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- PDB-2xi1: Crystal structure of the HIV-1 Nef sequenced from a patient's sample -

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Basic information

Entry
Database: PDB / ID: 2xi1
TitleCrystal structure of the HIV-1 Nef sequenced from a patient's sample
Components(NEF) x 2
KeywordsVIRAL PROTEIN / AIDS
Function / homology
Function and homology information


symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host autophagy / host cell Golgi membrane / SH3 domain binding / virion component / GTP binding / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
MethodX-RAY DIFFRACTION / OTHER / Resolution: 3.5 Å
AuthorsYadav, G.P. / Singh, P. / Gupta, S. / Tripathi, A.K. / Tripathi, R.K. / Ramachandran, R.
CitationJournal: Plos One / Year: 2011
Title: A Novel Dimer-Tetramer Transition Captured by the Crystal Structure of the HIV-1 Nef.
Authors: Singh, P. / Yadav, G.P. / Gupta, S. / Tripathi, A.K. / Ramachandran, R. / Tripathi, R.K.
History
DepositionJun 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

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Assembly

Deposited unit
A: NEF
B: NEF


Theoretical massNumber of molelcules
Total (without water)47,2252
Polymers47,2252
Non-polymers00
Water00
1
A: NEF


Theoretical massNumber of molelcules
Total (without water)23,6131
Polymers23,6131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NEF


Theoretical massNumber of molelcules
Total (without water)23,6131
Polymers23,6131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.030, 123.030, 130.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein NEF / HIV-1 NEF


Mass: 23612.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (BH5 ISOLATE)
Description: PATIENT SAMPLE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6KEI3
#2: Protein NEF / HIV-1 NEF


Mass: 23612.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (BH5 ISOLATE)
Description: PATIENT SAMPLE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C6KEI3
Sequence detailsGENBANK ACCESSION NUMBER GQ184340 CORRESPONDS TO THE SEQUENCE OF NEF FROM THE PATIENT.

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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: 3.02 Å3/Da / Density % sol: 59.22 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: VARIMAX-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→29.9 Å / Num. obs: 7262 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 56.37 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.5→29.551 Å / SU ML: 0.45 / σ(F): 1.36 / Phase error: 26.11 / Stereochemistry target values: ML / Details: 1-75 AND 152-178 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.288 331 4.6 %
Rwork0.2239 --
obs0.2268 7239 92.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.873 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 0 0 1681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011747
X-RAY DIFFRACTIONf_angle_d1.3932372
X-RAY DIFFRACTIONf_dihedral_angle_d19.225608
X-RAY DIFFRACTIONf_chiral_restr0.075235
X-RAY DIFFRACTIONf_plane_restr0.008294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5001-4.40750.28941560.2193280X-RAY DIFFRACTION91
4.4075-29.55190.28671750.22733628X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -35.9128 Å / Origin y: 40.169 Å / Origin z: 10.8204 Å
111213212223313233
T0.106 Å2-0.0405 Å2-0.0282 Å2-0.1779 Å20.0557 Å2--0.1009 Å2
L0.9383 °20.3268 °20.0565 °2-1.1059 °20.022 °2--0.749 °2
S0.0649 Å °-0.328 Å °-0.1363 Å °0.3199 Å °-0.179 Å °0.0845 Å °0.086 Å °-0.0703 Å °-0.2082 Å °
Refinement TLS groupSelection details: ALL

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