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- EMDB-8977: Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-dir... -

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Basic information

Entry
Database: EMDB / ID: EMD-8977
TitleCryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody, A12V163-b.01, elicited by vaccination of Rhesus macaques, in complex with stabilized HIV-1 Env BG505 DS-SOSIP, which was also bound to antibodies VRC03 and PGT122
Map data
SampleQuaternary complex of HIV-1 Env BG505 DS-SOSIP with antibodies A12V163-b.01, VRC03 and PGT122.:
(HIV-1 Env BG505 DS-SOSIP ...) x 4 / A12V163-b.01 / VRC03 / PGT122 / (A12V163-b.01 ...) x 2 / VRC03 heavy chain / VRC03 light chain / PGT122 heavy chain / PGT122 light chain
Function / homology
Function and homology information


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 / 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 ...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 / 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
Gp120 core superfamily / Retroviral envelope protein / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Envelope glycoprotein GP120 / Envelope glycoprotein Gp160
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsAcharya P / Eng ET / Kwong PD
CitationJournal: Cell / Year: 2019
Title: Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.
Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou / Gwo-Yu Chuang / Cara W Chao / Ying Gu / Alexander J Jafari / Mark K Louder / Sijy O'Dell / Ariana P Rowshan / Elise G Viox / Yiran Wang / Chang W Choi / Martin M Corcoran / Angela R Corrigan / Venkata P Dandey / Edward T Eng / Hui Geng / Kathryn E Foulds / Yicheng Guo / Young D Kwon / Bob Lin / Kevin Liu / Rosemarie D Mason / Martha C Nason / Tiffany Y Ohr / Li Ou / Reda Rawi / Edward K Sarfo / Arne Schön / John P Todd / Shuishu Wang / Hui Wei / Winston Wu / / James C Mullikin / Robert T Bailer / Nicole A Doria-Rose / Gunilla B Karlsson Hedestam / Diana G Scorpio / Julie Overbaugh / Jesse D Bloom / Bridget Carragher / Clinton S Potter / Lawrence Shapiro / Peter D Kwong / John R Mascola /
Abstract: The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be ...The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization.
Validation ReportPDB-ID: 6mpg

SummaryFull reportAbout validation report
History
DepositionJul 15, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseSep 11, 2019-
UpdateSep 11, 2019-
Current statusSep 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.19
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.19
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6mpg
  • Surface level: 1.19
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8977.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 384 pix.
= 410.88 Å
1.07 Å/pix.
x 384 pix.
= 410.88 Å
1.07 Å/pix.
x 384 pix.
= 410.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 1.19 / Movie #1: 1.19
Minimum - Maximum-2.859975 - 6.317193
Average (Standard dev.)0.010769986 (±0.12592092)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z410.880410.880410.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-2.8606.3170.011

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Supplemental data

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Sample components

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Entire Quaternary complex of HIV-1 Env BG505 DS-SOSIP with antibodies A1...

EntireName: Quaternary complex of HIV-1 Env BG505 DS-SOSIP with antibodies A12V163-b.01, VRC03 and PGT122.
Number of components: 14

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Component #1: protein, Quaternary complex of HIV-1 Env BG505 DS-SOSIP with anti...

ProteinName: Quaternary complex of HIV-1 Env BG505 DS-SOSIP with antibodies A12V163-b.01, VRC03 and PGT122.
Recombinant expression: No
MassTheoretical: 630 kDa

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Component #2: protein, HIV-1 Env BG505 DS-SOSIP gp120

ProteinName: HIV-1 Env BG505 DS-SOSIP gp120 / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, HIV-1 Env BG505 DS-SOSIP gp41

ProteinName: HIV-1 Env BG505 DS-SOSIP gp41 / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, A12V163-b.01

ProteinName: A12V163-b.01 / Recombinant expression: No
SourceSpecies: Macaca mulatta (Rhesus monkey)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, VRC03

ProteinName: VRC03 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, PGT122

ProteinName: PGT122 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, HIV-1 Env BG505 DS-SOSIP gp120

ProteinName: HIV-1 Env BG505 DS-SOSIP gp120 / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: protein, HIV-1 Env BG505 DS-SOSIP gp41

ProteinName: HIV-1 Env BG505 DS-SOSIP gp41 / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: protein, A12V163-b.01 Heavy chain

ProteinName: A12V163-b.01 Heavy chain / Recombinant expression: No
SourceSpecies: Macaca mulatta (Rhesus monkey)
Source (engineered)Expression System: Homo sapiens (human)

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Component #10: protein, A12V163-b.01 Light chain

ProteinName: A12V163-b.01 Light chain / Recombinant expression: No
SourceSpecies: Macaca mulatta (Rhesus monkey)
Source (engineered)Expression System: Homo sapiens (human)

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Component #11: protein, VRC03 heavy chain

ProteinName: VRC03 heavy chain / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #12: protein, VRC03 light chain

ProteinName: VRC03 light chain / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #13: protein, PGT122 heavy chain

ProteinName: PGT122 heavy chain / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #14: protein, PGT122 light chain

ProteinName: PGT122 light chain / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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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: 7.5
Support filmunspecified
VitrificationInstrument: SPOTITON / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 90 %

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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: 69.98 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 138170
3D reconstructionSoftware: cryoSPARC / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Correlation coefficient / Refinement space: REAL
Output model

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