[English] 日本語
Yorodumi
- PDB-6i2m: Crystal structure of vaccinia virus protein A55 BTB-Back domain i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i2m
TitleCrystal structure of vaccinia virus protein A55 BTB-Back domain in complex with human Cullin-3 N-terminus
Components
  • Cullin-3
  • Kelch repeat and BTB domain-containing protein A55
KeywordsVIRAL PROTEIN / BTB-Kelch / Cul3 / vaccinia virus
Function / homology
Function and homology information


positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / regulation protein catabolic process at postsynapse / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / RHOBTB3 ATPase cycle ...positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / regulation protein catabolic process at postsynapse / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / RHOBTB3 ATPase cycle / positive regulation of mitotic metaphase/anaphase transition / embryonic cleavage / cell projection organization / Notch binding / fibroblast apoptotic process / RHOBTB1 GTPase cycle / negative regulation of type I interferon production / stem cell division / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / stress fiber assembly / ubiquitin ligase complex scaffold activity / negative regulation of Rho protein signal transduction / positive regulation of cytokinesis / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / sperm flagellum / RHOBTB2 GTPase cycle / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / protein autoubiquitination / gastrulation / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / cyclin binding / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / kidney development / Hedgehog 'on' state / G1/S transition of mitotic cell cycle / protein destabilization / Wnt signaling pathway / protein polyubiquitination / Regulation of RAS by GAPs / spindle pole / mitotic spindle / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / cell migration / Neddylation / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / gene expression / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / host cell cytoplasm / postsynapse / protein ubiquitination / inflammatory response / positive regulation of cell population proliferation / ubiquitin protein ligase binding / centrosome / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / Golgi apparatus / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Vaccinia virus A55R / Cullin Repeats / 5 helical Cullin repeat like / Cullin protein neddylation domain / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily ...Vaccinia virus A55R / Cullin Repeats / 5 helical Cullin repeat like / Cullin protein neddylation domain / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Kelch motif / Kelch / Kelch repeat type 1 / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Kelch repeat and BTB domain-containing protein A55 / Cullin-3
Similarity search - Component
Biological speciesVaccinia virus WR
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGao, G. / Graham, S.C.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust098406/Z/12/B United Kingdom
Royal Society098406/Z/12/B United Kingdom
Wellcome Trust090315 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Molecular basis of cullin-3 (Cul3) ubiquitin ligase subversion by vaccinia virus protein A55.
Authors: Gao, C. / Pallett, M.A. / Croll, T.I. / Smith, G.L. / Graham, S.C.
History
DepositionNov 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 1, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kelch repeat and BTB domain-containing protein A55
B: Cullin-3


Theoretical massNumber of molelcules
Total (without water)75,6852
Polymers75,6852
Non-polymers00
Water00
1
A: Kelch repeat and BTB domain-containing protein A55
B: Cullin-3

A: Kelch repeat and BTB domain-containing protein A55
B: Cullin-3


Theoretical massNumber of molelcules
Total (without water)151,3704
Polymers151,3704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6470 Å2
ΔGint-29 kcal/mol
Surface area54300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.820, 42.520, 148.770
Angle α, β, γ (deg.)90.00, 128.41, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Kelch repeat and BTB domain-containing protein A55


Mass: 29960.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal GSKH6 represent the cloning site and purification tag
Source: (gene. exp.) Vaccinia virus WR / Gene: KBTB1, VACWR180, A55R / Plasmid: pOPTnH / Details (production host): C-terminal Lys-His6 tag / Production host: Escherichia coli (E. coli) / References: UniProt: P24768
#2: Protein Cullin-3 / CUL-3


Mass: 45723.953 Da / Num. of mol.: 1 / Mutation: I342R and L346D
Source method: isolated from a genetically manipulated source
Details: ENLYFQSHHHHHHDYKDDDDK sequence represents TEV protease site, His6 purification tag and FLAG epitope tag. I342R and L346D mutations stabilise the N-terminal domain as previously published (PMID 23349464).
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL3, KIAA0617 / Plasmid: CUL3A-c013
Details (production host): pNIC-CTHF backbone vector with Kanamycin selectable marker.
Production host: Escherichia coli (E. coli) / References: UniProt: Q13618

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 3.29% tacsimate pH 6.5, 9.92% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2017 / Details: toroidal mirrors
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→99.23 Å / Num. obs: 44144 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 76.887 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.04 / Rrim(I) all: 0.146 / Net I/σ(I): 8.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 12.6 % / Rmerge(I) obs: 17.224 / Mean I/σ(I) obs: 0.1 / Num. unique obs: 3279 / CC1/2: 0.302 / Rpim(I) all: 4.996 / Rrim(I) all: 17.953 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
DIALSdata reduction
xia2data scaling
STARANISOdata scaling
PHASERphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EOZ, 1R29

4eoz

1r29


Resolution: 2.3→58.29 Å / Cross valid method: FREE R-VALUE
Details: Structure was refined against data processed with an anisotropic/elliptical resolution cutoff. Overall ellipsoidal completeness is 92.9% overall and 86.4% in the highest resolution shell. ...Details: Structure was refined against data processed with an anisotropic/elliptical resolution cutoff. Overall ellipsoidal completeness is 92.9% overall and 86.4% in the highest resolution shell. Structure factors against which the model was refined and final map coefficients are deposited in addition to the un-truncated original observed intensities.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1170 5 %random selection
Rwork0.266 ---
obs0.267 23488 53 %-
Displacement parametersBiso mean: 73.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→58.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 0 0 4402

+
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