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

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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 / homologyRetroviral envelope protein GP41-like / Gp120 core superfamily / Immunoglobulin C1-set / Immunoglobulin/major histocompatibility complex, conserved site / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Envelope glycoprotein Gp160 ...Retroviral envelope protein GP41-like / Gp120 core superfamily / Immunoglobulin C1-set / Immunoglobulin/major histocompatibility complex, conserved site / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Envelope glycoprotein Gp160 / Envelope glycoprotein GP120 / Retroviral envelope protein / Immunoglobulin C1-set domain / Immunoglobulin V-set domain / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin subtype / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization / host cell endosome membrane / evasion or tolerance by virus of host immune response / viral protein processing / antigen binding / adaptive immune response / fusion of virus membrane with host plasma membrane / clathrin-dependent endocytosis of virus by host cell / 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 / Envelope glycoprotein gp160 / Immunoglobulin kappa light chain / IgG H chain
Function and homology information
Specimen sourceHuman immunodeficiency virus 1
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsFang, Q. / Rossmann, M.G.
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 Robb / Michael G Rossmann / Venigalla B Rao
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 21, 2019 / Release: Mar 6, 2019

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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
Polyers374,05912
Non-polymers29,343141
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)73450
ΔGint (kcal/M)264
Surface area (Å2)105690

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Components

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Protein/peptide , 2 types, 6 molecules AEIBFJ

#1: Protein/peptide T/F100 Env gp120


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


Mass: 20333.879 Da / Num. of mol.: 3 / Fragment: UNP residues 513-665 / 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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8ANC195 G52K5 ... , 2 types, 6 molecules CGKDHL

#3: Protein/peptide 8ANC195 G52K5 heavy chain, IG gamma-1 chain


Mass: 26153.283 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6B2A6
#4: Protein/peptide 8ANC195 G52K5 light chain


Mass: 23460.047 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX7

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Non-polymers , 3 types, 141 molecules

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


Mass: 221.208 Da / Num. of mol.: 96 / Formula: C8H15NO6 / N-Acetylglucosamine
#6: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 12 / Formula: C6H12O6
#7: Chemical...
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 33 / Formula: C6H12O6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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 IDNcbi tax IDOrganism
1211676Human immunodeficiency virus 1
239606Homo sapiens (human)
Source (recombinant)
IDEntity assembly IDCellNcbi tax IDOrganism
12HEK293S9606Homo sapiens (human)
239606Homo sapiens (human)
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
MicroscopyMicroscope model: 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 / Number of particles: 170716 / Symmetry type: POINT

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