[English] 日本語
Yorodumi
- PDB-5khq: Rasip1 RA domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5khq
TitleRasip1 RA domain
ComponentsRas-interacting protein 1
KeywordsSIGNALING PROTEIN / Rasip1 / Ras-Association domain / Rap effector
Function / homology
Function and homology information


negative regulation of membrane permeability / negative regulation of Rho-dependent protein serine/threonine kinase activity / positive regulation of integrin activation / Golgi stack / negative regulation of Rho protein signal transduction / branching morphogenesis of an epithelial tube / regulation of GTPase activity / vasculogenesis / negative regulation of autophagy / cell-cell junction ...negative regulation of membrane permeability / negative regulation of Rho-dependent protein serine/threonine kinase activity / positive regulation of integrin activation / Golgi stack / negative regulation of Rho protein signal transduction / branching morphogenesis of an epithelial tube / regulation of GTPase activity / vasculogenesis / negative regulation of autophagy / cell-cell junction / GTPase binding / angiogenesis / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / protein-containing complex
Similarity search - Function
Rasip1/Radil, cargo-binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / SMAD/FHA domain superfamily ...Rasip1/Radil, cargo-binding domain / Ras association (RalGDS/AF-6) domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / SMAD/FHA domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ras-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsGingras, A.R.
Funding support United States, 2items
OrganizationGrant numberCountry
American Heart Association12SDG11610043 United States
American Heart Association16GRNT29650005 United States
CitationJournal: Structure / Year: 2016
Title: Structural Basis of Dimeric Rasip1 RA Domain Recognition of the Ras Subfamily of GTP-Binding Proteins.
Authors: Gingras, A.R. / Puzon-McLaughlin, W. / Bobkov, A.A. / Ginsberg, M.H.
History
DepositionJun 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Oct 4, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras-interacting protein 1
B: Ras-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7833
Polymers32,6912
Non-polymers921
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-5 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.200, 89.200, 177.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Ras-interacting protein 1 / Rain


Mass: 16345.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASIP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5U651
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.5M Ammonium Sulfate and MES pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryojet
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2016 / Details: Mirror: Rh coated
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 10877 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 24.8 % / Biso Wilson estimate: 88.416 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.106 / Net I/σ(I): 26.35
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.8-325.72.8142.1197.6
3-3.21.3554.19199.9
3.2-3.40.6158.271100
3.4-3.80.23817.54199.9
3.8-4.20.10533.261100
4.2-4.80.05847.75199.9
4.8-5.90.05554.75199.9
5.9-8.30.04462.591100
8.3-500.02882.09198.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0151refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KHO

5kho


Resolution: 2.8→47.05 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.932 / SU B: 17.109 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.417 / ESU R Free: 0.291 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 544 5 %RANDOM
Rwork0.2344 ---
obs0.2358 10332 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 182.11 Å2 / Biso mean: 105.201 Å2 / Biso min: 65.08 Å2
Baniso -1Baniso -2Baniso -3
1-3.29 Å21.64 Å20 Å2
2--3.29 Å20 Å2
3----10.66 Å2
Refinement stepCycle: final / Resolution: 2.8→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 6 9 1573
Biso mean--97.09 91.85 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191588
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9692136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4535192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84420.475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.99715257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6911527
X-RAY DIFFRACTIONr_chiral_restr0.0920.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211201
X-RAY DIFFRACTIONr_mcbond_it5.60210.536792
X-RAY DIFFRACTIONr_mcangle_it8.63815.742976
X-RAY DIFFRACTIONr_scbond_it6.72110.853796
LS refinement shellResolution: 2.803→2.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 38 -
Rwork0.413 732 -
all-770 -
obs--99.48 %

+
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://pdbjlvh1.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