[English] 日本語
Yorodumi
- PDB-9b4q: Crystal structure of RRAS2 (RAS-Related protein) bound to GMPPNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9b4q
TitleCrystal structure of RRAS2 (RAS-Related protein) bound to GMPPNP
ComponentsRas-related protein R-Ras2
KeywordsONCOPROTEIN / RAS / RRAS2 / TC21
Function / homology
Function and homology information


Schwann cell migration / positive regulation of Schwann cell migration / RND1 GTPase cycle / small monomeric GTPase / osteoblast differentiation / GDP binding / Ras protein signal transduction / Golgi membrane / focal adhesion / GTPase activity ...Schwann cell migration / positive regulation of Schwann cell migration / RND1 GTPase cycle / small monomeric GTPase / osteoblast differentiation / GDP binding / Ras protein signal transduction / Golgi membrane / focal adhesion / GTPase activity / GTP binding / endoplasmic reticulum / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein R-Ras2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsCzyzyk, D.J. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)75N91019D00024 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into isoform-specific RAS-PI3K alpha interactions and the role of RAS in PI3K alpha activation.
Authors: Czyzyk, D. / Yan, W. / Messing, S. / Gillette, W. / Tsuji, T. / Yamaguchi, M. / Furuzono, S. / Turner, D.M. / Esposito, D. / Nissley, D.V. / McCormick, F. / Simanshu, D.K.
History
DepositionMar 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras-related protein R-Ras2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1003
Polymers19,5531
Non-polymers5472
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.299, 62.797, 66.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ras-related protein R-Ras2 / Ras-like protein TC21 / Teratocarcinoma oncogene


Mass: 19553.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRAS2, TC21 / Production host: Escherichia coli (E. coli)
References: UniProt: P62070, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 0.1 M Tris, 5%w/v PGA-LM, 30%w/v PEG MME 550

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.46→45.52 Å / Num. obs: 29226 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.087 / Net I/σ(I): 15.46
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.46-1.541.2345940.9041.2841
1.54-1.650.68844090.9690.7191
1.65-1.780.38840660.9840.4051
1.78-1.950.21437770.9950.2231
1.95-2.180.12734530.9970.1321
2.18-2.520.09930490.9970.1031
2.52-3.080.08226090.9980.0851
3.08-4.350.06320550.9980.0661
4.35-45.520.05112140.9980.0531

-
Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→45.52 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 1456 4.99 %
Rwork0.1819 --
obs0.1836 29153 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→45.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 33 175 1564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121483
X-RAY DIFFRACTIONf_angle_d1.3162017
X-RAY DIFFRACTIONf_dihedral_angle_d13.717574
X-RAY DIFFRACTIONf_chiral_restr0.143220
X-RAY DIFFRACTIONf_plane_restr0.012260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.510.60041410.52142667X-RAY DIFFRACTION98
1.51-1.570.38221360.34482748X-RAY DIFFRACTION100
1.57-1.640.28361480.24872698X-RAY DIFFRACTION99
1.64-1.730.27151420.21042725X-RAY DIFFRACTION99
1.73-1.840.25621490.21092755X-RAY DIFFRACTION100
1.84-1.980.26681410.18332760X-RAY DIFFRACTION100
1.98-2.180.22021480.16022760X-RAY DIFFRACTION100
2.18-2.490.18231530.16582796X-RAY DIFFRACTION100
2.49-3.140.19981440.18042833X-RAY DIFFRACTION100
3.14-45.520.18531540.15772955X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -9.0766 Å / Origin y: 15.232 Å / Origin z: -17.2461 Å
111213212223313233
T0.1662 Å2-0.0048 Å20.0083 Å2-0.1673 Å2-0.0078 Å2--0.1191 Å2
L2.5564 °2-0.2913 °2-0.0359 °2-3.1901 °2-0.2902 °2--0.9612 °2
S0.0298 Å °-0.0511 Å °-0.0434 Å °0.1991 Å °0.0308 Å °0.1585 Å °0.0351 Å °-0.0789 Å °0.0035 Å °
Refinement TLS groupSelection details: all

+
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