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- PDB-6nqd: Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex... -

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Basic information

Entry
Database: PDB / ID: 6nqd
TitleCryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab
Components
  • (8ANC195 G52K5 ...) x 2
  • T/F100 Env gp120
  • T/F100 Env gp41
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / Env / trimer / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


immunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / host cell endosome membrane / actin filament reorganization / mitigation of host immune response by virus / viral protein processing / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host plasma membrane ...immunoglobulin complex / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / host cell endosome membrane / actin filament reorganization / mitigation of host immune response by virus / viral protein processing / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host plasma membrane / adaptive immune response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / integral component of membrane / extracellular region / plasma membrane
Retroviral envelope protein GP41-like / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set / Immunoglobulin subtype / Immunoglobulin-like domain / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Gp120 core superfamily ...Retroviral envelope protein GP41-like / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set / Immunoglobulin subtype / Immunoglobulin-like domain / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Gp120 core superfamily / Envelope glycoprotein Gp160 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Envelope glycoprotein gp160 / Immunoglobulin kappa light chain / IgG H chain
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsFang, Q. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Nat Commun / Year: 2019
Title: A sequestered fusion peptide in the structure of an HIV-1 transmitted founder envelope trimer.
Authors: Neeti Ananthaswamy / Qianglin Fang / Wadad AlSalmi / Swati Jain / Zhenguo Chen / Thomas Klose / Yingyuan Sun / Yue Liu / Marthandan Mahalingam / Subhash Chand / Sodsai Tovanabutra / Merlin L ...Authors: Neeti Ananthaswamy / Qianglin Fang / Wadad AlSalmi / Swati Jain / Zhenguo Chen / Thomas Klose / Yingyuan Sun / Yue Liu / Marthandan Mahalingam / Subhash Chand / Sodsai Tovanabutra / Merlin L Robb / Michael G Rossmann / Venigalla B Rao /
Abstract: The envelope protein of human immunodeficiency virus-1 (HIV-1) and its fusion peptide are essential for cell entry and vaccine design. Here, we describe the 3.9-Å resolution structure of an envelope ...The envelope protein of human immunodeficiency virus-1 (HIV-1) and its fusion peptide are essential for cell entry and vaccine design. Here, we describe the 3.9-Å resolution structure of an envelope protein trimer from a very early transmitted founder virus (CRF01_AE T/F100) complexed with Fab from the broadly neutralizing antibody (bNAb) 8ANC195. The overall T/F100 trimer structure is similar to other reported "closed" state prefusion trimer structures. In contrast, the fusion peptide, which is exposed to solvent in reported closed structures, is sequestered (buried) in the hydrophobic core of the T/F100 trimer. A buried conformation has previously been observed in "open" state structures formed after CD4 receptor binding. The T/F100 trimer binds poorly to bNAbs including the fusion peptide-specific bNAbs PGT151 and VRC34.01. The T/F100 structure might represent a prefusion state, intermediate between the closed and open states. These observations are relevant to mechanisms of HIV-1 transmission and vaccine design.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: T/F100 Env gp120
B: T/F100 Env gp41
C: 8ANC195 G52K5 heavy chain, IG gamma-1 chain
D: 8ANC195 G52K5 light chain
E: T/F100 Env gp120
F: T/F100 Env gp41
G: 8ANC195 G52K5 heavy chain, IG gamma-1 chain
H: 8ANC195 G52K5 light chain
I: T/F100 Env gp120
J: T/F100 Env gp41
K: 8ANC195 G52K5 heavy chain, IG gamma-1 chain
L: 8ANC195 G52K5 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,402153
Polymers374,05912
Non-polymers29,343141
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area73450 Å2
ΔGint264 kcal/mol
Surface area105690 Å2

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Components

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Protein , 2 types, 6 molecules AEIBFJ

#1: Protein T/F100 Env gp120


Mass: 54739.133 Da / Num. of mol.: 3 / Fragment: UNP residues 29-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: A0A140EMT3
#2: Protein T/F100 Env gp41


Mass: 20333.879 Da / Num. of mol.: 3 / Fragment: UNP residues 513-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: A0A140EMT3

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Antibody , 2 types, 6 molecules CGKDHL

#3: Antibody 8ANC195 G52K5 heavy chain, IG gamma-1 chain


Mass: 26153.283 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6B2A6
#4: Antibody 8ANC195 G52K5 light chain


Mass: 23460.047 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX7

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Sugars , 3 types, 141 molecules

#5: Sugar...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Mass: 221.208 Da / Num. of mol.: 96
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
#6: Sugar
ChemComp-BMA / BETA-D-MANNOSE / Mannose


Mass: 180.156 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#7: Sugar...
ChemComp-MAN / ALPHA-D-MANNOSE / Mannose


Mass: 180.156 Da / Num. of mol.: 33
Source method: isolated from a genetically manipulated source
Formula: C6H12O6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1T/F100 Env trimer-8anc195 Fab complexCOMPLEX1, 2, 3, 40MULTIPLE SOURCES
2T/F100 Env trimerCOMPLEX1, 21RECOMBINANT
38anc195 FabCOMPLEX3, 41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Human immunodeficiency virus 111676
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
12Homo sapiens (human)9606HEK293S
23Homo sapiens (human)9606
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170716 / Symmetry type: POINT

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