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- PDB-7jhp: Crystal structure of HRas in complex with the Ras-binding and cys... -

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Basic information

Entry
Database: PDB / ID: 7jhp
TitleCrystal structure of HRas in complex with the Ras-binding and cysteine-rich domains of CRaf-kinase
Components
  • GTPase HRasHRAS
  • RAF proto-oncogene serine/threonine-protein kinase
KeywordsSIGNALING PROTEIN / Ras / Raf / RBD / CRD
Function / homology
Function and homology information


death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / GTPase complex / oncogene-induced cell senescence ...death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / GTPase complex / oncogene-induced cell senescence / insulin secretion involved in cellular response to glucose stimulus / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / Negative feedback regulation of MAPK pathway / T-helper 1 type immune response / GP1b-IX-V activation signalling / IFNG signaling activates MAPKs / positive regulation of wound healing / ERBB2-ERBB3 signaling pathway / defense response to protozoan / regulation of cell differentiation / face development / pseudopodium / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / somatic stem cell population maintenance / Activation of RAS in B cells / neurotrophin TRK receptor signaling pathway / thyroid gland development / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of protein-containing complex assembly / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / type II interferon-mediated signaling pathway / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / response to muscle stretch / activation of adenylate cyclase activity / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / intrinsic apoptotic signaling pathway / small monomeric GTPase / G protein activity / insulin-like growth factor receptor signaling pathway / thymus development / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / animal organ morphogenesis / positive regulation of JNK cascade
Similarity search - Function
Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / 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 / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / RAF proto-oncogene serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.766 Å
AuthorsCookis, T. / Mattos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1517295 United States
Citation
Journal: Biomolecules / Year: 2021
Title: Crystal Structure Reveals the Full Ras-Raf Interface and Advances Mechanistic Understanding of Raf Activation.
Authors: Cookis, T. / Mattos, C.
#1: Journal: Biorxiv / Year: 2020
Title: Crystal structure reveals the full Ras:Raf interface and advances mechanistic understanding of Raf activation
Authors: Cookis, T. / Mattos, C.
History
DepositionJul 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
C: RAF proto-oncogene serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8626
Polymers34,1852
Non-polymers6774
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-13 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.487, 44.353, 74.395
Angle α, β, γ (deg.)90.000, 103.945, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

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Components

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Protein , 2 types, 2 molecules AC

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


Mass: 18821.141 Da / Num. of mol.: 1 / Fragment: UNP residues 1-166 / Mutation: R97C
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
#2: Protein RAF proto-oncogene serine/threonine-protein kinase / Proto-oncogene c-RAF / cRaf / Raf-1


Mass: 15364.019 Da / Num. of mol.: 1 / Fragment: UNP residues 55-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Production host: Escherichia coli (E. coli)
References: UniProt: P04049, non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 52 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 17% w/v PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.76→36.61 Å / Num. obs: 7159 / % possible obs: 91.48 % / Redundancy: 7.2 % / Biso Wilson estimate: 43.52 Å2 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.048 / Rrim(I) all: 0.129 / Χ2: 0.955 / Net I/σ(I): 15.63
Reflection shellResolution: 2.766→2.865 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 369 / CC1/2: 0.795 / CC star: 0.941 / Rpim(I) all: 0.308 / Rrim(I) all: 0.819 / % possible all: 49.27

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4G0N & 1FAR

4g0n

1far


Resolution: 2.766→36.61 Å / SU ML: 0.2829 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 26.2282
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2637 716 10 %
Rwork0.211 6443 -
obs0.2162 7159 91.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.88 Å2
Refinement stepCycle: LAST / Resolution: 2.766→36.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2228 0 35 48 2311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222297
X-RAY DIFFRACTIONf_angle_d0.44153118
X-RAY DIFFRACTIONf_chiral_restr0.0401362
X-RAY DIFFRACTIONf_plane_restr0.0029397
X-RAY DIFFRACTIONf_dihedral_angle_d7.51071358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.980.2946990.2398889X-RAY DIFFRACTION64.58
2.98-3.280.29381510.24141363X-RAY DIFFRACTION96.93
3.28-3.750.26781520.20711367X-RAY DIFFRACTION97.31
3.75-4.720.26661540.17581386X-RAY DIFFRACTION98.4
4.72-36.610.23931600.22841438X-RAY DIFFRACTION98.52
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)
12.714928662740.4431093902780.8012264459492.37153339578-0.2737126930472.594139389430.01160432620730.0232205311872-0.3050817639470.003307898309030.1014879370430.2499983713520.392261340505-0.308041280681-0.04803574586540.303080748859-0.104865361310.02201305270730.21323829248-0.03486979350210.23994440906428.07934549074.2863189800525.449089521
22.6217966522-0.825660671709-0.2077438340361.20039045577-0.2891753205591.54977381681-0.04396469266110.7467288055720.6026553529550.248664012584-0.179965837645-0.0393225553688-0.768916337943-0.06948111127990.1375101185890.475127399168-0.0670251776885-0.1210517178720.3898712380110.07530011169680.61149331167114.579129970918.74684146027.68813706521
31.804405578470.840876905373-0.7249009886361.84474735430.2845647286110.959419560063-0.4175996937070.9067693742270.27702134788-0.6727867092860.6845961167720.0562042601817-0.106900343340.230558122820.2335073092380.500364367714-0.487552797109-0.007375536852250.70896216293-0.03962750791130.31191940414445.180674583719.973574067211.1499860481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 166)
2X-RAY DIFFRACTION2(chain 'C' and resid 55 through 133)
3X-RAY DIFFRACTION3(chain 'C' and resid 136 through 187)

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