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- PDB-6xqj: Structure of HIV-1 Vpr in complex with the human nucleotide excis... -

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Basic information

Entry
Database: PDB / ID: 6xqj
TitleStructure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A
ComponentsProtein Vpr,UV excision repair protein RAD23 homolog A
KeywordsANTIVIRAL PROTEIN / Vpr / hHR23A / NER
Function / homology
Function and homology information


symbiont-mediated arrest of host cell cycle during G2/M transition / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / Josephin domain DUBs / proteasome complex / ubiquitin binding ...symbiont-mediated arrest of host cell cycle during G2/M transition / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / Josephin domain DUBs / proteasome complex / ubiquitin binding / DNA Damage Recognition in GG-NER / nucleotide-excision repair / symbiont-mediated activation of host apoptosis / Formation of Incision Complex in GG-NER / protein destabilization / protein homooligomerization / virion component / kinase binding / viral penetration into host nucleus / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / single-stranded DNA binding / host cell / monoatomic ion transmembrane transport / damaged DNA binding / host extracellular space / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular membrane-bounded organelle / DNA-templated transcription / symbiont entry into host cell / regulation of DNA-templated transcription / host cell nucleus / Golgi apparatus / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Retroviral VpR/VpX protein / VPR/VPX protein / RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / UBA/TS-N domain ...Retroviral VpR/VpX protein / VPR/VPX protein / RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Protein Vpr / UV excision repair protein RAD23 homolog A
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsByeon, I.-J.L. / Calero, G. / Wu, Y. / Byeon, C.H. / Gronenborn, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50AI150481 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A.
Authors: Byeon, I.L. / Calero, G. / Wu, Y. / Byeon, C.H. / Jung, J. / DeLucia, M. / Zhou, X. / Weiss, S. / Ahn, J. / Hao, C. / Skowronski, J. / Gronenborn, A.M.
History
DepositionJul 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Vpr,UV excision repair protein RAD23 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8582
Polymers26,7931
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)55 / 960lowest energy structures
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein Vpr,UV excision repair protein RAD23 homolog A / R ORF protein / Viral protein R / hHR23A


Mass: 26792.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate NY5), (gene. exp.) Homo sapiens (human)
Strain: isolate NY5 / Gene: vpr, RAD23A / Production host: Escherichia coli (E. coli) / References: UniProt: P12520, UniProt: P54725
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic33D TROSY-HN(CA)CB
121isotropic33D TROSY-HN(CO)CACB
134isotropic33D HNCA
144isotropic33D (H)CCH-TOCSY
1135isotropic13D 1H-15N NOESY
154isotropic13D similtaneously 13C/15C-edited NOESY (aliphatic)
267isotropic13D similtaneously 13C/15C-edited NOESY (aliphatic)
174isotropic13D similtaneously 13C/15C-edited NOESY (aromatic)
185isotropic12D 1H-15N HSQC
1175isotropic22D 1H-15N HSQC
191isotropic32D 1H-15N HSQC
1104isotropic12D 1H-15N HSQC
2114isotropic12D 1H-15N HSQC
1124isotropic12D 1H-13C HSQC aliphatic
1144isotropic42D 1H-13C HSQC aromatic
1154isotropic33D HBHA(CO)NH
1166isotropic12D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1927 uM [U-100% 2H; U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O2H,15N,13C-labeled93% H2O/7% D2O
solution41100 uM [U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O15N,13C-labeled93% H2O/7% D2O
solution7745 uM [U-100% 13C; U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O15N,13C-labeled93% H2O/7% D2O
solution51110 uM [U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2O15N-labeled93% H2O/7% D2O
solution61000 uM [U-100% 15N] Vpr-hHR23A complex, 25 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.1 mM ZnSO4, 0.1 mM EDTA, 0.02 % sodium azide, 93% H2O/7% D2Ounlabeled93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
927 uMVpr-hHR23A complex[U-100% 2H; U-100% 13C; U-100% 15N]1
25 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
1 mMTCEPnatural abundance1
0.1 mMZnSO4natural abundance1
0.1 mMEDTAnatural abundance1
0.02 %sodium azidenatural abundance1
1100 uMVpr-hHR23A complex[U-100% 13C; U-100% 15N]4
25 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
2 mMDTTnatural abundance4
1 mMTCEPnatural abundance4
0.1 mMZnSO4natural abundance4
0.1 mMEDTAnatural abundance4
0.02 %sodium azidenatural abundance4
745 uMVpr-hHR23A complex[U-100% 13C; U-100% 15N]7
25 mMsodium phosphatenatural abundance7
50 mMsodium chloridenatural abundance7
2 mMDTTnatural abundance7
1 mMTCEPnatural abundance7
0.1 mMZnSO4natural abundance7
0.1 mMEDTAnatural abundance7
0.02 %sodium azidenatural abundance7
1110 uMVpr-hHR23A complex[U-100% 15N]5
25 mMsodium phosphatenatural abundance5
50 mMsodium chloridenatural abundance5
2 mMDTTnatural abundance5
1 mMTCEPnatural abundance5
0.1 mMZnSO4natural abundance5
0.1 mMEDTAnatural abundance5
0.02 %sodium azidenatural abundance5
1000 uMVpr-hHR23A complex[U-100% 15N]6
25 mMsodium phosphatenatural abundance6
50 mMsodium chloridenatural abundance6
2 mMDTTnatural abundance6
1 mMTCEPnatural abundance6
0.1 mMZnSO4natural abundance6
0.1 mMEDTAnatural abundance6
0.02 %sodium azidenatural abundance6
Sample conditions

Ionic strength: 100 mM / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.1

Conditions-IDLabelpH
1condition_17.2
2condition_27.5

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE7003
Bruker AVANCEBrukerAVANCE6004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospincollection
NMRPipe8.7Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.3.1CCPNchemical shift assignment
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorestructure calculation
TALOS+Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy structures / Conformers calculated total number: 960 / Conformers submitted total number: 55

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