[English] 日本語
Yorodumi
- PDB-4g0n: Crystal Structure of wt H-Ras-GppNHp bound to the RBD of Raf Kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g0n
TitleCrystal Structure of wt H-Ras-GppNHp bound to the RBD of Raf Kinase
Components
  • GTPase HRas
  • RAF proto-oncogene serine/threonine-protein kinase
KeywordsPROTEIN BINDING/TRANSFERASE / H-Ras / Ras / Raf kinase / Raf / GTPase / allosteric regulation / intrinsic hydrolysis / protein-protein interaction / Ras/Raf/MEK/ERK / kinase / GTP binding / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


phospholipase C activator activity / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling ...phospholipase C activator activity / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / positive regulation of wound healing / ERBB2-ERBB3 signaling pathway / adipose tissue development / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of cell differentiation / pseudopodium / neuromuscular junction development / 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 / positive regulation of peptidyl-serine phosphorylation / positive regulation of protein targeting to membrane / MAP kinase kinase kinase activity / SOS-mediated signalling / type II interferon-mediated signaling pathway / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Schwann cell development / Signalling to RAS / negative regulation of protein-containing complex assembly / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of Ras protein signal transduction / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / myelination / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / insulin-like growth factor receptor signaling pathway / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / animal organ morphogenesis / Tie2 Signaling / EPHB-mediated forward signaling / Signaling by FGFR2 in disease / positive regulation of epithelial cell proliferation / protein-membrane adaptor activity / Signaling by FLT3 fusion proteins / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / adenylate cyclase activator activity / wound healing / regulation of actin cytoskeleton organization / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by SCF-KIT / RAF activation / cellular response to gamma radiation / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / cellular senescence / positive regulation of JNK cascade / insulin receptor signaling pathway / chemotaxis / Stimuli-sensing channels / 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
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) ...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 domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / P-loop containing nucleotide triphosphate hydrolases / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / RAF proto-oncogene serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å
AuthorsFetics, S.K. / Kearney, B.M. / Buhrman, G. / Mattos, C.
CitationJournal: Structure / Year: 2015
Title: Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD.
Authors: Fetics, S.K. / Guterres, H. / Kearney, B.M. / Buhrman, G. / Ma, B. / Nussinov, R. / Mattos, C.
History
DepositionJul 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,6068
Polymers27,7662
Non-polymers8406
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.440, 90.440, 92.703
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-204-

CA

21A-363-

HOH

31B-208-

HOH

-
Components

-
Protein , 2 types, 2 molecules AB

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


Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: UNP residues 1-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: pET21 / 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: 8890.394 Da / Num. of mol.: 1 / Fragment: UNP residues 54-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Plasmid: pET302/NT-His / Production host: Escherichia coli (E. coli)
References: UniProt: P04049, non-specific serine/threonine protein kinase

-
Non-polymers , 6 types, 88 molecules

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


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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: Protein solution: 10 - 16 mg/mL, 50 mM HEPES, pH 7.2, 50 mM NaCl, 10mM MgCl2 5% Glycerol, 1mM DTE, 10 M ZnCl2 Reservoir solution:200mM calcium acetate, 100mM sodium cacodylate pH 6.5, 18% ...Details: Protein solution: 10 - 16 mg/mL, 50 mM HEPES, pH 7.2, 50 mM NaCl, 10mM MgCl2 5% Glycerol, 1mM DTE, 10 M ZnCl2 Reservoir solution:200mM calcium acetate, 100mM sodium cacodylate pH 6.5, 18% PEG 8000. Drop: 1uL protein, 1uL reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→32.4 Å / Num. all: 16218 / Num. obs: 16218 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.15

-
Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.45→32.368 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1628 10.09 %
Rwork0.1809 --
obs0.1858 16133 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.1703 Å20 Å2-0 Å2
2--7.1703 Å2-0 Å2
3----14.3406 Å2
Refinement stepCycle: LAST / Resolution: 2.45→32.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 47 82 2004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081956
X-RAY DIFFRACTIONf_angle_d0.682662
X-RAY DIFFRACTIONf_dihedral_angle_d14.171711
X-RAY DIFFRACTIONf_chiral_restr0.04305
X-RAY DIFFRACTIONf_plane_restr0.003335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4459-2.51780.28841120.2724930X-RAY DIFFRACTION77
2.5178-2.59910.28591250.24441138X-RAY DIFFRACTION92
2.5991-2.69190.3151350.24161194X-RAY DIFFRACTION98
2.6919-2.79960.27711360.22751225X-RAY DIFFRACTION99
2.7996-2.9270.25851370.20741212X-RAY DIFFRACTION99
2.927-3.08120.2781390.19231238X-RAY DIFFRACTION100
3.0812-3.2740.2611370.18751223X-RAY DIFFRACTION100
3.274-3.52660.21331360.1721234X-RAY DIFFRACTION99
3.5266-3.88090.22081390.15631244X-RAY DIFFRACTION100
3.8809-4.44130.17761400.14521255X-RAY DIFFRACTION100
4.4413-5.59080.21381380.15681279X-RAY DIFFRACTION100
5.5908-32.37080.21791540.19291333X-RAY DIFFRACTION100
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)
10.9234-1.0697-0.14292.56960.97712.25890.13220.25470.2298-0.6232-0.19820.0351-0.4634-0.29260.07350.3970.0934-0.00860.3040.0420.321836.79560.1928-16.3778
23.48080.8697-0.25752.04240.50230.93760.10781.2138-0.3911-1.16440.226-1.1516-0.09430.8422-0.13080.74920.26840.20870.75680.05310.475948.9844-5.7599-23.9836
32.9213-0.5191-0.32723.50160.53352.09490.16660.03950.1641-0.108-0.055-0.3898-0.17220.2145-0.06680.236-0.00790.04780.2162-0.00170.282745.7901-8.3891-8.1924
43.2141.02630.33374.64772.03834.7943-0.1221-0.0255-0.07350.10490.3614-0.44370.24940.05-0.1350.77090.2019-0.00450.53020.11370.341936.8981-0.1013-31.7044
56.109-0.73450.54112.54020.36070.1222-0.3261-0.8296-0.95360.60760.14970.17020.57290.0242-0.12880.9538-0.1001-0.05891.12110.030.59827.3695-9.717-37.3794
61.2207-0.2321-0.48951.221-0.80693.6684-0.3260.16820.0599-0.55160.06880.46030.152-1.2648-0.12890.76580.2638-0.08610.85660.15890.413926.5713-0.9302-28.9974
71.4201-0.05140.4481.39221.63224.0042-0.0737-0.07670.5309-0.4609-0.01610.1662-1.2581-0.10850.08060.96640.3934-0.0540.7230.08020.33332.40797.8645-37.6765
83.9756-1.1067-1.56332.71130.74771.6414-0.25620.37130.57990.09680.43460.17350.0001-1.2304-0.13960.90370.2372-0.15250.8030.15390.442330.15044.1186-39.1303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 166 )
4X-RAY DIFFRACTION4chain 'B' and (resid 54 through 71 )
5X-RAY DIFFRACTION5chain 'B' and (resid 72 through 77 )
6X-RAY DIFFRACTION6chain 'B' and (resid 78 through 89 )
7X-RAY DIFFRACTION7chain 'B' and (resid 90 through 108 )
8X-RAY DIFFRACTION8chain 'B' and (resid 109 through 131 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more