[English] 日本語
Yorodumi
- PDB-2bf8: Crystal structure of SUMO modified ubiquitin conjugating enzyme E... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bf8
TitleCrystal structure of SUMO modified ubiquitin conjugating enzyme E2- 25K
Components
  • UBIQUITIN-CONJUGATING ENZYME E2-25 KDA
  • UBIQUITIN-LIKE PROTEIN SMT3C
KeywordsLIGASE / LIGASE-COMPLEX / E2-25K / E2 UBIQUITIN CONJUGATING ENZYME / SUMO / SUMO-TARGET STRUCTURE / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / small protein activating enzyme binding / negative regulation of action potential / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / regulation of calcium ion transmembrane transport / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of DNA binding / Maturation of nucleoprotein / E2 ubiquitin-conjugating enzyme / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / cellular response to cadmium ion / ubiquitin-specific protease binding / transcription factor binding / ubiquitin conjugating enzyme activity / roof of mouth development / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / potassium channel regulator activity / Regulation of IFNG signaling / nuclear pore / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / protein K48-linked ubiquitination / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / protein tag activity / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / nuclear membrane / protein stabilization / nuclear speck / nuclear body / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Small ubiquitin-related modifier 1, Ubl domain / UBA/TS-N domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Small ubiquitin-related modifier 1, Ubl domain / UBA/TS-N domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 K / Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPichler, A. / Knipscheer, P. / Oberhofer, E. / Van Dijk, W.J. / Korner, R. / Velgaard Olsen, J. / Jentsch, S. / Melchior, F. / Sixma, T.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Sumo Imodification of the Ubiquitin Conjugating Enzyme E2-25K
Authors: Pichler, A. / Knipscheer, P. / Oberhofer, E. / Van Dijk, W.J. / Korner, R. / Velgaard Olsen, J. / Jentsch, S. / Melchior, F. / Sixma, T.K.
History
DepositionDec 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2-25 KDA
B: UBIQUITIN-LIKE PROTEIN SMT3C


Theoretical massNumber of molelcules
Total (without water)26,8172
Polymers26,8172
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.391, 58.391, 162.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2-25 KDA / E2-25K / UBIQUITIN-PROTEIN LIGASE / UBIQUITIN CARRIER PROTEIN / E2(25K) / HUNTINGTIN INTERACTING ...E2-25K / UBIQUITIN-PROTEIN LIGASE / UBIQUITIN CARRIER PROTEIN / E2(25K) / HUNTINGTIN INTERACTING PROTEIN 2 / HIP-2


Mass: 17846.412 Da / Num. of mol.: 1 / Fragment: CONSERVED CORE DOMAIN, RESIDUES 1-154
Source method: isolated from a genetically manipulated source
Details: COVALENT ISOPEPTIDE LINK BETWEEN E2-25K LYSINE 14 AND SUMO C-TERMINUS
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61085, ubiquitin-protein ligase
#2: Protein UBIQUITIN-LIKE PROTEIN SMT3C / SUMO / UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1 / UBIQUITIN-LIKE PROTEIN UBL1 / UBIQUITIN-RELATED ...SUMO / UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1 / UBIQUITIN-LIKE PROTEIN UBL1 / UBIQUITIN-RELATED PROTEIN SUMO-1 / GAP MODIFYING PROTEIN 1 / GMP1 / SENTRIN


Mass: 8970.248 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-97
Source method: isolated from a genetically manipulated source
Details: COVALENT ISOPEPTIDE LINK BETWEEN E2-25K LYSINE 14 AND SUMO C-TERMINUS
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63165
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCOVALENT ISOPEPTIDE BOND BETWEEN E2-25K LYSINE 14 AND SUMO C-TERMINUS

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 20

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.2 %
Crystal growpH: 8.5
Details: 100 MM TRIS PH 8.5 200 MM MAGNESIUM CHLORIDE 17% PEG 4000 10 % GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC ADSC Q4R / Date: Sep 7, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL, SI(111), SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13257 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 13 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.8 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FZY

1fzy


Resolution: 2.3→55.05 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.029 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 651 4.9 %RANDOM
Rwork0.21 ---
obs0.213 12545 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.66 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å20 Å2
2---2.04 Å20 Å2
3---4.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→55.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 0 83 1936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221905
X-RAY DIFFRACTIONr_bond_other_d0.0020.021729
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9482577
X-RAY DIFFRACTIONr_angle_other_deg0.92734052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2765231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69725.05591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64415347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.631510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022095
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
X-RAY DIFFRACTIONr_nbd_refined0.1980.2403
X-RAY DIFFRACTIONr_nbd_other0.190.21782
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2900
X-RAY DIFFRACTIONr_nbtor_other0.0890.21064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0750.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3190.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8131.51512
X-RAY DIFFRACTIONr_mcbond_other0.1731.5467
X-RAY DIFFRACTIONr_mcangle_it0.97921884
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7553866
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4964.5693
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.411 56 -
Rwork0.293 871 -
obs--98.51 %
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)
13.5484-1.0822-1.95759.48252.94183.35540.0625-0.0756-0.09220.4331-0.1307-0.79760.3162-0.10590.0682-0.1357-0.10810.0391-0.2368-0.0434-0.296140.19517.78369.772
24.7404-4.0568-2.56669.49910.29818.47150.76841.07861.1827-0.7803-0.457-0.425-1.6759-0.7391-0.31140.36630.12060.0810.35770.30020.163817.99152.24774.211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 155
2X-RAY DIFFRACTION2B20 - 97

+
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