[English] 日本語
Yorodumi
- PDB-3uin: Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uin
TitleComplex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2
Components
  • E3 SUMO-protein ligase RanBP2
  • Ran GTPase-activating protein 1
  • SUMO-conjugating enzyme UBC9
  • Small ubiquitin-related modifier 2
KeywordsLigase/Isomerase/Protein Binding / E3 / ligase / SUMO / UBC9 / RanBP2 / nuclear pore complex / Ligase-Isomerase-Protein Binding complex
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 / SUMO ligase activity / annulate lamellae / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors ...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 / SUMO ligase activity / annulate lamellae / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / transferase complex / mitotic nuclear membrane reassembly / Vitamin D (calciferol) metabolism / nuclear pore cytoplasmic filaments / synaptonemal complex / small protein activating enzyme binding / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / SUMOylation of DNA methylation proteins / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Maturation of nucleoprotein / negative regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / nuclear export / Nuclear import of Rev protein / activation of GTPase activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / SUMO transferase activity / aggresome / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / nucleocytoplasmic transport / centrosome localization / Viral Messenger RNA Synthesis / regulation of gluconeogenesis / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / Regulation of HSF1-mediated heat shock response / response to axon injury / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / 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 / response to amphetamine / SUMOylation of chromatin organization proteins / GTPase activator activity / SUMOylation of transcription cofactors / HCMV Late Events / transcription coregulator binding / chromosome segregation / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / SUMOylation of intracellular receptors / protein modification process / PKR-mediated signaling / mitotic spindle / ISG15 antiviral mechanism / PML body / kinetochore / small GTPase binding / Formation of Incision Complex in GG-NER / HCMV Early Events / Separation of Sister Chromatids / protein tag activity / Signaling by ALK fusions and activated point mutants / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / snRNP Assembly / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process
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 / : / Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain ...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 / : / Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Leucine rich repeat, ribonuclease inhibitor type / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Zinc finger domain / Leucine Rich repeat / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / TPR repeat region circular profile. / TPR repeat profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Tetratricopeptide repeats / Tetratricopeptide repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Alpha Horseshoe / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ran GTPase-activating protein 1 / E3 SUMO-protein ligase RanBP2 / Small ubiquitin-related modifier 2 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.597 Å
AuthorsGareau, J.R. / Reverter, D. / Lima, C.D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2.
Authors: Gareau, J.R. / Reverter, D. / Lima, C.D.
History
DepositionNov 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2012Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SUMO-conjugating enzyme UBC9
B: Small ubiquitin-related modifier 2
C: Ran GTPase-activating protein 1
D: E3 SUMO-protein ligase RanBP2


Theoretical massNumber of molelcules
Total (without water)53,7074
Polymers53,7074
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.407, 155.407, 57.931
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein SUMO-conjugating enzyme UBC9 / SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin carrier protein I / Ubiquitin- ...SUMO-protein ligase / Ubiquitin carrier protein 9 / Ubiquitin carrier protein I / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / p18


Mass: 18030.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC9, UBCE9, UBE2I / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Small ubiquitin-related modifier 2 / SUMO-2 / HSMT3 / SMT3 homolog 2 / SUMO-3 / Sentrin-2 / Ubiquitin-like protein SMT3A / Smt3A


Mass: 9177.270 Da / Num. of mol.: 1 / Fragment: UNP residues 14-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMT3A, SMT3H2, SUMO2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61956
#3: Protein Ran GTPase-activating protein 1 / RanGAP1


Mass: 18572.506 Da / Num. of mol.: 1 / Fragment: UNP residues 419-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1835, RANGAP1, SD / Plasmid: pSmt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46060
#4: Protein E3 SUMO-protein ligase RanBP2 / 358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding ...358 kDa nucleoporin / Nuclear pore complex protein Nup358 / Nucleoporin Nup358 / Ran-binding protein 2 / RanBP2 / p270


Mass: 7926.794 Da / Num. of mol.: 1 / Fragment: UNP residues 2629-2695
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP358, RANBP2 / Plasmid: pSmt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49792
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsVAL TO MET CONFLICT IN UNP ENTRY P61956

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.41 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K

-
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: Aug 11, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.597→25 Å / Num. all: 25030 / Num. obs: 24830 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 63.73 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.7
Reflection shellResolution: 2.597→2.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 1.8 / % possible all: 98

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z5S

1z5s


Resolution: 2.597→24.411 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 27.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 1263 5.09 %RANDOM
Rwork0.2113 ---
obs0.2139 24821 99.19 %-
all-25024 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.633 Å2 / ksol: 0.274 e/Å3
Displacement parametersBiso mean: 79.1316 Å2
Baniso -1Baniso -2Baniso -3
1--4.1551 Å2-0 Å20 Å2
2---4.1551 Å20 Å2
3---8.3102 Å2
Refinement stepCycle: LAST / Resolution: 2.597→24.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3609 0 0 42 3651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093690
X-RAY DIFFRACTIONf_angle_d1.1764996
X-RAY DIFFRACTIONf_dihedral_angle_d18.041403
X-RAY DIFFRACTIONf_chiral_restr0.081553
X-RAY DIFFRACTIONf_plane_restr0.006651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.597-2.7010.41510.35912511266297
2.701-2.82380.34781470.32762568271599
2.8238-2.97240.32451400.30252580272099
2.9724-3.15830.3531280.283926122740100
3.1583-3.40160.32871270.259826662793100
3.4016-3.74280.27981400.211826092749100
3.7428-4.28190.22971470.186526182765100
4.2819-5.38510.23181400.17226722812100
5.3851-24.41190.22291430.17292722286599

+
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