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- PDB-5ka6: HIV-1 gp41 variant Q552R and L555M resistance mutations -

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Basic information

Entry
Database: PDB / ID: 5ka6
TitleHIV-1 gp41 variant Q552R and L555M resistance mutations
ComponentsTransmembrane protein gp41Transmembrane protein
KeywordsMEMBRANE 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: 1.85 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 protein gp41
B: Transmembrane protein gp41
C: Transmembrane protein gp41


Theoretical massNumber of molelcules
Total (without water)31,8993
Polymers31,8993
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-66 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.591, 43.591, 113.048
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Transmembrane protein gp41 / Transmembrane protein / Glycoprotein 41


Mass: 10632.926 Da / Num. of mol.: 3 / Fragment: UNP residues 543-582 and 625-661 linked via GGRGG / Mutation: Q552R, L555M
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.: 96 / 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: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.3M Calcium Acetate, 0.1M Sodium Cacodylate Sample concentration: 6.35 mg/ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 25, 2011 / Details: Oxford Danfysik toroidal focusing mirror.
RadiationMonochromator: Si(111) channel cut monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→35.81 Å / Num. obs: 41094 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.9
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.489 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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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: 1.85→35.807 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2776 1692 9.72 %
Rwork0.2309 --
obs0.2354 39786 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→35.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 0 96 2035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031962
X-RAY DIFFRACTIONf_angle_d0.5322644
X-RAY DIFFRACTIONf_dihedral_angle_d22.7391184
X-RAY DIFFRACTIONf_chiral_restr0.038297
X-RAY DIFFRACTIONf_plane_restr0.003341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.87260.45841370.47771231X-RAY DIFFRACTION93
1.8726-1.89630.65251100.5538971X-RAY DIFFRACTION69
1.8963-1.92130.44091250.45971186X-RAY DIFFRACTION91
1.9213-1.94760.5741310.4731074X-RAY DIFFRACTION85
1.9476-1.97540.42451400.38221339X-RAY DIFFRACTION99
1.9754-2.00490.34821430.33351228X-RAY DIFFRACTION99
2.0049-2.03620.38661480.32131383X-RAY DIFFRACTION100
2.0362-2.06960.39361360.36091342X-RAY DIFFRACTION100
2.0696-2.10530.37891470.32061317X-RAY DIFFRACTION100
2.1053-2.14360.32161360.27341271X-RAY DIFFRACTION100
2.1436-2.18480.34561640.2621374X-RAY DIFFRACTION100
2.1848-2.22940.33141200.28651282X-RAY DIFFRACTION99
2.2294-2.27790.33171420.30441354X-RAY DIFFRACTION98
2.2779-2.33090.30321230.27471272X-RAY DIFFRACTION99
2.3309-2.38910.30061510.23721322X-RAY DIFFRACTION100
2.3891-2.45370.31991510.22471292X-RAY DIFFRACTION99
2.4537-2.52590.31431280.21911327X-RAY DIFFRACTION98
2.5259-2.60740.23061480.2221291X-RAY DIFFRACTION99
2.6074-2.70060.27711320.22551363X-RAY DIFFRACTION99
2.7006-2.80860.28261420.23121244X-RAY DIFFRACTION98
2.8086-2.93640.28231390.21651296X-RAY DIFFRACTION98
2.9364-3.09120.29191510.2291301X-RAY DIFFRACTION99
3.0912-3.28470.26141350.23291331X-RAY DIFFRACTION99
3.2847-3.53810.25291160.1921295X-RAY DIFFRACTION100
3.5381-3.89380.27341480.17311344X-RAY DIFFRACTION100
3.8938-4.45630.18491420.16861321X-RAY DIFFRACTION100
4.4563-5.6110.22131420.19011286X-RAY DIFFRACTION98
5.611-35.81390.21161420.20341280X-RAY DIFFRACTION96
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)
11.65920.12580.47241.4594-0.97866.5038-0.08540.0159-0.1637-0.0751-0.0942-0.05760.3832-0.07120.10360.2104-0.02280.02260.2543-0.01950.2486-3.19017.5148.5783
20.8069-0.12550.87391.9072-1.76476.1197-0.09820.06030.13760.0797-0.4998-0.31760.09480.67420.55910.1662-0.0066-0.00870.33640.03790.27024.343511.56837.8709
31.7203-0.1418-0.04461.8822-0.09626.10860.0701-0.14650.17780.134-0.04530.1207-0.3602-0.51910.0370.1775-0.06130.02850.1942-0.01820.2748-4.13917.15899.0525
43.2419-0.67521.5621.71070.74536.3757-0.2741-0.44070.4021-0.1446-0.22170.289-0.9789-1.13320.35140.18230.02410.01490.3083-0.02920.2748-11.903221.63457.4196
56.1187-0.05091.43944.16152.67566.3670.5859-0.08080.1142-0.4110.5539-0.33160.56930.709-0.60130.5215-0.031-0.17930.4761-0.05040.4902-14.11046.3454-12.2112
62.1924-0.36890.08461.4612-0.09181.9301-0.0692-0.21540.18240.24130.01040.1587-0.0073-0.11550.02330.267-0.06780.07880.3838-0.05740.2969-12.081113.654118.6399
71.6361-1.3086-2.16841.9651.13267.8323-0.40180.0935-0.38190.1751-0.07180.37371.1851-0.24910.24060.2798-0.07560.10130.2774-0.09360.3787-11.55742.09946.0053
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 542 through 580 )
2X-RAY DIFFRACTION2chain 'A' and (resid 581 through 661 )
3X-RAY DIFFRACTION3chain 'B' and (resid 543 through 580 )
4X-RAY DIFFRACTION4chain 'B' and (resid 581 through 663 )
5X-RAY DIFFRACTION5chain 'C' and (resid 544 through 553 )
6X-RAY DIFFRACTION6chain 'C' and (resid 554 through 626 )
7X-RAY DIFFRACTION7chain 'C' and (resid 627 through 663 )

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