[English] 日本語
Yorodumi
- PDB-1lxd: CRYSTAL STRUCTURE OF THE RAS INTERACTING DOMAIN OF RALGDS, A GUAN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lxd
TitleCRYSTAL STRUCTURE OF THE RAS INTERACTING DOMAIN OF RALGDS, A GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR OF RAL PROTEIN
ComponentsRALGDSB
KeywordsPHOSPHORYLATION / RALGDS / RAS BINDING / UBIQUITIN FOLD / CDC25 FAMILY / SIGNAL TRANSDUCTION / CROSS-TALK
Function / homology
Function and homology information


p38MAPK events / GTPase regulator activity / RAF/MAP kinase cascade / small GTPase-mediated signal transduction / brush border / guanyl-nucleotide exchange factor activity / Ras protein signal transduction / nucleus / plasma membrane / cytosol
Similarity search - Function
Ral guanine nucleotide dissociation stimulator / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal ...Ral guanine nucleotide dissociation stimulator / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ral guanine nucleotide dissociation stimulator
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsHuang, L. / Weng, X.W. / Hofer, F. / Martin, G.S. / Kim, S.H.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Three-dimensional structure of the Ras-interacting domain of RalGDS.
Authors: Huang, L. / Weng, X. / Hofer, F. / Martin, G.S. / Kim, S.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary Crystallographic Analysis of the Ras Binding Domain of Ralgds, a Guanine Nucleotide Dissociation Stimulator of the Ral Protein
Authors: Huang, L. / Jancarik, J. / Kim, S.-H. / Hofer, F. / Martin, G.S.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Activated Ras Interacts with the Ral Guanine Nucleotide Dissociation Stimulator
Authors: Hofer, F. / Fields, S. / Schneider, C. / Martin, G.S.
History
DepositionMar 5, 1997Processing site: BNL
Revision 1.0Mar 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RALGDSB
B: RALGDSB


Theoretical massNumber of molelcules
Total (without water)22,7022
Polymers22,7022
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-5 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.282, 30.714, 51.326
Angle α, β, γ (deg.)90.00, 94.57, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.219734, -0.826478, -0.518316), (-0.811699, -0.139838, 0.567089), (-0.541167, 0.545325, -0.640124)
Vector: 90.1868, 3.1041, 130.4588)

-
Components

#1: Protein RALGDSB


Mass: 11350.771 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN WHICH BINDS TO ACTIVE RAS
Mutation: N-TERMINAL GS INHERITED FROM THE LINKER SEQUENCE OF THE CLONING VECTOR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RALGDS C-TERMINAL DOMAIN / Plasmid: PGEX98 FROM PGEX2T
Gene (production host): C-TERMINAL DOMAIN OF RALGDS FUSED TO GLUTATHIONINE S TRANSFERASE
Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: Q03386
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTERMINAL RESIDUE LYS 100 IN THE PDB FILE IS LYS 864 IN THE RAT RALGDS SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 30 %
Description: THIS STRUCTURE WAS SOLVED USING THE MAD DATA ON THE SELENOMETHIONINE MUTANT OF THE PROTEIN AT X4A NSLS. BUT THE STRUCTURE WAS REFINED AGAINST THE NATIVE DATA ABOVE.
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 8000, 0.1 M TRIS PH 8.5, AND 0.2 M CALCIUM ACETATE.
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.5 mMdithiothreitol1drop
30.5 mMPMSF1drop
40.5 mMEDTA1drop
50.1 Mcalcium acetate1drop
60.05 mMTris-HCl1drop
710 %PEG80001drop
80.2 Mcalcium acetate1reservoir
90.1 MTris-HCl1reservoir
1020 %PEG80001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.4→10 Å / Num. obs: 6485 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.09 / Net I/σ(I): 16.7
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.92 / Rsym value: 0.251 / % possible all: 99.5
Reflection
*PLUS
Rmerge(I) obs: 0.09

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MADSYSphasing
X-PLOR3.85model building
X-PLOR3.85refinement
X-PLOR3.85phasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→6 Å / Rfactor Rfree error: 0.04 / Data cutoff high absF: 15000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: H19A.PEP IS THE PEPTIDE BOND FIL
RfactorNum. reflection% reflectionSelection details
Rfree0.298 -10 %RANDOM
Rwork0.212 ---
obs0.212 6209 84 %-
Displacement parametersBiso mean: 15 Å2
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 0 58 1453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: NO RESTRAINTS.
LS refinement shellResolution: 2.4→2.48 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.31 -10 %
Rwork0.261 408 -
obs--70.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1P19.PROX19.PRO
X-RAY DIFFRACTION2P11.WATH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.85 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.31

+
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