[English] 日本語
Yorodumi
- PDB-3tug: Crystal structure of the HECT domain of ITCH E3 ubiquitin ligase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tug
TitleCrystal structure of the HECT domain of ITCH E3 ubiquitin ligase
ComponentsE3 ubiquitin-protein ligase Itchy homolog
KeywordsLIGASE / Structural Genomics / Structural Genomics Consortium / SGC / Catalytic domain / E3 Ligase
Function / homology
Function and homology information


regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / protein K29-linked ubiquitination / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / T cell anergy / positive regulation of T cell anergy / CXCR chemokine receptor binding / regulation of necroptotic process ...regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / protein K29-linked ubiquitination / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / T cell anergy / positive regulation of T cell anergy / CXCR chemokine receptor binding / regulation of necroptotic process / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of JNK cascade / HECT-type E3 ubiquitin transferase / arrestin family protein binding / regulation of hematopoietic stem cell differentiation / negative regulation of type I interferon production / positive regulation of receptor catabolic process / negative regulation of NF-kappaB transcription factor activity / ubiquitin-like protein ligase binding / protein monoubiquitination / ligase activity / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / ribonucleoprotein complex binding / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / regulation of cell growth / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / receptor internalization / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / cell cortex / early endosome membrane / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / inflammatory response / symbiont entry into host cell / intracellular membrane-bounded organelle / innate immune response / apoptotic process / negative regulation of apoptotic process / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with ...Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Itchy homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsDong, A. / Dobrovetsky, E. / Xue, S. / Butler, C. / Wernimont, A. / Walker, J.R. / Tempel, W. / Dhe-Paganon, S. / Arrowsmith, C.H. / Edwards, A.M. ...Dong, A. / Dobrovetsky, E. / Xue, S. / Butler, C. / Wernimont, A. / Walker, J.R. / Tempel, W. / Dhe-Paganon, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the HECT domain of ITCH E3 ubiquitin ligase
Authors: Dobrovetsky, E. / Dong, A. / Xue, S. / Butler, C. / Wernimont, A. / Walker, J.R. / Tempel, W. / Dhe-Paganon, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Tong, Y.
History
DepositionSep 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Itchy homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,52611
Polymers47,4901
Non-polymers3510
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.779, 82.779, 109.943
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein E3 ubiquitin-protein ligase Itchy homolog / Itch / Atrophin-1-interacting protein 4 / AIP4 / NFE2-associated polypeptide 1 / NAPP1


Mass: 47490.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITCH / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R
References: UniProt: Q96J02, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG1500, 0.2M NaCl 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.27→40 Å / Num. all: 20717 / Num. obs: 20717 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 38.7
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 3 / Num. unique all: 2048 / Rsym value: 0.89 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
BUSTER2.8.0refinement
Coot0.6model building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OML

3oml


Resolution: 2.27→38.74 Å / Cor.coef. Fo:Fc: 0.9365 / Cor.coef. Fo:Fc free: 0.9071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 668 3.23 %RANDOM
Rwork0.1962 ---
all0.198 20717 --
obs0.198 20665 --
Displacement parametersBiso mean: 52.05 Å2
Baniso -1Baniso -2Baniso -3
1--4.8086 Å20 Å20 Å2
2---4.8086 Å20 Å2
3---9.6172 Å2
Refine analyzeLuzzati coordinate error obs: 0.317 Å
Refinement stepCycle: LAST / Resolution: 2.27→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 10 78 2760
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012760HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.943746HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d910SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes409HARMONIC5
X-RAY DIFFRACTIONt_it2760HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion16.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion348SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3184SEMIHARMONIC4
LS refinement shellResolution: 2.27→2.39 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2587 109 3.66 %
Rwork0.2089 2867 -
all0.2108 2976 -
Refinement TLS params.Method: refined / Origin x: -3.1384 Å / Origin y: -37.1045 Å / Origin z: -18.8237 Å
111213212223313233
T-0.157 Å2-0.0475 Å20.0051 Å2--0.1233 Å2-0.0004 Å2---0.1882 Å2
L1.5333 °2-0.0886 °2-0.1021 °2-1.7899 °2-0.6521 °2--2.4305 °2
S0.0474 Å °0.0785 Å °0.2314 Å °0.0129 Å °-0.0551 Å °0.0427 Å °-0.0621 Å °0.0227 Å °0.0077 Å °
Refinement TLS groupSelection details: chain A

+
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