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- EMDB-8981: Cryo-EM reconstruction of domain-swapped, glycan-reactive, neutra... -

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Entry
Database: EMDB / ID: 8981
TitleCryo-EM reconstruction 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
Map dataRefined map from cryoSparc postprocessed in Relion using map fro cryoSparc
SampleTernary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies 2G12 and VRC03.:
2G12 Light chain / 2G12 heavy chain / (Envelope glycoprotein ...) x 2 / VRC03 heavy chain / VRC03 Light chain / (ligand) x 3
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
SourceHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 8.8 Å resolution
AuthorsAcharya P / Kwong PD
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 ReportPDB-ID: 6e5p

SummaryFull reportAbout validation report
DateDeposition: Jul 21, 2018 / Header (metadata) release: Aug 29, 2018 / Map release: Feb 13, 2019 / Last update: Feb 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.734
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.734
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6e5p
  • Surface level: 0.734
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8981.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.1 Å/pix.
= 420.902 Å
384 pix
1.1 Å/pix.
= 420.902 Å
384 pix
1.1 Å/pix.
= 420.902 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0961 Å
Density
Contour Level:0.734 (by author), 0.734 (movie #1):
Minimum - Maximum-0.083880894 - 0.7352861
Average (Standard dev.)0.0114334095 (0.061371464)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin0.00.00.0
Limit383.0383.0383.0
Spacing384384384
CellA=B=C: 420.9024 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.09609895833331.09609895833331.0960989583333
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z420.902420.902420.902
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.2942.2030.019

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Supplemental data

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Sample components

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Entire Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of an...

EntireName: Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies 2G12 and VRC03.
Number of components: 10

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Component #1: protein, Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragme...

ProteinName: Ternary complex HIV-1 Env BG505 DS-SOSIP with Fab fragments of antibodies 2G12 and VRC03.
Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, 2G12 Light chain

ProteinName: 2G12 Light chain / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 23.130762 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, 2G12 heavy chain

ProteinName: 2G12 heavy chain / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 23.932869 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Envelope glycoprotein gp120

ProteinName: Envelope glycoprotein gp120 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 53.086102 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Envelope glycoprotein gp160

ProteinName: Envelope glycoprotein gp160 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 19.102811 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, VRC03 heavy chain

ProteinName: VRC03 heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 24.699861 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, VRC03 Light chain

ProteinName: VRC03 Light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 23.043652 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 54 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #9: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 24 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #10: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/ml / pH: 7.01
VitrificationInstrument: OTHER / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 90 %
Details: 0.005% dodecyl maltoside was added to sample before vitification. The value given for _emd_vitrification.instrument is SPOTITON. This is not in a list of allowed values set(['FEI VITROBOT MARK I', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', 'FEI VITROBOT MARK II', 'HOMEMADE PLUNGER', 'LEICA EM CPC', 'LEICA KF80', 'FEI VITROBOT MARK III', 'LEICA EM GP', 'OTHER', 'REICHERT-JUNG PLUNGER', 'FEI VITROBOT MARK IV']) so OTHER is written into the XML file.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 63.84 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000.0 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 2000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2206

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 5245
3D reconstructionSoftware: cryoSPARC / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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