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- EMDB-2753: PGT124 in complex with BG505 SOSIP.664 Env trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-2753
TitlePGT124 in complex with BG505 SOSIP.664 Env trimer
Map dataReconstruction of PGT124 Fab in complex with BG505 SOSIP.664 Env trimer
Sample
  • Sample: Fab fragment of PGT124 monoclonal antibody isolated from human patient in Protocol G cohort. SOSIP.664 soluble Env trimer from HIV-1 virus infecting infant (BG505).
  • Protein or peptide: Fragment antigen binding
  • Protein or peptide: BG505 SOSIP.664 gp140
KeywordsPGT124 / HIV-1 / envelope glycoprotein trimer / SOSIP / broadly neutralizing antibody
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 17.8 Å
AuthorsGarces F / Sok D / Kong L / McBride R / Kim HJ / Saye-Francisco KF / Julien J-P / Hua Y / Cupo A / Moore JP ...Garces F / Sok D / Kong L / McBride R / Kim HJ / Saye-Francisco KF / Julien J-P / Hua Y / Cupo A / Moore JP / Ward AB / Paulson JC / Burton DR / Wilson IA
CitationJournal: Cell / Year: 2014
Title: Structural evolution of glycan recognition by a family of potent HIV antibodies.
Authors: Fernando Garces / Devin Sok / Leopold Kong / Ryan McBride / Helen J Kim / Karen F Saye-Francisco / Jean-Philippe Julien / Yuanzi Hua / Albert Cupo / John P Moore / James C Paulson / Andrew B ...Authors: Fernando Garces / Devin Sok / Leopold Kong / Ryan McBride / Helen J Kim / Karen F Saye-Francisco / Jean-Philippe Julien / Yuanzi Hua / Albert Cupo / John P Moore / James C Paulson / Andrew B Ward / Dennis R Burton / Ian A Wilson /
Abstract: The HIV envelope glycoprotein (Env) is densely covered with self-glycans that should help shield it from recognition by the human immune system. Here, we examine how a particularly potent family of ...The HIV envelope glycoprotein (Env) is densely covered with self-glycans that should help shield it from recognition by the human immune system. Here, we examine how a particularly potent family of broadly neutralizing antibodies (Abs) has evolved common and distinct structural features to counter the glycan shield and interact with both glycan and protein components of HIV Env. The inferred germline antibody already harbors potential binding pockets for a glycan and a short protein segment. Affinity maturation then leads to divergent evolutionary branches that either focus on a single glycan and protein segment (e.g., Ab PGT124) or engage multiple glycans (e.g., Abs PGT121-123). Furthermore, other surrounding glycans are avoided by selecting an appropriate initial antibody shape that prevents steric hindrance. Such molecular recognition lessons are important for engineering proteins that can recognize or accommodate glycans.
History
DepositionAug 11, 2014-
Header (metadata) releaseAug 27, 2014-
Map releaseApr 15, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2753-PGT...

Downloads & links

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Map

FileDownload / File: emd_2753.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of PGT124 Fab in complex with BG505 SOSIP.664 Env trimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.8 / Movie #1: 2.8
Minimum - Maximum-3.73774481 - 11.876063350000001
Average (Standard dev.)0.0 (±0.90726209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-39-39-39
Dimensions160160160
Spacing160160160
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-39-39-39
NC/NR/NS160160160
D min/max/mean-3.73811.8760.000

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Supplemental data

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Sample components

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Entire : Fab fragment of PGT124 monoclonal antibody isolated from human pa...

EntireName: Fab fragment of PGT124 monoclonal antibody isolated from human patient in Protocol G cohort. SOSIP.664 soluble Env trimer from HIV-1 virus infecting infant (BG505).
Components
  • Sample: Fab fragment of PGT124 monoclonal antibody isolated from human patient in Protocol G cohort. SOSIP.664 soluble Env trimer from HIV-1 virus infecting infant (BG505).
  • Protein or peptide: Fragment antigen binding
  • Protein or peptide: BG505 SOSIP.664 gp140

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Supramolecule #1000: Fab fragment of PGT124 monoclonal antibody isolated from human pa...

SupramoleculeName: Fab fragment of PGT124 monoclonal antibody isolated from human patient in Protocol G cohort. SOSIP.664 soluble Env trimer from HIV-1 virus infecting infant (BG505).
type: sample / ID: 1000 / Oligomeric state: One SOSIP trimer binds 3 PGT124 Fabs / Number unique components: 2
Molecular weightExperimental: 750 KDa / Theoretical: 750 KDa

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Macromolecule #1: Fragment antigen binding

MacromoleculeName: Fragment antigen binding / type: protein_or_peptide / ID: 1 / Name.synonym: Fab / Details: Fab consists of heavy and light chain / Number of copies: 3 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Molecular weightExperimental: 50 KDa / Theoretical: 50 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Macromolecule #2: BG505 SOSIP.664 gp140

MacromoleculeName: BG505 SOSIP.664 gp140 / type: protein_or_peptide / ID: 2 / Name.synonym: SOSIP trimer / Details: SOSIP trimer consists of 3 gp140 subunits / Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Molecular weightExperimental: 600 KDa / Theoretical: 600 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.4 / Details: TBS
StainingType: NEGATIVE / Details: 2% uranyl formate
GridDetails: 400 copper mesh with thin carbon support glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
DateJul 23, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 2.05 µm / Number real images: 594 / Average electron dose: 25 e/Å2
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000
Sample stageSpecimen holder: room temp / Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 55
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected with DoG Picker, an automatic selection program
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.8 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 12245
Final two d classificationNumber classes: 120

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