[English] 日本語
Yorodumi
- PDB-6zrn: Crystal structure of the RLIP76 Ral binding domain mutant (E427S/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zrn
TitleCrystal structure of the RLIP76 Ral binding domain mutant (E427S/L429M/Q433L/K440R) in complex with RalB-GMPPNP
Components
  • RalA-binding protein 1
  • Ras-related protein Ral-B
KeywordsPROTEIN BINDING / RalB / RLIP76 / Ral binding domain / coiled-coil / small GTPase / G protein
Function / homology
Function and homology information


doxorubicin transport / regulation of exocyst assembly / regulation of exocyst localization / ABC-type glutathione S-conjugate transporter activity / ABC-type glutathione-S-conjugate transporter / positive regulation of autophagosome assembly / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter / regulation of Cdc42 protein signal transduction / regulation of small GTPase mediated signal transduction ...doxorubicin transport / regulation of exocyst assembly / regulation of exocyst localization / ABC-type glutathione S-conjugate transporter activity / ABC-type glutathione-S-conjugate transporter / positive regulation of autophagosome assembly / xenobiotic detoxification by transmembrane export across the plasma membrane / ABC-type xenobiotic transporter / regulation of Cdc42 protein signal transduction / regulation of small GTPase mediated signal transduction / regulation of GTPase activity / ABC-type xenobiotic transporter activity / positive regulation of epidermal growth factor receptor signaling pathway / small GTPase-mediated signal transduction / positive regulation of mitochondrial fission / cellular response to exogenous dsRNA / CDC42 GTPase cycle / positive regulation of GTPase activity / positive regulation of protein serine/threonine kinase activity / transmembrane transporter activity / xenobiotic transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / positive regulation of protein binding / negative regulation of protein binding / p38MAPK events / RAC1 GTPase cycle / receptor-mediated endocytosis / GTPase activator activity / cellular response to starvation / small monomeric GTPase / receptor internalization / small GTPase binding / transmembrane transport / positive regulation of protein phosphorylation / chemotaxis / spindle pole / GDP binding / G protein activity / ATPase binding / midbody / Ras protein signal transduction / nuclear body / cell division / GTPase activity / apoptotic process / ubiquitin protein ligase binding / GTP binding / signal transduction / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
RalA-binding protein 1 / : / RLIP76, Ral binding domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / Small GTPase, Ras-type / Small GTPase Ras domain profile. ...RalA-binding protein 1 / : / RLIP76, Ral binding domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Ral-B / RalA-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.482 Å
AuthorsHurd, C. / Brear, P. / Revell, J. / Ross, S. / Mott, H. / Owen, D.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Affinity maturation of the RLIP76 Ral binding domain to inform the design of stapled peptides targeting the Ral GTPases.
Authors: Hurd, C.A. / Brear, P. / Revell, J. / Ross, S. / Mott, H.R. / Owen, D.
History
DepositionJul 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: 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-related protein Ral-B
B: Ras-related protein Ral-B
C: RalA-binding protein 1
D: RalA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,98810
Polymers55,7114
Non-polymers1,2776
Water4,396244
1
A: Ras-related protein Ral-B
D: RalA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4945
Polymers27,8562
Non-polymers6393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Ral-B
C: RalA-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4945
Polymers27,8562
Non-polymers6393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.196, 77.517, 65.767
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Ras-related protein Ral-B


Mass: 20998.691 Da / Num. of mol.: 2 / Mutation: Q72L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALB / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P11234
#2: Protein RalA-binding protein 1 / RalBP1 / 76 kDa Ral-interacting protein / Dinitrophenyl S-glutathione ATPase / DNP-SG ATPase / Ral- ...RalBP1 / 76 kDa Ral-interacting protein / Dinitrophenyl S-glutathione ATPase / DNP-SG ATPase / Ral-interacting protein 1


Mass: 6856.937 Da / Num. of mol.: 2 / Mutation: C411S, E427S, L429M, Q433L, K440R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALBP1, RLIP1, RLIP76 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q15311

-
Non-polymers , 4 types, 250 molecules

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


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bicine 9.0 pH, 30% w/v PEG 6000

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.48→65.77 Å / Num. obs: 78582 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.069 / Rrim(I) all: 0.264 / Net I/σ(I): 8 / Num. measured all: 1159648 / Scaling rejects: 4407
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.48-1.5615.46.167176059114420.4461.6046.3761.3100
4.69-65.7713.40.1363433825630.9930.0370.14120.599.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KWI

2kwi


Resolution: 1.482→50.15 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 3868 4.93 %
Rwork0.2086 74603 -
obs0.2101 78471 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.41 Å2 / Biso mean: 30.8218 Å2 / Biso min: 12.63 Å2
Refinement stepCycle: final / Resolution: 1.482→50.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 78 244 3994
Biso mean--21.76 36.56 -
Num. residues----454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.482-1.49990.41211550.3734259498
1.4999-1.51890.32621350.3442691100
1.5189-1.53880.32281230.32372634100
1.5388-1.55990.36581380.30752670100
1.5599-1.58220.3501980.30662686100
1.5822-1.60580.30081350.29132618100
1.6058-1.63090.28811290.28592696100
1.6309-1.65770.29421290.27532624100
1.6577-1.68630.32281850.28392688100
1.6863-1.71690.33051270.2962621100
1.7169-1.74990.32731390.30052675100
1.7499-1.78570.35271430.29532611100
1.7857-1.82450.32781230.29992694100
1.8245-1.86690.281550.26552627100
1.8669-1.91360.2561350.24272669100
1.9136-1.96540.28911230.23792703100
1.9654-2.02320.23351360.21882659100
2.0232-2.08850.25561600.22122622100
2.0885-2.16320.21151480.2082683100
2.1632-2.24980.22431180.18592689100
2.2498-2.35220.22141390.18162660100
2.3522-2.47620.25421430.19982657100
2.4762-2.63130.22851600.19362642100
2.6313-2.83440.26851380.19572674100
2.8344-3.11960.2471500.19372703100
3.1196-3.5710.20231250.17912662100
3.571-4.49860.19261530.15682699100
4.4986-50.150.18331260.18522752100

+
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