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

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Basic information

Entry
Database: PDB / ID: 6xqi
TitleStructure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A
Components
  • ASN-PRO-LEU-GLU-PHE-LEU
  • Protein Vpr
  • UV excision repair protein RAD23 homolog A
KeywordsVIRAL PROTEIN / HIV / viral accessory protein / hHR23A / human
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 / proteasome complex / Josephin domain DUBs / 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 / proteasome complex / Josephin domain DUBs / ubiquitin binding / nucleotide-excision repair / symbiont-mediated activation of host apoptosis / DNA Damage Recognition in GG-NER / protein homooligomerization / protein destabilization / virion component / kinase binding / Formation of Incision Complex in GG-NER / viral penetration into host nucleus / host cell / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / single-stranded DNA binding / monoatomic ion transmembrane transport / proteasome-mediated ubiquitin-dependent protein catabolic process / host extracellular space / damaged DNA binding / symbiont entry into host cell / intracellular membrane-bounded organelle / DNA-templated transcription / regulation of DNA-templated transcription / host cell nucleus / apoptotic process / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.34 Å
AuthorsCalero, G.C. / Wu, Y. / Weiss, S.C.
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 1.0Aug 11, 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 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Vpr
B: Protein Vpr
C: Protein Vpr
D: Protein Vpr
F: UV excision repair protein RAD23 homolog A
G: UV excision repair protein RAD23 homolog A
H: ASN-PRO-LEU-GLU-PHE-LEU
I: ASN-PRO-LEU-GLU-PHE-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,28212
Polymers41,0218
Non-polymers2624
Water84747
1
A: Protein Vpr
B: Protein Vpr
F: UV excision repair protein RAD23 homolog A
I: ASN-PRO-LEU-GLU-PHE-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6416
Polymers20,5104
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-24 kcal/mol
Surface area9670 Å2
MethodPISA
2
C: Protein Vpr
D: Protein Vpr
G: UV excision repair protein RAD23 homolog A
H: ASN-PRO-LEU-GLU-PHE-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6416
Polymers20,5104
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-22 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.165, 130.165, 81.305
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11G-307-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31(chain C and (resid 17 through 78 or resid 79))
41(chain D and (resid 17 through 78 or resid 79))
12(chain F and (resid 166 through 167 or (resid 168...
22(chain G and (resid 166 through 192 or resid 194 through 205))
13chain H
23chain I

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA17 - 78
211chain BB17 - 78
311(chain C and (resid 17 through 78 or resid 79))C0
411(chain D and (resid 17 through 78 or resid 79))D0
112(chain F and (resid 166 through 167 or (resid 168...F166 - 167
122(chain F and (resid 166 through 167 or (resid 168...F168
132(chain F and (resid 166 through 167 or (resid 168...F166 - 205
142(chain F and (resid 166 through 167 or (resid 168...F166 - 205
152(chain F and (resid 166 through 167 or (resid 168...F166 - 205
162(chain F and (resid 166 through 167 or (resid 168...F166 - 205
212(chain G and (resid 166 through 192 or resid 194 through 205))G166 - 192
222(chain G and (resid 166 through 192 or resid 194 through 205))G194 - 205
113chain HH74 - 79
213chain II74 - 79

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Protein Vpr / R ORF protein / Viral protein R


Mass: 7623.708 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
Strain: isolate NY5 / Gene: vpr / Production host: Escherichia coli (E. coli) / References: UniProt: P12520
#2: Protein/peptide UV excision repair protein RAD23 homolog A / hHR23A


Mass: 4531.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD23A / Production host: Escherichia coli (E. coli) / References: UniProt: P54725
#3: Protein/peptide ASN-PRO-LEU-GLU-PHE-LEU


Mass: 731.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.91 Å3/Da / Density % sol: 74.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Tris, pH 7.5, 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2017
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.34→24.783 Å / Num. obs: 41494 / % possible obs: 89.4 % / Redundancy: 4.508 % / Biso Wilson estimate: 73.981 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.125 / Χ2: 1.095 / Net I/σ(I): 6.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible allCC1/2
2.34-2.391.8389.90.1242414.77471.5
2.34-2.342.0553.9760.2625634.99177.6
2.34-2.382.3463.1590.3526663.87682.30.121
2.34-2.352.7612.2480.5627702.65488.50.177
2.35-2.423.4272.0870.7728402.37693.50.253
2.42-2.513.9341.3241.227921.47995.10.462
2.51-2.64.0621.3321.6727101.47994.90.564
2.6-2.715.771.9912.4325962.1695.70.488
2.71-2.835.2331.3213.2725141.44795.40.707
2.83-2.976.1540.6745.1623920.72895.10.85
2.97-3.136.010.4566.6322710.49494.60.91
3.13-3.325.8430.2649.2721120.28693.60.967
3.32-3.555.4960.16412.0220080.1893.80.986
3.55-3.836.1380.10315.418460.11291.90.992
3.83-4.25.8680.08317.5716850.0991.80.992
4.2-4.75.4660.06719.6115240.073910.994
4.7-5.426.1070.06721.0313410.07290.40.995
5.42-6.645.6630.07419.6211110.08187.80.993
6.64-9.396.0080.05423.078510.05985.40.997
9.39-24.7835.5840.04124.144780.04582.10.998

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.15.1_3469refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.34→24.783 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 933 2.99 %
Rwork0.2016 30237 -
obs0.2022 31170 92.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 200.33 Å2 / Biso mean: 76.5794 Å2 / Biso min: 40.17 Å2
Refinement stepCycle: final / Resolution: 2.34→24.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 4 47 2906
Biso mean--62.81 88.83 -
Num. residues----343
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1222X-RAY DIFFRACTION19.763TORSIONAL
12B1222X-RAY DIFFRACTION19.763TORSIONAL
13C1222X-RAY DIFFRACTION19.763TORSIONAL
14D1222X-RAY DIFFRACTION19.763TORSIONAL
21F364X-RAY DIFFRACTION19.763TORSIONAL
22G364X-RAY DIFFRACTION19.763TORSIONAL
31H52X-RAY DIFFRACTION19.763TORSIONAL
32I52X-RAY DIFFRACTION19.763TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3401-2.46340.37511220.3081432493
2.4634-2.61760.2611140.2833439494
2.6176-2.81940.25711410.2435435994
2.8194-3.10270.24931330.205432693
3.1027-3.55050.20891320.1829431592
3.5505-4.4690.17921560.1759425791
4.469-24.7830.22661350.1992426288
Refinement TLS params.Method: refined / Origin x: 64.9542 Å / Origin y: -17.6203 Å / Origin z: 6.7735 Å
111213212223313233
T0.584 Å2-0.0026 Å20.1343 Å2-0.3365 Å20.0047 Å2--0.4407 Å2
L1.0041 °2-0.0668 °20.9871 °2-1.7096 °2-0.1306 °2--2.3974 °2
S-0.011 Å °-0.024 Å °0.0759 Å °-0.0148 Å °0.1776 Å °0.0147 Å °-0.1933 Å °-0.0106 Å °-0.1609 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA17 - 78
2X-RAY DIFFRACTION1allA79
3X-RAY DIFFRACTION1allB17 - 78
4X-RAY DIFFRACTION1allB79
5X-RAY DIFFRACTION1allC16 - 78
6X-RAY DIFFRACTION1allC79
7X-RAY DIFFRACTION1allD15 - 78
8X-RAY DIFFRACTION1allD79
9X-RAY DIFFRACTION1allF166 - 205
10X-RAY DIFFRACTION1allG166 - 205
11X-RAY DIFFRACTION1allH74 - 79
12X-RAY DIFFRACTION1allI74 - 79
13X-RAY DIFFRACTION1allS1 - 47

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