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- PDB-6i2m: Crystal structure of vaccinia virus protein A55 BTB-Back domain i... -

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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


: / liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating ...: / liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / Notch binding / RHOBTB1 GTPase cycle / fibroblast apoptotic process / negative regulation of Rho protein signal transduction / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / stress fiber assembly / positive regulation of cytokinesis / protein monoubiquitination / sperm flagellum / protein autoubiquitination / protein K48-linked ubiquitination / RHOBTB2 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / gastrulation / positive regulation of TORC1 signaling / cyclin binding / intrinsic apoptotic signaling pathway / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / Hedgehog 'on' state / protein destabilization / G1/S transition of mitotic cell cycle / mitotic spindle / Wnt signaling pathway / spindle pole / Regulation of RAS by GAPs / protein polyubiquitination / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / cell migration / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / gene expression / ubiquitin-dependent protein catabolic process / postsynapse / symbiont-mediated perturbation of host ubiquitin-like protein modification / proteasome-mediated ubiquitin-dependent protein catabolic process / host cell cytoplasm / Potential therapeutics for SARS / protein ubiquitination / inflammatory response / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / Golgi apparatus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vaccinia virus A55R / Cullin Repeats / 5 helical Cullin repeat like / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin ...Vaccinia virus A55R / Cullin Repeats / 5 helical Cullin repeat like / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Kelch / Kelch repeat type 1 / Kelch motif / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water0
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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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