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- EMDB-7858: Ectodomain of full length, wild type HIV-1 glycoprotein clone PC6... -

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Entry
Database: EMDB / ID: 7858
TitleEctodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab
Map dataEctodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab
SampleFull length, wild type HIV-1 Envelope glycoprotein in complex with PGT151 Fab:
(Envelope glycoprotein ...) x 2 / (Immunoglobulin G PGT151 Fab, ...) x 2 / (ligand) x 5
Function / homologyImmunoglobulin V-set domain / Immunoglobulin-like domain / Immunoglobulin C1-set domain / Retroviral envelope protein / Envelope glycoprotein GP120 / Envelope glycoprotein Gp160 / Gp120 core superfamily / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Ig-like domain profile. ...Immunoglobulin V-set domain / Immunoglobulin-like domain / Immunoglobulin C1-set domain / Retroviral envelope protein / Envelope glycoprotein GP120 / Envelope glycoprotein Gp160 / Gp120 core superfamily / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Ig-like domain profile. / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C1-set / Immunoglobulin/major histocompatibility complex, conserved site / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Immunoglobulin V-set domain / membrane fusion involved in viral entry into host cell / host cell endosome membrane / viral envelope / virion attachment to host cell / virion membrane / structural molecule activity / integral component of membrane / Envelope glycoprotein gp160 / Uncharacterized protein / IgG H chain
Function and homology information
SourceHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsBerndsens ZB / Rantalainen KR / Ward AB
CitationJournal: Cell Rep / Year: 2018
Title: Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design.
Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais / James C Paulson / Ian A Wilson / Andrew B Ward
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at ...Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex.
Validation ReportPDB-ID: 6dcq

SummaryFull reportAbout validation report
DateDeposition: May 8, 2018 / Header (metadata) release: Jun 27, 2018 / Map release: Jun 27, 2018 / Last update: Jul 4, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6dcq
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6dcq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7858.png

Downloads & links

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Map

Fileemd_7858.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.03 Å/pix.
= 329.6 Å		320 pix
1.03 Å/pix.
= 329.6 Å		320 pix
1.03 Å/pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.0583 (by emdb), 0.05 (movie #1):
Minimum - Maximum-0.14663479 - 0.30068433
Average (Standard dev.)-0.00029263593 (0.008385066)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin0.0.0.
Limit319.319.319.
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.600329.600329.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1470.301-0.000

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Supplemental data

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Mask #1

Fileemd_7858_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire Full length, wild type HIV-1 Envelope glycoprotein in complex wit...

EntireName: Full length, wild type HIV-1 Envelope glycoprotein in complex with PGT151 Fab
Details: Full length HIV-1 Envelope glycoprotein clone C043 collected 18 months post infection from donor 64 of Protocol C cohort study. Expressed as recombinant protein in HEK293F cell line.
Number of components: 10

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Component #1: protein, Full length, wild type HIV-1 Envelope glycoprotein in co...

ProteinName: Full length, wild type HIV-1 Envelope glycoprotein in complex with PGT151 Fab
Details: Full length HIV-1 Envelope glycoprotein clone C043 collected 18 months post infection from donor 64 of Protocol C cohort study. Expressed as recombinant protein in HEK293F cell line.
Recombinant expression: No
MassExperimental: 389 kDa
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Envelope glycoprotein gp160

ProteinName: Envelope glycoprotein gp160 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 53.392359 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Envelope glycoprotein gp160

ProteinName: Envelope glycoprotein gp160 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 40.020207 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Immunoglobulin G PGT151 Fab, Heavy chain

ProteinName: Immunoglobulin G PGT151 Fab, Heavy chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.087438 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Immunoglobulin G PGT151 Fab, Light chain

ProteinName: Immunoglobulin G PGT151 Fab, Light chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.057809 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 100 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #7: ligand, ALPHA-L-FUCOSE

LigandName: ALPHA-L-FUCOSE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.164156 kDa

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Component #8: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #9: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #10: ligand, BETA-D-GALACTOSE

LigandName: BETA-D-GALACTOSEGalactose / Number of Copies: 4 / 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.: 7 mg/ml
Buffer solution: Detergent removed with Biobeads prior to grid freezing
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 % / Details: Blot force 0 Blot time 5 sec.

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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: 1.885 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4039

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 236179
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

6dcq

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