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- PDB-2xxn: Structure of the vIRF4-HAUSP TRAF domain complex -

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Basic information

Entry
Database: PDB / ID: 2xxn
TitleStructure of the vIRF4-HAUSP TRAF domain complex
Components
  • K10
  • UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7
KeywordsHYDROLASE / KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS VIRAL INTERFERON REGULATORY FACTOR 4
Function / homology
Function and homology information


regulation of telomere capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation ...regulation of telomere capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of circadian rhythm / regulation of protein stability / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / PML body / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / rhythmic process / p53 binding / Regulation of TP53 Degradation / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / transcription cis-regulatory region binding / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / host cell nucleus / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
MATH domain / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : ...MATH domain / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / Winged helix-like DNA-binding domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Viral IRF4-like protein / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HUMAN HERPESVIRUS 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChoi, W.C. / Hwang, J. / Kim, M.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Bilateral Inhibition of Hausp Deubiquitinase by a Viral Interferon Regulatory Factor Protein
Authors: Lee, H.R. / Choi, W.C. / Lee, S. / Hwang, J. / Hwang, E. / Guchhait, K. / Haas, J. / Toth, Z. / Jeon, Y.H. / Oh, T.K. / Kim, M.H. / Jung, J.U.
History
DepositionNov 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Mar 28, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7
B: K10


Theoretical massNumber of molelcules
Total (without water)18,3502
Polymers18,3502
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-4.5 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.462, 72.462, 53.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2057-

HOH

21B-2001-

HOH

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Components

#1: Protein UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7 / DEUBIQUITINATING ENZYME 7 / HERPESVIRUS-ASSOCIATED UBIQUITIN-SPECIFIC PROTEASE / UBIQUITIN ...DEUBIQUITINATING ENZYME 7 / HERPESVIRUS-ASSOCIATED UBIQUITIN-SPECIFIC PROTEASE / UBIQUITIN THIOESTERASE 7 / UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 7 / HAUSP


Mass: 16814.838 Da / Num. of mol.: 1 / Fragment: TRAF DOMAIN, RESIDUES 63-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein/peptide K10 / VIRF-4


Mass: 1534.690 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN HERPESVIRUS 8 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q2HR73
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.7 % / Description: NONE
Crystal growpH: 5.9 / Details: 5% PEG3350, 0.2 M MAGNESIUM FORMATE, PH 5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9999
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 21908 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 21.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 65.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 11.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F1W

2f1w


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.754 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17426 1118 5.1 %RANDOM
Rwork0.15777 ---
obs0.15861 20747 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.858 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 0 238 1533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221369
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9021865
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45623.18869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67615213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.77159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021086
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.2607
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2943
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3763841
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91251332
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3678623
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.33411533
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.331464
X-RAY DIFFRACTIONr_sphericity_free1.823240
X-RAY DIFFRACTIONr_sphericity_bonded1.46631322
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 72 -
Rwork0.143 1539 -
obs--100 %

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