[English] 日本語
Yorodumi
- PDB-8vm2: Crystal Structure of NRAS Q61K bound to GTP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vm2
TitleCrystal Structure of NRAS Q61K bound to GTP
ComponentsGTPase NRas
KeywordsHYDROLASE/ONCOPROTEIN / NRAS / oncogenic mutation / RAS superfamily small GTPases / HYDROLASE / HYDROLASE-ONCOPROTEIN complex
Function / homology
Function and homology information


myoblast differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / 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 ...myoblast differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / 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 / Signalling to RAS / 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 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / 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 / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of endothelial cell proliferation / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / 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 / MAPK cascade / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / RAF/MAP kinase cascade / Ras protein signal transduction / Golgi membrane / GTPase activity / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol
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
GUANOSINE-5'-TRIPHOSPHATE / GTPase NRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsGebregiworgis, T. / Chan, J.Y.L. / Kuntz, D.A. / Prive, G.G. / Marshall, C.B. / Ikura, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-1542284 Canada
CitationJournal: Eur J Cell Biol / Year: 2024
Title: Crystal structure of NRAS Q61K with a ligand-induced pocket near switch II.
Authors: Gebregiworgis, T. / Chan, J.Y. / Kuntz, D.A. / Prive, G.G. / Marshall, C.B. / Ikura, M.
History
DepositionJan 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTPase NRas
B: GTPase NRas
C: GTPase NRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,04313
Polymers65,3183
Non-polymers2,72510
Water7,404411
1
A: GTPase NRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8615
Polymers21,7731
Non-polymers1,0894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase NRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8434
Polymers21,7731
Non-polymers1,0713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase NRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3384
Polymers21,7731
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.789, 55.699, 149.291
Angle α, β, γ (deg.)90.00, 98.15, 90.00
Int Tables number5
Space group name H-MI121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

-
Components

#1: Protein GTPase NRas / Transforming protein N-Ras


Mass: 21772.666 Da / Num. of mol.: 3 / Fragment: residues 1-172 / Mutation: Q61K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01111, small monomeric GTPase
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: PEG/Ion (containing 0.06 M Citric acid, 0.04 M BIS-TRIS propane)/pH 4.1, 16% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.542 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.74→29.74 Å / Num. obs: 63393 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.032 / Rrim(I) all: 0.065 / Net I/σ(I): 15.8 / Num. measured all: 234839
Reflection shellResolution: 1.74→1.77 Å / % possible obs: 99.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.749 / Num. measured all: 7765 / Num. unique obs: 3430 / CC1/2: 0.578 / Rpim(I) all: 0.616 / Rrim(I) all: 0.975 / Net I/σ(I) obs: 1.2

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→29.74 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2026 2002 3.16 %
Rwork0.1721 --
obs0.173 63374 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 165 411 4684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d2.069
X-RAY DIFFRACTIONf_dihedral_angle_d24.321688
X-RAY DIFFRACTIONf_chiral_restr0.107677
X-RAY DIFFRACTIONf_plane_restr0.014753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.30481390.284300X-RAY DIFFRACTION100
1.78-1.830.27811430.26354345X-RAY DIFFRACTION100
1.83-1.890.26731430.24344363X-RAY DIFFRACTION100
1.89-1.950.27141430.21714390X-RAY DIFFRACTION100
1.95-2.020.21051400.20044335X-RAY DIFFRACTION100
2.02-2.10.21551430.18144392X-RAY DIFFRACTION100
2.1-2.190.20761430.17364351X-RAY DIFFRACTION100
2.19-2.310.2091430.16674375X-RAY DIFFRACTION100
2.31-2.450.19521430.1654400X-RAY DIFFRACTION100
2.45-2.640.2041420.16254364X-RAY DIFFRACTION100
2.64-2.910.1831440.16154395X-RAY DIFFRACTION100
2.91-3.330.17681440.15034405X-RAY DIFFRACTION100
3.33-4.190.16211440.14114443X-RAY DIFFRACTION100
4.19-29.740.20731480.16654514X-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)
15.749-0.70681.8060.764-0.16491.55730.0626-0.1303-0.55910.04140.0915-0.06380.05490.186-0.14020.16140.00550.00260.1634-0.01770.15548.0441-17.6798-16.5166
21.8799-0.53490.34680.8534-0.13650.71250.22241.1942-0.5641-0.6836-0.2261-0.05530.24610.26550.02240.26040.06370.01160.4263-0.09280.12422.0406-18.4593-31.9914
33.40010.47390.70521.42690.50890.6310.03830.0802-0.2649-0.0889-0.0036-0.05230.04710.1023-0.0890.1615-0.01180.00820.165-0.02820.15678.9164-18.3559-20.8864
43.9470.62151.03161.73681.33591.4474-0.1983-0.0793-0.72760.1384-0.05950.440.103-0.1721-0.3150.2448-0.01110.01250.15460.04460.4742-6.4126-25.2251-15.9744
52.8295-0.25810.77041.40140.05781.06650.0281-0.1054-0.07070.0658-0.00430.12990.0389-0.0483-0.03780.1247-0.00330.02340.13330.01370.1092-6.8532-12.004-16.1733
60.70490.1917-0.57030.0654-0.16960.47330.13310.84290.3555-0.6484-0.11230.2291-0.2466-0.0999-0.00430.27350.0162-0.04380.37270.11030.191-7.9515-3.4689-33.038
73.2343-0.0108-0.26482.0843-1.46636.0611-0.02620.00630.5820.1530.10750.1127-0.6231-0.34630.03860.17810.01070.02220.15230.01730.256-8.40060.7841-17.6943
80.972-0.1842-0.60720.57190.09331.8770.05020.55920.5138-0.2032-0.1021-0.133-0.11610.0997-0.24170.16730.00940.04770.30720.11010.09641.7978-5.4302-27.6501
93.7512-0.19590.28952.91190.19383.2788-0.1212-0.13990.48890.26160.0202-0.23-0.26140.3081-0.04210.1382-0.00990.00640.1781-0.01940.1578.4019-8.3969-14.0023
103.45960.5075-0.22410.41350.01680.52870.161-0.4832-0.09160.051-0.13940.08240.0618-0.2645-0.00990.1215-0.02360.00740.25770.01880.1579-40.298-11.0761-11.2507
112.6627-0.8047-0.15691.7469-0.57620.9280.0288-0.48030.38790.23890.06190.0154-0.1713-0.050.00910.1544-0.00440.03770.2576-0.08660.1777-32.90581.7914-3.6776
122.5678-0.15691.52870.2146-0.50982.57830.0224-0.36280.10930.0418-0.0290.0096-0.056-0.1511-0.01830.13890.00630.01410.3104-0.00660.1556-42.0014-6.7735-6.9865
132.7979-0.2488-0.45570.29110.05990.8855-0.0409-0.4171-0.18960.00120.0059-0.01520.0850.0038-0.0070.1416-0.00450.02350.230.04390.1422-28.8523-9.4875-10.0577
144.89742.5168-0.46343.17490.91291.7812-0.1029-0.0691-0.52170.00730.0448-0.2220.37110.09020.02810.16530.01270.01810.16640.01870.218-23.2951-16.79-15.5139
152.4517-0.1801-0.19310.83410.5431.77170.10360.3180.2221-0.2604-0.0908-0.041-0.17240.0705-0.04320.14410.00240.02260.19250.02970.1822-24.1834-2.9796-21.0558
162.2592-0.8757-0.76272.29481.4892.42550.15660.27230.5159-0.2011-0.03460.0057-0.3945-0.1267-0.05910.16210.01680.03030.16880.03580.2489-31.07042.9003-18.0288
173.9580.68680.29741.99880.19813.0619-0.02650.1589-0.0585-0.08350.1049-0.05790.2742-0.0984-0.00880.130.00090.00960.19060.01970.1036-39.7467-9.8964-21.371
182.5971-0.2311-0.32281.55060.08771.47250.06110.19140.0211-0.1079-0.0224-0.1626-0.02010.1455-0.09180.16380.0043-0.00640.09340.00190.1547-35.1613-6.8327-44.2038
192.9674-0.09110.15941.0437-0.42751.09030.01910.00620.33160.1512-0.0549-0.1035-0.07450.0907-0.10790.2069-0.0049-0.01820.12740.02440.2508-34.9407-1.0319-42.058
202.90880.1075-0.2911.5645-0.41461.5470.08090.5089-0.0155-0.2607-0.00980.08160.1348-0.2346-0.0610.2106-0.007-0.05710.1837-0.00210.1853-43.0721-10.7766-48.925
212.3011-0.11570.74081.08470.16691.01550.1634-0.1163-0.43390.06570.05270.02910.4235-0.37220.23820.1989-0.0404-0.03340.1350.01270.2225-45.1323-15.2276-38.6908
221.80890.1725-0.41821.1710.21630.9496-0.0143-0.3804-0.56480.05360.01360.39550.4072-0.16070.02150.274-0.0447-0.0470.11620.03280.337-43.8429-18.7397-35.869
231.3983-1.0099-1.44592.45822.04163.2129-0.02550.0517-0.073-0.09360.0323-0.07680.21640.1176-0.01460.2340.0341-0.02340.1044-0.0180.1917-31.1556-19.4432-46.8296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 61 )
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 116 )
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 126 )
7X-RAY DIFFRACTION7chain 'A' and (resid 127 through 137 )
8X-RAY DIFFRACTION8chain 'A' and (resid 138 through 151 )
9X-RAY DIFFRACTION9chain 'A' and (resid 152 through 170 )
10X-RAY DIFFRACTION10chain 'B' and (resid -4 through 15 )
11X-RAY DIFFRACTION11chain 'B' and (resid 16 through 36 )
12X-RAY DIFFRACTION12chain 'B' and (resid 37 through 46 )
13X-RAY DIFFRACTION13chain 'B' and (resid 47 through 92 )
14X-RAY DIFFRACTION14chain 'B' and (resid 93 through 104 )
15X-RAY DIFFRACTION15chain 'B' and (resid 105 through 137 )
16X-RAY DIFFRACTION16chain 'B' and (resid 138 through 151 )
17X-RAY DIFFRACTION17chain 'B' and (resid 152 through 171 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 25 )
19X-RAY DIFFRACTION19chain 'C' and (resid 26 through 46 )
20X-RAY DIFFRACTION20chain 'C' and (resid 47 through 104 )
21X-RAY DIFFRACTION21chain 'C' and (resid 105 through 126 )
22X-RAY DIFFRACTION22chain 'C' and (resid 127 through 151 )
23X-RAY DIFFRACTION23chain 'C' and (resid 152 through 171 )

+
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