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- PDB-6dln: Oligomeric Structure of the HIV gp41 MPER-TMD in Phospholipid Bilayers -

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Basic information

Entry
Database: PDB / ID: 6dln
TitleOligomeric Structure of the HIV gp41 MPER-TMD in Phospholipid Bilayers
ComponentsTransmembrane protein gp41Transmembrane protein
KeywordsMEMBRANE PROTEIN / HIV / MPER-TMD
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
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodSOLID-STATE NMR / molecular dynamics
AuthorsKwon, B. / Lee, M. / Waring, A.J. / Hong, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM066976 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Oligomeric Structure and Three-Dimensional Fold of the HIV gp41 Membrane-Proximal External Region and Transmembrane Domain in Phospholipid Bilayers.
Authors: Kwon, B. / Lee, M. / Waring, A.J. / Hong, M.
History
DepositionJun 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)14,0183
Polymers14,0183
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: 19F Spin diffusion (CODEX) NMR Experiments
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1950 Å2
ΔGint-26 kcal/mol
Surface area10070 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Transmembrane protein gp41 / Transmembrane protein / Envelope glycoprotein gp160 / Env polyprotein


Mass: 4672.646 Da / Num. of mol.: 3 / Fragment: residues 665-703 / Source method: obtained synthetically
Source: (synth.) Human immunodeficiency virus type 1 group M subtype B
References: UniProt: P04578

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
213isotropic32D 13C-13C DARR
223isotropic32D water Edited DARR
332isotropic113C-19F REDOR
242isotropic22D water Edited DARR
351isotropic119F CODEX
363isotropic119F CODEX
372isotropic119F CODEX

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
membrane133 % w/w 4-19F-F699 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5Peptides were reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.519F-sample10 mM HEPES buffer pH 7.5
membrane333 % w/w [U-13C; U-15N]-L669,I686, A700, 13C'-G694, 19F-5F-W680 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5Peptides were reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.513C, 15N, 19F_sample 110 mM HEPES buffer pH 7.5
membrane233 % w/w [U-13C; U-15N]-L684,I686, G694, 19F-5F-W678, 19F-4F-F699 HIV gp41 MPER-TMD, reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.5Peptides were reconstituted into the virus mimetic membrane (POPC:POPE:POPS:sphingomyelin: cholesterol = 30:15:15:10:30), 10 mM HEPES buffer pH 7.513C, 15N, 19F_sample 210 mM HEPES buffer pH 7.5
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
33 % w/wHIV gp41 MPER-TMD4-19F-F6991
33 % w/wHIV gp41 MPER-TMD[U-13C; U-15N]-L669,I686, A700, 13C'-G694, 19F-5F-W6803
33 % w/wHIV gp41 MPER-TMD[U-13C; U-15N]-L684,I686, G694, 19F-5F-W678, 19F-4F-F6992
10 mMHEPES buffernatural abundance1
10 mMHEPES buffernatural abundance2
10 mMHEPES buffernatural abundance3
Sample conditions
Conditions-IDDetailsIonic strength unitsLabelpHPressure (kPa)Temperature (K)
29-10.5 KHz MASNot definedCondition 17.5 1 atm263 K
35 - 10 kHzNot definedCondition 27.5 1 atm233 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker BrukerBrukerBruker4001
Bruker BrukerBrukerBruker6002
Bruker BrukerBrukerBruker8003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinchemical shift assignment
MatlabMathworkdata analysis
GROMACSUniversity of GroningenRoyal Institute of TechnologyUppsala Universityrefinement
CHARMM-GUILehigh University / Department of Biological Sciences / Department of Bioengineering/ Im Labrefinement
GROMACSUniversity of GroningenRoyal Institute of TechnologyUppsala Universitystructure calculation
CHARMM-GUILehigh University / Department of Biological Sciences / Department of Bioengineering/ Im Labstructure calculation
Refinement
MethodSoftware ordinal
molecular dynamics3
molecular dynamics4
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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