[English] 日本語
Yorodumi
- PDB-2a7l: Structure of the human hypothetical ubiquitin-conjugating enzyme,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a7l
TitleStructure of the human hypothetical ubiquitin-conjugating enzyme, LOC55284
ComponentsHypothetical ubiquitin-conjugating enzyme LOC55284
KeywordsLIGASE / STRUCTURAL GENOMICS CONSORTIUM / (SGC) / UBIQUITIN / UBIQUITIN- CONJUGATING ENZYME
Function / homology
Function and homology information


N-terminal E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein quality control for misfolded or incompletely synthesized proteins / protein monoubiquitination / negative regulation of TORC1 signaling / antiviral innate immune response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...N-terminal E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / cellular response to misfolded protein / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein quality control for misfolded or incompletely synthesized proteins / protein monoubiquitination / negative regulation of TORC1 signaling / antiviral innate immune response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA repair / ubiquitin protein ligase binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 W
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Mol Cell Proteomics / Year: 2012
Title: A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.
Authors: Sheng, Y. / Hong, J.H. / Doherty, R. / Srikumar, T. / Shloush, J. / Avvakumov, G.V. / Walker, J.R. / Xue, S. / Neculai, D. / Wan, J.W. / Kim, S.K. / Arrowsmith, C.H. / Raught, B. / Dhe-Paganon, S.
History
DepositionJul 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 28, 2012Group: Database references
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical ubiquitin-conjugating enzyme LOC55284
B: Hypothetical ubiquitin-conjugating enzyme LOC55284
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3654
Polymers30,3192
Non-polymers462
Water3,603200
1
A: Hypothetical ubiquitin-conjugating enzyme LOC55284
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1822
Polymers15,1591
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical ubiquitin-conjugating enzyme LOC55284
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1822
Polymers15,1591
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.595, 60.655, 133.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a monomer.

-
Components

#1: Protein Hypothetical ubiquitin-conjugating enzyme LOC55284


Mass: 15159.265 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLJ11011 / Plasmid: PET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96B02, ubiquitin-protein ligase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.63 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3 M NaCl, 0.1 M bisTris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 5, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 27952 / Num. obs: 27952 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 36.68
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.94 / Num. unique all: 1475 / % possible all: 50.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y6L

1y6l


Resolution: 1.82→24.44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.446 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29982 1403 5 %RANDOM
Rwork0.26179 ---
obs0.26378 26406 95.15 %-
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: 36.259 Å2
Baniso -1Baniso -2Baniso -3
1--2.26 Å20 Å20 Å2
2--4.09 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 1.82→24.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 2 200 2124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221970
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9752676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7125244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17125.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31615342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.118156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021472
X-RAY DIFFRACTIONr_nbd_refined0.220.2850
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21351
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2150
X-RAY DIFFRACTIONr_metal_ion_refined0.1310.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.235
X-RAY DIFFRACTIONr_mcbond_it1.69531234
X-RAY DIFFRACTIONr_mcangle_it2.77442012
X-RAY DIFFRACTIONr_scbond_it3.7055762
X-RAY DIFFRACTIONr_scangle_it5.6457664
LS refinement shellResolution: 1.82→1.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.521 69 -
Rwork0.454 1241 -
obs--61.91 %

+
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