[English] 日本語
Yorodumi
- PDB-2qgx: Ubiquitin-conjugating enzyme E2Q -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qgx
TitleUbiquitin-conjugating enzyme E2Q
ComponentsUbiquitin-conjugating enzyme E2 Q1
KeywordsLIGASE / ubiquitin conjugating protein / UBC / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


prolactin secretion / suckling behavior / reproductive system development / fertilization / mating behavior / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / embryo implantation / filopodium / protein polyubiquitination ...prolactin secretion / suckling behavior / reproductive system development / fertilization / mating behavior / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / embryo implantation / filopodium / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / ATP binding / nucleus / cytosol
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 Q1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsNeculai, D. / Avvakumov, G.V. / Xue, S. / Walker, J.R. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Neculai, D. / Avvakumov, G.V. / Xue, S. / Walker, J.R. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Sicheri, F. / 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
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Aug 30, 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: Ubiquitin-conjugating enzyme E2 Q1
B: Ubiquitin-conjugating enzyme E2 Q1
C: Ubiquitin-conjugating enzyme E2 Q1
D: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)75,4744
Polymers75,4744
Non-polymers00
Water1,62190
1
A: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)18,8681
Polymers18,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)18,8681
Polymers18,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)18,8681
Polymers18,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)18,8681
Polymers18,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Ubiquitin-conjugating enzyme E2 Q1
B: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)37,7372
Polymers37,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
MethodPISA
6
C: Ubiquitin-conjugating enzyme E2 Q1
D: Ubiquitin-conjugating enzyme E2 Q1


Theoretical massNumber of molelcules
Total (without water)37,7372
Polymers37,7372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.390, 60.390, 172.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Detailsbiological unit is 1/4 asymmetric unit.

-
Components

#1: Protein
Ubiquitin-conjugating enzyme E2 Q1 / Ubiquitin-protein ligase Q1 / Ubiquitin carrier protein Q1 / Protein NICE-5


Mass: 18868.420 Da / Num. of mol.: 4 / Fragment: UBC domain; residues 248-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2Q1, NICE5, UBE2Q / Plasmid: pET28a-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7Z7E8, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 22% PEG4000, 0.1 M Tris-Cl, pH7.5, 0.12 M MgCl2, 1 mM DTT, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 15.81 / Number: 122268 / Rmerge(I) obs: 0.039 / D res high: 2.55 Å / Num. obs: 44274 / % possible obs: 96.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obs
5.438.72299.210.028
4.415.499.510.024
3.834.4197.710.03
3.423.8396.610.042
3.133.4299.310.068
2.893.1399.410.117
2.712.8999.610.202
2.552.7189.310.315
ReflectionResolution: 2.55→38.722 Å / Num. obs: 22493 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 63.455 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 15.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.55-2.710.3153.114601657589.3
2.71-2.890.2025.120165695999.6
2.89-3.130.1178.618691642799.4
3.13-3.420.06813.416980586999.3
3.42-3.830.04221.214742524196.6
3.83-4.410.032713051463297.7
4.41-5.40.02431.611535400499.5
5.40.028328878312699.2

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.87 Å57.61 Å
Translation2.87 Å57.61 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZUO

1zuo


Resolution: 2.56→38.722 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.807 / Stereochemistry target values: twin_lsq_f
RfactorNum. reflection% reflection
Rfree0.208 1126 5.01 %
Rwork0.168 21367 -
obs-22493 99.06 %
Solvent computationBsol: 88.392 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso max: 593.55 Å2 / Biso mean: 84.773 Å2 / Biso min: 23.96 Å2
Baniso -1Baniso -2Baniso -3
1-8.559 Å2-0 Å2-0 Å2
2--8.559 Å2-0 Å2
3----17.118 Å2
Refinement stepCycle: LAST / Resolution: 2.56→38.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5020 0 0 90 5110
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.3381
X-RAY DIFFRACTIONf_bond_d0.0021
X-RAY DIFFRACTIONf_chiral_restr0.0291
X-RAY DIFFRACTIONf_dihedral_angle_d8.6851
X-RAY DIFFRACTIONf_plane_restr0.0011
X-RAY DIFFRACTIONf_nbd_refined4.0751
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)
11.23891.50533.12793.48364.66627.86140.073-0.2427-0.02230.3930.1986-0.23540.5727-0.0235-0.27020.1347-0.0411-0.16080.437-0.03190.2848-37.164213.54318.3474
21.17690.07040.51311.35773.90868.23870.23510.0185-0.1910.25270.1923-0.10240.81990.0206-0.32690.44090.03660.00020.1447-0.01240.2622-43.9213-0.2212-23.6404
31.55141.1124-2.3163.8474-4.79518.03140.13340.56060.1291-0.28650.07480.25010.284-0.5318-0.33160.08070.07990.00290.43950.15470.1858-60.061527.2631-8.0752
41.15010.6697-2.63341.2128-1.4776.88780.22240.04880.13710.0290.28830.07380.268-0.323-0.35130.2484-0.1421-0.01380.20240.02330.2197-68.831414.26824.1603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 159
2X-RAY DIFFRACTION2chain BB1 - 161
3X-RAY DIFFRACTION3chain CC2 - 162
4X-RAY DIFFRACTION4chain DD1 - 160

+
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