[English] 日本語
Yorodumi
- PDB-3ong: Crystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ong
TitleCrystal structure of UBA2ufd-Ubc9: insights into E1-E2 interactions in Sumo pathways
Components
  • SUMO-conjugating enzyme UBC9
  • Ubiquitin-activating enzyme E1-like
KeywordsLIGASE
Function / homology
Function and homology information


SUMO activating enzyme complex / SUMO activating enzyme activity / SUMO conjugating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / mitotic spindle elongation / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation ...SUMO activating enzyme complex / SUMO activating enzyme activity / SUMO conjugating enzyme activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMOylation of SUMOylation proteins / mitotic spindle elongation / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / SUMOylation of chromatin organization proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / protein sumoylation / condensed nuclear chromosome / cell division / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme ...Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / SUMO-activating enzyme subunit Uba2 / Ubiquitin activating enzyme, alpha domain superfamily / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
SUMO-conjugating enzyme UBC9 / Ubiquitin-activating enzyme E1-like
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, J. / Taherbhoy, A.M. / Hunt, H.W. / Seyedin, S.N. / Miller, D.W. / Huang, D.T. / Schulman, B.A.
CitationJournal: Plos One / Year: 2010
Title: Crystal structure of UBA2(ufd)-Ubc9: insights into E1-E2 interactions in Sumo pathways.
Authors: Wang, J. / Taherbhoy, A.M. / Hunt, H.W. / Seyedin, S.N. / Miller, D.W. / Miller, D.J. / Huang, D.T. / Schulman, B.A.
History
DepositionAug 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Sep 18, 2013Group: Derived calculations
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.6Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Ubiquitin-activating enzyme E1-like
B: SUMO-conjugating enzyme UBC9
C: Ubiquitin-activating enzyme E1-like
D: SUMO-conjugating enzyme UBC9


Theoretical massNumber of molelcules
Total (without water)64,8094
Polymers64,8094
Non-polymers00
Water68538
1
B: SUMO-conjugating enzyme UBC9
C: Ubiquitin-activating enzyme E1-like


Theoretical massNumber of molelcules
Total (without water)32,4052
Polymers32,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ubiquitin-activating enzyme E1-like
D: SUMO-conjugating enzyme UBC9


Theoretical massNumber of molelcules
Total (without water)32,4052
Polymers32,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.465, 134.038, 62.012
Angle α, β, γ (deg.)90.00, 94.44, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ubiquitin-activating enzyme E1-like / SMT3-activating enzyme subunit 2 / Polymerase-interacting protein 2


Mass: 14324.036 Da / Num. of mol.: 2 / Fragment: UNP residues 439-563
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBA2, PIP2, UAL1, YDR390C, D9509.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P52488
#2: Protein SUMO-conjugating enzyme UBC9 / Ubiquitin-conjugating enzyme E2-18 kDa / Ubiquitin-protein ligase / Ubiquitin carrier protein 9


Mass: 18080.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBC9, YDL064W / Production host: Escherichia coli (E. coli)
References: UniProt: P50623, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG3350, 0.1 M Bis-Tris pH 5.5, 0.2 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 23, 2008
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 22536 / % possible obs: 94.03 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.35 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 21.582 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25099 1143 5.1 %RANDOM
Rwork0.2228 ---
obs0.22423 21393 81.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.864 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.26 Å2
2---0.18 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4267 0 0 38 4305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224369
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.9785935
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2795538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46625200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91715737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.181522
X-RAY DIFFRACTIONr_chiral_restr0.0690.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213354
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2591.52719
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.5124388
X-RAY DIFFRACTIONr_scbond_it0.76831650
X-RAY DIFFRACTIONr_scangle_it1.3514.51547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 55 -
Rwork0.334 903 -
obs--47.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.2878-2.12291.42568.9888-2.48646.94210.2093-0.0340.2799-0.078-0.2624-0.5850.05920.16010.05310.0215-0.0298-0.00650.26670.00140.264729.798380.591547.3162
22.42020.41181.29498.4511.48784.00610.02090.3456-0.0317-0.4366-0.00210.05360.28820.0966-0.01880.15070.00990.09660.24560.04530.124112.423387.102423.458
39.14612.01743.02889.67424.69338.24940.75140.0059-0.63050.9666-0.2173-0.24871.2376-0.3339-0.53411.1219-0.1723-0.19190.27870.04030.29663.86454.474421.0474
42.1273-0.20450.47659.289-0.01452.6480.18210.0785-0.03931.0613-0.128-0.17430.3584-0.293-0.05410.3868-0.079-0.06930.3386-0.0210.174428.853248.10254.6122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

+
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