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- PDB-6e5p: Backbone model based on cryo-EM map at 8.5 A of domain-swapped, g... -

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Entry
Database: PDB / ID: 6e5p
TitleBackbone model based on cryo-EM map at 8.5 A of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 Env BG505 DS-SOSIP, which was also bound to CD4-binding site antibody VRC03
Components
  • (Envelope glycoprotein ...) x 2
  • 2G12 Light chain
  • 2G12 heavy chain
  • VRC03 Light chain
  • VRC03 heavy chain
KeywordsVIRAL PROTEIN / HIV-1 Env / complex / neutralizing / domain-swapped antibody
Function / homologyGp120 core superfamily / Envelope glycoprotein Gp160 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Envelope glycoprotein GP120 / Retroviral envelope protein / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization ...Gp120 core superfamily / Envelope glycoprotein Gp160 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Envelope glycoprotein GP120 / Retroviral envelope protein / 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 / 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 / identical protein binding / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Function and homology information
Specimen sourceHomo sapiens (human)
Human immunodeficiency virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8.8 Å resolution
AuthorsAcharya, P. / Kwong, P.D.
CitationJournal: Structure / Year: 2019
Title: Structural Survey of Broadly Neutralizing Antibodies Targeting the HIV-1 Env Trimer Delineates Epitope Categories and Characteristics of Recognition.
Authors: Gwo-Yu Chuang / Jing Zhou / Priyamvada Acharya / Reda Rawi / Chen-Hsiang Shen / Zizhang Sheng / Baoshan Zhang / Tongqing Zhou / Robert T Bailer / Venkata P Dandey / Nicole A Doria-Rose / Mark K Louder / Krisha McKee / John R Mascola / Lawrence Shapiro / Peter D Kwong
Abstract: Over the past decade, structures have been determined for broadly neutralizing antibodies that recognize all major exposed surfaces of the prefusion-closed HIV-1-envelope (Env) trimer. To understand ...Over the past decade, structures have been determined for broadly neutralizing antibodies that recognize all major exposed surfaces of the prefusion-closed HIV-1-envelope (Env) trimer. To understand this recognition and its implications, we analyzed 206 antibody-HIV-1 Env structures from the Protein Data Bank with resolution suitable to define interaction chemistries and measured antibody neutralization on a 208-strain panel. Those with >25% breadth segregated into almost two dozen classes based on ontogeny and recognition and into six epitope categories based on recognized Env residues. For paratope, the number of protruding loops and level of somatic hypermutation were significantly higher for broad HIV-1 neutralizing antibodies than for a comparison set of non-HIV-1 antibodies (p < 0.0001). For epitope, the number of independent sequence segments was higher (p < 0.0001), as well as the glycan component surface area (p = 0.0005). The unusual characteristics of epitope and paratope delineated here are likely to reflect respectively virus-immune evasion and antibody-recognition solutions that allow effective neutralization of HIV-1.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 21, 2018 / Release: Feb 13, 2019

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-8981
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: 2G12 Light chain
2: 2G12 heavy chain
3: 2G12 heavy chain
4: 2G12 Light chain
A: Envelope glycoprotein gp120
B: Envelope glycoprotein gp160
C: Envelope glycoprotein gp120
D: Envelope glycoprotein gp160
E: Envelope glycoprotein gp120
F: Envelope glycoprotein gp160
H: 2G12 heavy chain
I: VRC03 heavy chain
J: VRC03 Light chain
K: 2G12 Light chain
L: 2G12 Light chain
M: 2G12 heavy chain
O: VRC03 heavy chain
P: VRC03 Light chain
Q: 2G12 Light chain
R: 2G12 heavy chain
S: 2G12 heavy chain
T: 2G12 Light chain
V: VRC03 heavy chain
W: VRC03 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)659,378114
Polyers642,17924
Non-polymers17,19990
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 4 types, 18 molecules 14KLQT23HMRSIOVJPW

#1: Protein/peptide
2G12 Light chain


Mass: 23130.762 Da / Num. of mol.: 6 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein/peptide
2G12 heavy chain


Mass: 23932.869 Da / Num. of mol.: 6 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Protein/peptide VRC03 heavy chain


Mass: 24699.861 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Protein/peptide VRC03 Light chain


Mass: 23043.652 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Envelope glycoprotein ... , 2 types, 6 molecules ACEBDF

#3: Protein/peptide Envelope glycoprotein gp120 /


Mass: 53086.102 Da / Num. of mol.: 3 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#4: Protein/peptide Envelope glycoprotein gp160


Mass: 19102.811 Da / Num. of mol.: 3 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S9

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Non-polymers , 3 types, 90 molecules

#7: Chemical...
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 54 / Formula: C6H12O6
#8: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 24 / Formula: C8H15NO6 / N-Acetylglucosamine
#9: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 12 / 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

ComponentName: Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies 2G12 and VRC03.
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.01
Buffer componentConc.: 150 mM / Name: HEPES
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: SPOTITON / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 kelvins
Details: 0.005% dodecyl maltoside was added to sample before vitification

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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 / Nominal magnification: 105000 / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 63.84 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2206
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2LeginonLeginonimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 463860
SymmetryPoint symmetry: C3
3D reconstructionResolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 5245 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL

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