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- EMDB-5921: Negative stain reconstruction of PGT151 Fab in complex with the s... -

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Basic information

Entry
Database: EMDB / ID: EMD-5921
TitleNegative stain reconstruction of PGT151 Fab in complex with the soluble Env trimer BG505 SOSIP
Map dataReconstruction of BG505 SOSIP trimer in complex with PGT151 Fab
Sample
  • Sample: Fab fragment of HIV-1 Env antibody PGT151 in complex with soluble Env trimer BG505 SOSIP
  • Protein or peptide: HIV-1 Envelope glycoprotein
  • Protein or peptide: PGT151 Antibody Fab fragment
KeywordsHIV-1 envelope glycoprotein trimer / broadly neutralizing antibody / PGT151
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 Å
AuthorsLee JH / Blattner C / Wilson IA / Ward AB
CitationJournal: IMMUNITY / Year: 2014
Title: Structural Delineation of a Quaternary, Cleavage-Dependent Epitope at the gp41-gp120 Interface on Intact HIV-1 Env Trimers.
Authors: Blattner C / Lee JH / Sliepen K / Derking R / Falkowska E / de la Pena AT / Cupo A / Julien JP / van Gils M / Lee PS / Peng W / Paulson JC / Poignard P / Burton DR / Moore JP / Sanders RW / Wilson IA / Ward AB
History
DepositionMar 10, 2014-
Header (metadata) releaseApr 16, 2014-
Map releaseMay 7, 2014-
UpdateMay 28, 2014-
Current statusMay 28, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.67
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.67
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_5921.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of BG505 SOSIP trimer in complex with PGT151 Fab
Voxel sizeX=Y=Z: 2.05 Å
Density
Contour LevelBy AUTHOR: 2.67 / Movie #1: 2.67
Minimum - Maximum-2.68402052 - 12.491912839999999
Average (Standard dev.)0.0 (±0.77874744)
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
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-39-39-39
NC/NR/NS160160160
D min/max/mean-2.68412.492-0.000

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Supplemental data

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Sample components

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Entire : Fab fragment of HIV-1 Env antibody PGT151 in complex with soluble...

EntireName: Fab fragment of HIV-1 Env antibody PGT151 in complex with soluble Env trimer BG505 SOSIP
Components
  • Sample: Fab fragment of HIV-1 Env antibody PGT151 in complex with soluble Env trimer BG505 SOSIP
  • Protein or peptide: HIV-1 Envelope glycoprotein
  • Protein or peptide: PGT151 Antibody Fab fragment

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Supramolecule #1000: Fab fragment of HIV-1 Env antibody PGT151 in complex with soluble...

SupramoleculeName: Fab fragment of HIV-1 Env antibody PGT151 in complex with soluble Env trimer BG505 SOSIP
type: sample / ID: 1000 / Oligomeric state: 2 Fabs bind one Env Trimer / Number unique components: 2
Molecular weightTheoretical: 520 KDa

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Macromolecule #1: HIV-1 Envelope glycoprotein

MacromoleculeName: HIV-1 Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: Env
Details: The SOSIP trimer was co-expressed with Furin. The soluble trimer contains stabilizing mutations
Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505 / synonym: HIV-1
Molecular weightTheoretical: 420 MDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Macromolecule #2: PGT151 Antibody Fab fragment

MacromoleculeName: PGT151 Antibody Fab fragment / type: protein_or_peptide / ID: 2 / Name.synonym: PGT151 Fab / Details: Heavy chain-light chain dimer of PGT151 Fab / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: B-cells
Molecular weightTheoretical: 49.5 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: 50 mM Tris, 150 mM NaCl
StainingType: NEGATIVE
Details: Sample was applied to grid briefly, then stained for 30-45 seconds with 2% uranyl formate.
GridDetails: plasma-cleaned carbon coated 400 mesh grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
TemperatureMin: 293 K / Max: 293 K
Alignment procedureLegacy - Astigmatism: Objective astigmatism corrected at 52,000 times magnification
DetailsData collected in 5 degree tilt increments
DateMar 20, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 0.205 µm / Number real images: 482 / Average electron dose: 30 e/Å2
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 45

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Image processing

CTF correctionDetails: not corrected
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: OTHER / Software - Name: XMIPP, EMAN, EMAN2, Sparx
Details: Reference free 2D class averages generated using XMIPP and Sparx to sort particles. EMAN2 was used to generate an initial model followed by projection matching carried out in EMAN.
Number images used: 12364

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Atomic model buiding 1

Initial modelPDB ID:

3j5m


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: E / Chain - #3 - Chain ID: F / Chain - #4 - Chain ID: I / Chain - #5 - Chain ID: J
SoftwareName: Chimera
DetailsThe PGV04 Fabs in the structure were removed prior to fitting.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

4nug


Chain - #0 - Chain ID: H / Chain - #1 - Chain ID: L
SoftwareName: Chimera
DetailsTwo Fabs were fit independently of each other into the EM reconstruction.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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