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- PDB-6k6m: Crystal structure of HIV-2 Nef protein -

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Basic information

Entry
Database: PDB / ID: 6k6m
TitleCrystal structure of HIV-2 Nef protein
ComponentsProtein Nef
KeywordsVIRAL PROTEIN / accessory protein
Biological speciesHuman immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.072 Å
AuthorsHirao, K. / Andrews, S. / Kuroki, K. / Kusaka, H. / Tadokoro, T. / Kita, S. / Ose, T. / Rowland-Jones, S. / Maenaka, K.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15H02384 Japan
Japan Society for the Promotion of Science22121007 Japan
Japan Society for the Promotion of ScienceJSPS Strategic Young Researcher Overseas Visits Program for Accelerating Brain Circulation Japan
Japan Agency for Medical Research and Development (AMED)18am0101093j0002 Japan
Japan Agency for Medical Research and Development (AMED)18ae0101047h Japan
Japan Science and TechnologySupport Program for Implementation of New Equipment Sharing System Japan
CitationJournal: Iscience / Year: 2020
Title: Structure of HIV-2 Nef Reveals Features Distinct from HIV-1 Involved in Immune Regulation.
Authors: Hirao, K. / Andrews, S. / Kuroki, K. / Kusaka, H. / Tadokoro, T. / Kita, S. / Ose, T. / Rowland-Jones, S.L. / Maenaka, K.
History
DepositionJun 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 21, 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.name
Revision 1.2Nov 22, 2023Group: 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: Protein Nef


Theoretical massNumber of molelcules
Total (without water)19,7491
Polymers19,7491
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9580 Å2
Unit cell
Length a, b, c (Å)43.577, 44.770, 103.636
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein Nef


Mass: 19749.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→44.77 Å / Num. obs: 12922 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 37.33 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.022 / Rrim(I) all: 0.059 / Net I/σ(I): 24.1 / Num. measured all: 91696
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.07-2.137.20.77969529700.7990.310.842.699.5
9.03-44.775.60.013107719210.0060.01473.199.1

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AVV

1avv


Resolution: 2.072→40.17 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.85
RfactorNum. reflection% reflection
Rfree0.2398 631 4.9 %
Rwork0.2046 --
obs0.2063 12874 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.66 Å2 / Biso mean: 45.4033 Å2 / Biso min: 22.29 Å2
Refinement stepCycle: final / Resolution: 2.072→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1202 0 0 53 1255
Biso mean---45.42 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021243
X-RAY DIFFRACTIONf_angle_d0.5551683
X-RAY DIFFRACTIONf_chiral_restr0.042164
X-RAY DIFFRACTIONf_plane_restr0.005217
X-RAY DIFFRACTIONf_dihedral_angle_d17.556471
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.072-2.2320.28081390.234223772516
2.232-2.45650.30521340.219823902524
2.4565-2.81190.26151130.216624352548
2.8119-3.54240.22761190.206724532572
3.5424-40.17780.21791260.193125882714

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