811.02198.2
4.26-5.374.90.06738880.9930.0330.0751.06294.9
5.37-504.90.0739650.9950.0340.0781.03394.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
REFMACv5.8.0238refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4g0n

4g0n


Resolution: 1.98→44.88 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.181 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1912 3851 5 %RANDOM
Rwork0.1594 ---
obs0.161 73461 95.53 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 130.2 Å2 / Biso mean: 35.681 Å2 / Biso min: 13.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å2-0.11 Å2
2--0.61 Å20 Å2
3----1.32 Å2
Refinement stepCycle: final / Resolution: 1.98→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8102 0 132 641 8875
Biso mean--23.98 39.13 -
Num. residues----1037
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11E52990.07
12A52990.07
21E51790.09
22G51790.09
31E51900.09
32L51900.09
41F26480.08
42B26480.08
51F26360.07
52H26360.07
61F26670.08
62M26670.08
71A52300.08
72G52300.08
81A52500.08
82L52500.08
91B26640.09
92H26640.09
101B26790.04
102M26790.04
111G52960.08
112L52960.08
121H26430.07
122M26430.07
LS refinement shellResolution: 1.982→2.033 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 273 -
Rwork0.213 5104 -
all-5377 -
obs--89.92 %
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)
11.5709-0.10590.07441.4530.13841.44770.0261-0.09140.0851-0.0083-0.02120.0621-0.0814-0.0603-0.00490.0154-0.0103-0.01940.1156-0.0020.0576-3.328-5.75747.149
22.39050.6260.28672.446-0.23081.072-0.03510.0674-0.2165-0.18430.0518-0.19160.15690.0783-0.01670.0446-0.0007-0.0040.0916-0.0280.061811.578-25.33644.732
31.39180.20990.28141.4285-0.08541.63320.00880.10230.05680.01610.0052-0.1172-0.04440.0543-0.0140.02080.0049-0.03520.15710.00410.0796-19.627-2.08614.807
43.1893-0.6720.32573.33650.50211.57080.02830.0944-0.40920.138-0.00370.17810.2731-0.1335-0.02460.1101-0.0388-0.03840.1338-0.00030.1053-34.593-21.61212.939
52.00980.3386-0.21782.96470.68172.14350.04840.2253-0.08350.0803-0.28650.58490.2511-0.33160.2380.0493-0.04470.04410.3301-0.09420.28158.589-4.2912.047
62.1667-0.5081-0.11874.0381-0.30651.7735-0.033-0.08250.16780.3096-0.0360.0244-0.1557-0.03270.0690.04270.00460.01250.1887-0.00540.078423.47915.01816.176
71.6804-0.3564-0.13171.40210.09491.38430.0320.0345-0.0666-0.00370.0016-0.11820.08410.116-0.03360.0076-0.00260.00340.1159-0.01770.1008-31.526-8.41249.531
84.0860.9007-0.36812.91420.43331.39910.0638-0.15080.5347-0.1237-0.08040.1729-0.1626-0.05680.01660.0293-0.00440.020.0735-0.00990.159-46.58311.1549.914
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E1 - 166
2X-RAY DIFFRACTION2F3 - 95
3X-RAY DIFFRACTION3A1 - 166
4X-RAY DIFFRACTION4B2 - 95
5X-RAY DIFFRACTION5G1 - 166
6X-RAY DIFFRACTION6H2 - 95
7X-RAY DIFFRACTION7L1 - 166
8X-RAY DIFFRACTION8M3 - 95

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