[English] 日本語
Yorodumi
- PDB-2grr: Crystal Structure of human RanGAP1-Ubc9-D127S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2grr
TitleCrystal Structure of human RanGAP1-Ubc9-D127S
Components
  • Ran GTPase-activating protein 1
  • Ubiquitin-conjugating enzyme E2 I
KeywordsLIGASE / ubiquitin / conjugation / small ubiquitin like modifer / smt3
Function / homology
Function and homology information


cellular response to vasopressin / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...cellular response to vasopressin / positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / cytoplasmic periphery of the nuclear pore complex / RING-like zinc finger domain binding / SUMO ligase complex / SUMOylation of nuclear envelope proteins / transferase complex / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / nuclear pore cytoplasmic filaments / small protein activating enzyme binding / synaptonemal complex / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / activation of GTPase activity / negative regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / nuclear export / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / aggresome / Maturation of nucleoprotein / nucleocytoplasmic transport / transcription factor binding / SUMOylation of ubiquitinylation proteins / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / response to axon injury / nuclear pore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / GTPase activator activity / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of endogenous retroelements by KRAB-ZFP proteins / transcription coregulator binding / chromosome segregation / RHO GTPases Activate Formins / SUMOylation of intracellular receptors / protein modification process / PKR-mediated signaling / PML body / mitotic spindle / kinetochore / small GTPase binding / Formation of Incision Complex in GG-NER / Separation of Sister Chromatids / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / nuclear membrane / positive regulation of cell migration / cadherin binding / cell division / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / dendrite / ubiquitin protein ligase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran-GTPase activating protein 1, C-terminal domain / Ran-GTPase activating protein 1, C-terminal / Ran-GTPase activating protein 1, C-terminal domain superfamily / RanGAP1 C-terminal domain / : / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...Ran-GTPase activating protein 1, C-terminal domain / Ran-GTPase activating protein 1, C-terminal / Ran-GTPase activating protein 1, C-terminal domain superfamily / RanGAP1 C-terminal domain / : / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Roll / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ran GTPase-activating protein 1 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsYunus, A.A. / Lima, C.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.
Authors: Yunus, A.A. / Lima, C.D.
History
DepositionApr 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 I
B: Ran GTPase-activating protein 1


Theoretical massNumber of molelcules
Total (without water)36,7442
Polymers36,7442
Non-polymers00
Water7,981443
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.150, 44.675, 61.013
Angle α, β, γ (deg.)72.610, 71.720, 75.350
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / Ubiquitin carrier protein I / SUMO-1-protein ligase / SUMO-1- ...Ubiquitin-protein ligase I / Ubiquitin carrier protein I / SUMO-1-protein ligase / SUMO-1-conjugating enzyme / Ubiquitin carrier protein 9 / p18


Mass: 18285.082 Da / Num. of mol.: 1 / Mutation: D127S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Plasmid: PET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 CODON PLUS RIL / References: UniProt: P63279, ubiquitin-protein ligase
#2: Protein Ran GTPase-activating protein 1


Mass: 18459.348 Da / Num. of mol.: 1 / Fragment: C-terminal domain (RESIDUES 419-587)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANGAP1 / Plasmid: PSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 CODON PLUS RIL / References: UniProt: P46060
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 86191 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.053 / Χ2: 0.542 / Net I/σ(I): 10.9
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.398 / Num. unique all: 8402 / Χ2: 0.254 / % possible all: 92.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→26.48 Å / Rfactor Rfree error: 0.003 / FOM work R set: 0.859 / Data cutoff high absF: 470500.375 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4268 5.1 %RANDOM
Rwork0.201 ---
all-90955 --
obs-84133 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.542 Å2 / ksol: 0.457 e/Å3
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0.84 Å2-1.59 Å2
2--0.36 Å21.27 Å2
3----1.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-6 Å
Luzzati sigma a0.12 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→26.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 0 443 2913
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.682
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.132.5
LS refinement shellResolution: 1.3→1.35 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.284 374 4.9 %
Rwork0.264 7310 -
obs-7684 84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

+
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