[English] 日本語
Yorodumi
- PDB-3h1d: Structure of the HUWE1 HECT Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h1d
TitleStructure of the HUWE1 HECT Domain
ComponentsE3 ubiquitin-protein ligase HUWE1
KeywordsLIGASE / E3Ligase / ubiquitin / HECT / lobe / Alternative splicing / Chromosomal rearrangement / Cytoplasm / Differentiation / Disease mutation / DNA-binding / Mental retardation / Nucleus / Phosphoprotein / Ubl conjugation pathway
Function / homology
Function and homology information


negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / protein monoubiquitination / Golgi organization / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair ...negative regulation of mitochondrial fusion / histone ubiquitin ligase activity / positive regulation of mitophagy in response to mitochondrial depolarization / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / protein monoubiquitination / Golgi organization / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / membrane fusion / cell differentiation / Golgi membrane / Neutrophil degranulation / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) ...Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Armadillo-type fold / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsPartridge, J.R. / Schwartz, T.U.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: A structural element within the HUWE1 HECT domain modulates self-ubiquitination and substrate ubiquitination activities.
Authors: Pandya, R.K. / Partridge, J.R. / Love, K.R. / Schwartz, T.U. / Ploegh, H.L.
History
DepositionApr 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HUWE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8095
Polymers47,4251
Non-polymers3844
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.654, 55.653, 69.585
Angle α, β, γ (deg.)90.00, 122.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-414-

HOH

-
Components

#1: Protein E3 ubiquitin-protein ligase HUWE1


Mass: 47424.609 Da / Num. of mol.: 1 / Fragment: HECT / Mutation: C4099A, C4184A, C4367A
Source method: isolated from a genetically manipulated source
Details: human rhinovirus 3c (HRV3C) protease site / Source: (gene. exp.) Homo sapiens (human) / Gene: HUWE1, KIAA0312, KIAA1578, UREB1, HSPC272 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta cells (Novagen)
References: UniProt: Q7Z6Z7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M citric acid, 1.8 M (NH4)2SO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.89→30 Å / Num. obs: 30294 / % possible obs: 98.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.072 / Net I/σ(I): 17.2
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.439 / % possible all: 96.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1nd7

1nd7


Resolution: 1.892→29.347 Å / SU ML: 0.68 / σ(F): 1.34 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1527 5.04 %
Rwork0.1656 --
obs0.1687 30294 97.75 %
all-30991 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.008 Å2 / ksol: 0.357 e/Å3
Refine analyzeLuzzati coordinate error obs: 0.68 Å
Refinement stepCycle: LAST / Resolution: 1.892→29.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 20 357 3547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113258
X-RAY DIFFRACTIONf_angle_d1.2024391
X-RAY DIFFRACTIONf_dihedral_angle_d15.81200
X-RAY DIFFRACTIONf_chiral_restr0.085460
X-RAY DIFFRACTIONf_plane_restr0.005567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.892-1.95310.30721220.23322430X-RAY DIFFRACTION92
1.9531-2.02290.27111650.19382629X-RAY DIFFRACTION99
2.0229-2.10380.26931370.17052625X-RAY DIFFRACTION100
2.1038-2.19960.26061490.17232645X-RAY DIFFRACTION99
2.1996-2.31550.23771200.16962663X-RAY DIFFRACTION99
2.3155-2.46050.25511370.16162656X-RAY DIFFRACTION99
2.4605-2.65040.24131490.16582648X-RAY DIFFRACTION99
2.6504-2.91690.24721340.17452644X-RAY DIFFRACTION99
2.9169-3.33840.20821370.16812638X-RAY DIFFRACTION99
3.3384-4.20410.19371510.14152551X-RAY DIFFRACTION95
4.2041-29.35010.19591260.1522639X-RAY DIFFRACTION95
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)
10.40340.176-0.07510.26540.11780.30110.01190.0471-0.0876-0.06970.00790.05230.0312-0.062-0.01370.08220.0372-0.00790.069-0.00870.0632-7.777625.53739.0372
20.7268-0.0723-0.04220.1146-0.10170.5222-0.1307-0.01790.16860.0791-0.0214-0.0260.00930.06110.08790.1380.0122-0.02640.0885-0.00070.0805-0.97438.309918.1191
30.3943-0.08020.20880.1585-0.09220.13070.0045-0.0108-0.0180.02950.0064-0.0328-0.019-0.0374-0.00660.0330.01910.00760.0112-0.00190.02512.497527.658925.8683
41.9189-0.8969-0.00430.2004-0.37190.3302-0.0944-0.321-0.37650.11580.07420.12560.06660.04920.00840.110.00710.00290.11340.04010.171729.165825.847919.0485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3980:4056)
2X-RAY DIFFRACTION2(chain A and resid 4057:4103)
3X-RAY DIFFRACTION3(chain A and resid 4104:4315)
4X-RAY DIFFRACTION4(chain A and resid 4316:4366)

+
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