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- EMDB-8643: BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV a... -

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Basic information

Entry
Database: EMDB / ID: 8643
TitleBG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibodies 3BNC117 and PGT145
Map dataBG505 SOSIP.664 trimer in complex with 3BNC117 and PGT145 Fabs
SampleBG505 SOSIP.664 trimer in complex with PGT145 and 3BNC117 Fabs
  • gp120Envelope glycoprotein GP120
  • gp41
  • (3BNC117 antibody, ...) x 2
  • (PGT145 antibody, ...) x 2
  • (ligand) x 3
Function/homologypositive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization / Envelope glycoprotein Gp160 / Retroviral envelope protein GP41-like / Retroviral envelope protein / Gp120 core superfamily / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / host cell endosome membrane ...positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization / Envelope glycoprotein Gp160 / Retroviral envelope protein GP41-like / Retroviral envelope protein / Gp120 core superfamily / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / host cell endosome membrane / evasion or tolerance by virus of host immune response / Envelope glycoprotein GP120 / 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
Function and homology information
SourceHuman immunodeficiency virus 1 / HIV / virus
MethodCryo EM / single particle reconstruction / 4.3 Å resolution
AuthorsLee JH / Nieusma T / Ward AB
CitationJournal: Immunity / Year: 2017
Title: A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic β-Hairpin Structure.
Authors: Jeong Hyun Lee / Raiees Andrabi / Ching-Yao Su / Anila Yasmeen / Jean-Philippe Julien / Leopold Kong / Nicholas C Wu / Ryan McBride / Devin Sok / Matthias Pauthner / Christopher A Cottrell / Travis Nieusma / Claudia Blattner / James C Paulson / Per Johan Klasse / Ian A Wilson / Dennis R Burton / Andrew B Ward
Abstract: Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the ...Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the surface HIV envelope (Env) trimer. Using cryo-electron microscopy, we solved the atomic structure of an apex bnAb, PGT145, in complex with Env. We showed that the long anionic HCDR3 of PGT145 penetrated between glycans at the trimer 3-fold axis, to contact peptide residues from all three Env protomers, and thus explains its highly trimer-specific nature. Somatic hypermutation in the other CDRs of PGT145 were crucially involved in stabilizing the structure of the HCDR3, similar to bovine antibodies, to aid in recognition of a cluster of conserved basic residues hypothesized to facilitate trimer disassembly during viral entry. Overall, the findings exemplify the creative solutions that the human immune system can evolve to recognize a conserved motif buried under a canopy of glycans.
Copyright: 2017 The Author(s). Published by Elsevier Inc. All rights reserved.
Validation ReportPDB-ID: 5v8l

SummaryFull reportAbout validation report
DateDeposition: Mar 22, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5v8l
  • Surface level: 0.03
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5v8l
  • Imaged by Jmol
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3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_8643.map.gz (map file in CCP4 format, 95552 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
1.31 Å/pix.
= 377.28 Å
288 pix
1.31 Å/pix.
= 377.28 Å
288 pix
1.31 Å/pix.
= 377.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.31 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.07770067 - 0.17263675
Average (Standard dev.)1.4130349E-6 (0.005214065)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin000
Limit287287287
Spacing288288288
CellA=B=C: 377.27997 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z377.280377.280377.280
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0780.1730.000

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Supplemental data

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Sample components

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Entire BG505 SOSIP.664 trimer in complex with PGT145 and 3BNC117 Fabs

EntireName: BG505 SOSIP.664 trimer in complex with PGT145 and 3BNC117 Fabs
Number of components: 10
MassTheoretical: 560 kDa

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Component #1: protein, BG505 SOSIP.664 trimer in complex with PGT145 and 3BNC11...

ProteinName: BG505 SOSIP.664 trimer in complex with PGT145 and 3BNC117 Fabs
Recombinant expression: No
MassTheoretical: 560 kDa
SourceSpecies: Human immunodeficiency virus 1 / Strain: BG505
Source (engineered)Expression System: Homo sapiens / Cell of expression system: HEK293F

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Component #2: protein, gp120

ProteinName: gp120Envelope glycoprotein GP120 / Recombinant expression: No
MassTheoretical: 54.064277 kDa
SourceSpecies:
Source (engineered)Expression System: Human immunodeficiency virus 1 / Strain: BG505

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Component #3: protein, gp41

ProteinName: gp41 / Recombinant expression: No
MassTheoretical: 17.146482 kDa
SourceSpecies:
Source (engineered)Expression System: Human immunodeficiency virus 1 / Strain: BG505

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Component #4: protein, 3BNC117 antibody, heavy chain

ProteinName: 3BNC117 antibody, heavy chain / Recombinant expression: No
MassTheoretical: 24.656484 kDa
SourceSpecies:
Source (engineered)Expression System: Homo sapiens

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Component #5: protein, PGT145 antibody, heavy chain

ProteinName: PGT145 antibody, heavy chain / Recombinant expression: No
MassTheoretical: 28.793164 kDa
SourceSpecies:
Source (engineered)Expression System: Homo sapiens

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Component #6: protein, 3BNC117 antibody, light chain

ProteinName: 3BNC117 antibody, light chain / Recombinant expression: No
MassTheoretical: 23.022658 kDa
SourceSpecies:
Source (engineered)Expression System: Homo sapiens

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Component #7: protein, PGT145 antibody, light chain

ProteinName: PGT145 antibody, light chain / Recombinant expression: No
MassTheoretical: 23.95375 kDa
SourceSpecies:
Source (engineered)Expression System: Homo sapiens

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Component #8: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 106 / Recombinant expression: No
MassTheoretical: 0.221208 kDa
SourceSpecies:

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Component #9: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 0.180156 kDa
SourceSpecies:

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Component #10: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 36 / Recombinant expression: No
MassTheoretical: 0.180156 kDa
SourceSpecies:

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: Cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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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: 32 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionDetails: Electron dose per image indicates total dose

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 65060
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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