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- PDB-6b72: A novel HIV-1 Nef dimer interface induced by a single octyl-gluco... -

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Basic information

Entry
Database: PDB / ID: 6b72
TitleA novel HIV-1 Nef dimer interface induced by a single octyl-glucoside molecule
ComponentsProtein Nef
KeywordsVIRAL PROTEIN / HIV-1 Nef / Dimer
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 / suppression by virus of host autophagy / activation of transmembrane receptor protein tyrosine kinase activity / host cell Golgi membrane / virion component / endocytosis involved in viral entry into host cell / SH3 domain binding / virus-mediated perturbation of host defense response / GTP binding ...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 / suppression by virus of host autophagy / activation of transmembrane receptor protein tyrosine kinase activity / host cell Golgi membrane / virion component / endocytosis involved in viral entry into host cell / SH3 domain binding / virus-mediated perturbation of host defense response / 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 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsWu, M. / Augelli-Szafran, C.E. / Ptak, R.G. / Smithgall, T.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400010I United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI102724 United States
CitationJournal: PLoS ONE / Year: 2018
Title: A single beta-octyl glucoside molecule induces HIV-1 Nef dimer formation in the absence of partner protein binding.
Authors: Wu, M. / Alvarado, J.J. / Augelli-Szafran, C.E. / Ptak, R.G. / Smithgall, T.E.
History
DepositionOct 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Nef
B: Protein Nef
C: Protein Nef
D: Protein Nef
E: Protein Nef
F: Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4619
Polymers106,5846
Non-polymers8773
Water00
1
A: Protein Nef
B: Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8203
Polymers35,5282
Non-polymers2921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-4 kcal/mol
Surface area13810 Å2
MethodPISA
2
C: Protein Nef
E: Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8203
Polymers35,5282
Non-polymers2921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-4 kcal/mol
Surface area13350 Å2
MethodPISA
3
D: Protein Nef
F: Protein Nef
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8203
Polymers35,5282
Non-polymers2921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-5 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.577, 109.577, 247.040
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Protein Nef / 3'ORF / Negative factor / F-protein


Mass: 17764.062 Da / Num. of mol.: 6 / Fragment: UNP residues 57-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B
Gene: nef / Production host: Escherichia coli (E. coli) / References: UniProt: P03407
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 18%-20% PEG5000 MME, 0.1 M Bis-Tris propane, pH 8.0, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→94.9 Å / Num. obs: 29203 / % possible obs: 100 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.024 / Rrim(I) all: 0.079 / Rsym value: 0.075 / Net I/av σ(I): 5.2 / Net I/σ(I): 20.5
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.828 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4209 / Rpim(I) all: 0.264 / Rrim(I) all: 0.869 / Rsym value: 0.828 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→94.9 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.94 / SU B: 40.713 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.158 / ESU R Free: 0.389 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 1494 5.1 %RANDOM
Rwork0.2331 ---
obs0.234 27655 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 217.34 Å2 / Biso mean: 120.113 Å2 / Biso min: 88.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.3 Å20 Å2
2---0.59 Å20 Å2
3---1.92 Å2
Refinement stepCycle: final / Resolution: 3.2→94.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6183 0 60 0 6243
Biso mean--119.96 --
Num. residues----729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196477
X-RAY DIFFRACTIONr_bond_other_d0.0010.025808
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9418794
X-RAY DIFFRACTIONr_angle_other_deg0.894313476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.35122.973333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.555151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2711542
X-RAY DIFFRACTIONr_chiral_restr0.060.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216979
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021479
LS refinement shellResolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 107 -
Rwork0.313 2017 -
all-2124 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4783-0.2164-1.37141.36750.46223.45690.0206-0.0938-0.3777-0.141-0.34150.18720.2933-0.3870.32080.31990.17510.1030.2753-0.00680.1556-36.3322-13.117-23.6563
22.8043-0.2651-2.14012.44831.57063.7263-0.1764-0.3205-0.1708-0.0683-0.23440.24180.44090.05140.41080.12370.08130.04740.4902-0.04950.0702-47.8375-5.64960.4572
34.4819-0.9466-1.52361.40340.23322.5344-0.0673-0.1668-0.37050.1673-0.1190.1649-0.0527-0.08310.18620.63580.29840.130.20040.08160.1684-44.6607-75.8617-33.3303
41.11470.57330.53054.6393-0.34882.86-0.19510.29920.0066-0.1409-0.0518-0.47180.03320.18130.24690.55350.28750.09720.3110.08760.1787-75.3294-30.1521-25.3239
54.3228-2.5873-1.97351.93580.63153.17510.0550.2288-0.17590.0257-0.13750.13890.24230.00180.08250.62940.28610.19550.14940.06580.1137-65.3464-62.755-20.292
61.13210.2369-0.78335.4313-1.90723.85740.07790.1099-0.07270.1472-0.1085-0.46950.02680.04030.03050.45630.27670.07110.20460.10120.1508-76.0801-5.9075-38.4614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 203
2X-RAY DIFFRACTION2B55 - 203
3X-RAY DIFFRACTION3C55 - 203
4X-RAY DIFFRACTION4D55 - 203
5X-RAY DIFFRACTION5E55 - 203
6X-RAY DIFFRACTION6F54 - 203

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