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- PDB-5ka5: HIV-1 gp41 variant V549E resistance mutation -

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Basic information

Entry
Database: PDB / ID: 5ka5
TitleHIV-1 gp41 variant V549E resistance mutation
ComponentsTransmembrane glycoprotein gp41
KeywordsVIRAL PROTEIN / Hiv-1 / membrane fusion / 5-helix / C-peptide
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Helix Hairpins - #210 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBhardwaj, A. / Khasnis, M.D. / Halkidis, K. / Root, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM066682 United States
CitationJournal: PLoS Pathog. / Year: 2016
Title: Receptor Activation of HIV-1 Env Leads to Asymmetric Exposure of the gp41 Trimer.
Authors: Khasnis, M.D. / Halkidis, K. / Bhardwaj, A. / Root, M.J.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Transmembrane glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)10,6161
Polymers10,6161
Non-polymers00
Water57632
1
A: Transmembrane glycoprotein gp41

A: Transmembrane glycoprotein gp41

A: Transmembrane glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)31,8473
Polymers31,8473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6340 Å2
ΔGint-57 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.716, 40.716, 115.521
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-701-

HOH

21A-720-

HOH

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Components

#1: Protein Transmembrane glycoprotein gp41 / Glycoprotein 41


Mass: 10615.807 Da / Num. of mol.: 1 / Fragment: UNP residues 543-582 and 625-661 linked via GGRGG / Mutation: V549E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: isolate HXB2 / Gene: env / Plasmid: P4 / Production host: Escherichia coli (E. coli) / Strain (production host): RP3098 / References: UniProt: P04578
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1.8 Å3/Da / Density % sol: 31.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3M Sodium chloride, 0.1M Sodium Acetate Sample concentration: 6 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2012 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→18 Å / Num. obs: 13238 / % possible obs: 99.8 % / Redundancy: 2.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.3
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 1.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AIK

1aik


Resolution: 1.8→17.998 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.25 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2225 1292 10.5 %
Rwork0.1871 --
obs0.1939 12745 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→17.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms647 0 0 32 679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002655
X-RAY DIFFRACTIONf_angle_d0.321882
X-RAY DIFFRACTIONf_dihedral_angle_d16.595392
X-RAY DIFFRACTIONf_chiral_restr0.02896
X-RAY DIFFRACTIONf_plane_restr0.001116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8012-1.87320.3321370.31051198X-RAY DIFFRACTION81
1.8732-1.95820.32271440.29511245X-RAY DIFFRACTION84
1.9582-2.06110.27481400.27591228X-RAY DIFFRACTION85
2.0611-2.18980.28331420.25281223X-RAY DIFFRACTION85
2.1898-2.35820.24051460.23021304X-RAY DIFFRACTION87
2.3582-2.59410.23321500.2161268X-RAY DIFFRACTION87
2.5941-2.96640.24711530.18651295X-RAY DIFFRACTION88
2.9664-3.72560.17911420.16061327X-RAY DIFFRACTION90
3.7256-13.98890.221380.14671328X-RAY DIFFRACTION90
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)
10.33050.079-0.24090.66360.76597.7584-0.01790.01840.03310.0048-0.09220.02550.0957-0.33250.06190.19580.014-0.00110.2445-0.02440.260714.1095-11.1729-5.5117
22.68511.00143.72440.38581.38065.3694-0.277-0.01320.2069-0.0466-0.09690.0655-0.4064-0.12010.13630.27730.0387-0.06540.2052-0.01710.245914.2055-1.8871-3.6067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 542 through 624 )
2X-RAY DIFFRACTION2chain 'A' and (resid 625 through 663 )

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