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- PDB-6ujv: Model of the HIV-1 gp41 membrane-proximal external region, transm... -

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Basic information

Entry
Database: PDB / ID: 6ujv
TitleModel of the HIV-1 gp41 membrane-proximal external region, transmembrane domain and cytoplasmic tail (LLP2)
ComponentsEnvelope glycoprotein GP41
KeywordsMEMBRANE PROTEIN / Viral protein / Membrane-proximal external region / Transmembrane domain / Cytoplasmic tail
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / : / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / : / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / apoptotic process / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane / plasma 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
AuthorsPiai, A. / Fu, Q. / Cai, Y. / Ghantous, F. / Xiao, T. / Shaik, M.M. / Peng, H. / Rits-Volloch, S. / Liu, Z. / Chen, W. ...Piai, A. / Fu, Q. / Cai, Y. / Ghantous, F. / Xiao, T. / Shaik, M.M. / Peng, H. / Rits-Volloch, S. / Liu, Z. / Chen, W. / Seaman, M.S. / Chen, B. / Chou, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127193 United States
Citation
Journal: Nat Commun / Year: 2020
Title: Structural basis of transmembrane coupling of the HIV-1 envelope glycoprotein.
Authors: Piai, A. / Fu, Q. / Cai, Y. / Ghantous, F. / Xiao, T. / Shaik, M.M. / Peng, H. / Rits-Volloch, S. / Chen, W. / Seaman, M.S. / Chen, B. / Chou, J.J.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of the membrane proximal external region of HIV-1 envelope glycoprotein.
Authors: Fu, Q. / Shaik, M.M. / Cai, Y. / Ghantous, F. / Piai, A. / Peng, H. / Rits-Volloch, S. / Liu, Z. / Harrison, S.C. / Seaman, M.S. / Chen, B. / Chou, J.J.
#2: Journal: Science / Year: 2016
Title: Structural basis for membrane anchoring of HIV-1 envelope spike.
Authors: Dev, J. / Park, D. / Fu, Q. / Chen, J. / Ha, H.J. / Ghantous, F. / Herrmann, T. / Chang, W. / Liu, Z. / Frey, G. / Seaman, M.S. / Chen, B. / Chou, J.J.
History
DepositionOct 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein GP41
B: Envelope glycoprotein GP41
C: Envelope glycoprotein GP41


Theoretical massNumber of molelcules
Total (without water)45,5183
Polymers45,5183
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, Performed on the MPER-TMD and TMD-CT(LLP2)
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8210 Å2
ΔGint-57 kcal/mol
Surface area23670 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Envelope glycoprotein GP41 / Env polyprotein


Mass: 15172.598 Da / Num. of mol.: 3 / Fragment: residues 658-786 / Mutation: C764S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: isolate 92UG024.2 / Gene: env / Plasmid: pMM-LR6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A060KRW4, UniProt: P04578*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N TROSY-HSQC
121isotropic13D TROSY HNCO
131isotropic13D TROSY HNCA
141isotropic22D 1H-15N TROSY-HSQC
151isotropic23D TROSY HN(CA)CO
161isotropic23D TROSY HN(CO)CA
171isotropic23D TROSY HN(CA)CB
182isotropic22D 1H-15N TROSY-HSQC
192isotropic23D 15N-edited NOESY-TROSY-HSQC
1103isotropic32D 1H-15N TROSY-HSQC
1113isotropic32D 1H-13C HSQC
1123isotropic33D 15N-edited NOESY-TROSY-HSQC
1133isotropic33D 13C-edited NOESY
1144isotropic42D 1H-15N TROSY-HSQC
1154isotropic43D 15N-edited NOESY-TROSY-HSQC
1165isotropic42D 1H-15N TROSY-HSQC
1175isotropic42D 1H-13C HSQC
1185isotropic43D 15N-edited NOESY-TROSY-HSQC
1195isotropic32D 1H-15N TROSY-HSQC
1205isotropic32D 1H-13C HSQC
1215isotropic33D J(CH)-MODULATED NOESY
1226isotropic12D 1H-15N TROSY-HSQC
1237isotropic12D 1H-15N TROSY-HSQC
1247isotropic13D TROSY HNCO
1257isotropic13D TROSY HNCA
1267isotropic13D TROSY HN(CA)CO
1277isotropic13D TROSY HN(CO)CA
1288isotropic22D 1H-15N TROSY-HSQC
1298isotropic23D 15N-edited NOESY-TROSY-HSQC
1309isotropic42D 1H-15N TROSY-HSQC
1319isotropic42D 1H-13C HSQC
1329isotropic43D 15N-edited NOESY-TROSY-HSQC
1339isotropic43D 13C-edited NOESY
13410isotropic42D 1H-15N TROSY-HSQC
13510isotropic43D 15N-edited NOESY-TROSY-HSQC
13611isotropic42D 1H-15N TROSY-HSQC
13711isotropic42D 1H-13C HSQC
13811isotropic43D 15N-edited NOESY-TROSY-HSQC
13911isotropic32D 1H-15N TROSY-HSQC
14011isotropic32D 1H-13C HSQC
14111isotropic33D J(CH)-MODULATED NOESY
14212isotropic12D 1H-15N TROSY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
bicelle10.7 mM [U-13C; U-15N; U-85% 2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2OBicelle q=0.513C,15N,85%2H_TMD-CT(LLP2)90% H2O/10% D2O
bicelle20.8 mM [U-15N; U-2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 80 mM DMPC, 80 mM DHPC, 90% H2O/10% D2OBicelle q=0.515N,2H_TMD-CT(LLP2)90% H2O/10% D2O
bicelle31.0 mM [U-13C; U-15N] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 80 mM DMPC, 80 mM DHPC, 90% H2O/10% D2OBicelle q=0.513C,15N_TMD-CT(LLP2)90% H2O/10% D2O
bicelle40.5 mM [U-15N; U-2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2OBicelle q=0.5control_sample_TMD-CT(LLP2)90% H2O/10% D2O
bicelle50.5 mM [U-15N; U-2H] HIV-1 gp41 TMD-CT(LLP2), 0.5 mM [U-13C] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2OBicelle q=0.5; The (15N,2H)-labeled and the (13C)-labeled proteins were mixed ~1:1mixed_sample_TMD-CT(LLP2)90% H2O/10% D2O
bicelle60.5 mM [U-15N; U-85% 2H] HIV-1 gp41 TMD-CT(LLP2), 40 mM MES, 40 mM DMPC, 80 mM DHPC, 90% H2O/10% D2OBicelle q=0.515N,85%2H_TMD-CT(LLP2)90% H2O/10% D2O
bicelle70.8 mM [U-13C; U-15N; U-85% 2H] HIV-1 gp41 MPER-TMD, 40 mM MOPS, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2OBicelle q=0.513C,15N,85%2H_MPER-TMD90% H2O/10% D2O
bicelle80.8 mM [U-15N; U-2H] HIV-1 gp41 MPER-TMD, 40 mM MOPS, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2OBicelle q=0.515N,2H_MPER-TMD90% H2O/10% D2O
bicelle90.8 mM [U-13C; U-15N] HIV-1 gp41 MPER-TMD, 40 mM MOPS, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2OBicelle q=0.513C,15N_MPER-TMD90% H2O/10% D2O
bicelle100.4 mM [U-15N; U-2H] HIV-1 gp41 MPER-TMD, 40 mM MOPS, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2OBicelle q=0.5control_sample_MPER-TMD90% H2O/10% D2O
bicelle110.4 mM [U-15N; U-2H] HIV-1 gp41 MPER-TMD, 0.4 mM [U-13C] HIV-1 gp41 MPER-TMD, 40 mM MOPS, 50 mM DMPC, 100 mM DHPC, 90% H2O/10% D2OBicelle q=0.5; The (15N,2H)-labeled and the (13C)-labeled proteins were mixed ~1:1mixed_sample_MPER-TMD90% H2O/10% D2O
bicelle120.8 mM [U-15N; U-85% 2H] HIV-1 gp41 MPER-TMD, 40 mM MOPS, 50 mM DMPC, 85 mM DPC, 90% H2O/10% D2OBicelle q=0.615N,85%2H_MPER-TMD90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMHIV-1 gp41 TMD-CT(LLP2)[U-13C; U-15N; U-85% 2H]1
40 mMMESnatural abundance1
40 mMDMPCnatural abundance1
80 mMDHPCnatural abundance1
0.8 mMHIV-1 gp41 TMD-CT(LLP2)[U-15N; U-2H]2
40 mMMESnatural abundance2
80 mMDMPCnatural abundance2
80 mMDHPCnatural abundance2
1.0 mMHIV-1 gp41 TMD-CT(LLP2)[U-13C; U-15N]3
40 mMMESnatural abundance3
80 mMDMPCnatural abundance3
80 mMDHPCnatural abundance3
0.5 mMHIV-1 gp41 TMD-CT(LLP2)[U-15N; U-2H]4
40 mMMESnatural abundance4
40 mMDMPCnatural abundance4
80 mMDHPCnatural abundance4
0.5 mMHIV-1 gp41 TMD-CT(LLP2)[U-15N; U-2H], [U-13C]5
40 mMMESnatural abundance5
40 mMDMPCnatural abundance5
80 mMDHPCnatural abundance5
0.5 mMHIV-1 gp41 TMD-CT(LLP2)[U-15N; U-85% 2H]6
40 mMMESnatural abundance6
40 mMDMPCnatural abundance6
80 mMDHPCnatural abundance6
0.8 mMHIV-1 gp41 MPER-TMD[U-13C; U-15N; U-85% 2H]7
40 mMMOPSnatural abundance7
50 mMDMPCnatural abundance7
100 mMDHPCnatural abundance7
0.8 mMHIV-1 gp41 MPER-TMD[U-15N; U-2H]8
40 mMMOPSnatural abundance8
50 mMDMPCnatural abundance8
100 mMDHPCnatural abundance8
0.8 mMHIV-1 gp41 MPER-TMD[U-13C; U-15N]9
40 mMMOPSnatural abundance9
50 mMDMPCnatural abundance9
100 mMDHPCnatural abundance9
0.4 mMHIV-1 gp41 MPER-TMD[U-15N; U-2H]10
40 mMMOPSnatural abundance10
50 mMDMPCnatural abundance10
100 mMDHPCnatural abundance10
0.4 mMHIV-1 gp41 MPER-TMD[U-15N; U-2H], [U-13C]11
40 mMMOPSnatural abundance11
50 mMDMPCnatural abundance11
100 mMDHPCnatural abundance11
0.8 mMHIV-1 gp41 MPER-TMD[U-15N; U-85% 2H]12
40 mMMOPSnatural abundance12
50 mMDMPCnatural abundance12
85 mMDPCnatural abundance12
Sample conditionsIonic strength: 0 M / Label: conditions_1 / pH: 6.7 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD6001Equipped with a cryogenic probe
Bruker AVANCE IIIBrukerAVANCE III7502Equipped with a cryogenic probe
Bruker AVANCE IIIBrukerAVANCE III8003Equipped with a cryogenic probe
Bruker AVANCE IIIBrukerAVANCE III9004Equipped with a cryogenic probe

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichpeak picking
XEASYBartels et al.peak picking
CARAKeller and Wuthrichchemical shift assignment
XEASYBartels et al.chemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 15

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