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- EMDB-7621: Cryo-EM structure at 4.0 A resolution of vaccine-elicited antibod... -

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Basic information

Entry
Database: EMDB / ID: 7621
TitleCryo-EM structure at 4.0 A resolution of vaccine-elicited antibody vFP7.04 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122
Map dataMap from RELION postprocess using tight mask
SamplevFP7.04-BG505 DS-SOSIP-VRC03-PGT122:
PGT122 / VRC03 / Glycoprotein / vFP7.04 / (Envelope glycoprotein ...) x 2 / vFP7.04 Heavy chain / vFP7.04 light chain / PGT122 heavy Chain / PGT122 Light chain / VRC03 Heavy chain ...PGT122 / VRC03 / Glycoprotein / vFP7.04 / (Envelope glycoprotein ...) x 2 / vFP7.04 Heavy chain / vFP7.04 light chain / PGT122 heavy Chain / PGT122 Light chain / VRC03 Heavy chain / VRC03 light chain / (ligand) x 3
Function / homologyGp120 core superfamily / Envelope glycoprotein Gp160 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Envelope glycoprotein GP120 / Retroviral envelope protein / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization ...Gp120 core superfamily / Envelope glycoprotein Gp160 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Envelope glycoprotein GP120 / Retroviral envelope protein / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization / host cell endosome membrane / 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 / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Function and homology information
SourceHomo sapiens (human) / Human immunodeficiency virus 1 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsAcharya P / Carragher B / Potter CS / Kwong PD
CitationJournal: PLoS Pathog. / Year: 2018
Title: Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV.
Authors: Adam S Dingens / Priyamvada Acharya / Hugh K Haddox / Reda Rawi / Kai Xu / Gwo-Yu Chuang / Hui Wei / Baoshan Zhang / John R Mascola / Bridget Carragher / Clinton S Potter / Julie Overbaugh / Peter D Kwong / Jesse D Bloom
Validation ReportPDB-ID: 6cue

SummaryFull reportAbout validation report
DateDeposition: Mar 26, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Jul 11, 2018 / Last update: Oct 3, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6cue
  • Surface level: 1.04
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6cue
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7621.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.1 Å/pix.
= 422.4 Å
384 pix
1.1 Å/pix.
= 422.4 Å
384 pix
1.1 Å/pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour Level:1.04 (by author), 1.04 (movie #1):
Minimum - Maximum-2.3151062 - 5.5166054
Average (Standard dev.)0.0153290685 (0.14115492)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin0.00.00.0
Limit383.0383.0383.0
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z422.400422.400422.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-2.3155.5170.015

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Supplemental data

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Sample components

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Entire vFP7.04-BG505 DS-SOSIP-VRC03-PGT122

EntireName: vFP7.04-BG505 DS-SOSIP-VRC03-PGT122 / Number of components: 16

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Component #1: protein, vFP7.04-BG505 DS-SOSIP-VRC03-PGT122

ProteinName: vFP7.04-BG505 DS-SOSIP-VRC03-PGT122 / Recombinant expression: No

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Component #2: protein, PGT122

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

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Component #3: protein, VRC03

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

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Component #4: protein, Glycoprotein

ProteinName: Glycoprotein / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, vFP7.04

ProteinName: vFP7.04 / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, Envelope glycoprotein gp120

ProteinName: Envelope glycoprotein gp120 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 52.986969 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, Envelope glycoprotein gp41

ProteinName: Envelope glycoprotein gp41 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 17.162525 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: protein, vFP7.04 Heavy chain

ProteinName: vFP7.04 Heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 13.152787 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: protein, vFP7.04 light chain

ProteinName: vFP7.04 light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 12.256805 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #10: protein, PGT122 heavy Chain

ProteinName: PGT122 heavy Chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 14.838731 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #11: protein, PGT122 Light chain

ProteinName: PGT122 Light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 11.591728 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #12: protein, VRC03 Heavy chain

ProteinName: VRC03 Heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 14.6395 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #13: protein, VRC03 light chain

ProteinName: VRC03 light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 11.386774 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #14: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 81 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #15: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #16: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 15 / 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.: 0.5 mg/ml / pH: 7
VitrificationInstrument: OTHER / Cryogen name: ETHANE
Details: The value given for _emd_vitrification.instrument is SPOTITON. This is not in a list of allowed values set(['LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', 'FEI VITROBOT MARK II', 'HOMEMADE PLUNGER', 'REICHERT-JUNG PLUNGER', 'FEI VITROBOT MARK I', 'LEICA KF80', 'FEI VITROBOT MARK III', 'LEICA EM GP', 'OTHER', 'FEI VITROBOT MARK IV']) so OTHER is written into the XML file.

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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: 53.11 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000.0 X (calibrated) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 978

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 64580
3D reconstructionSoftware: cryoSPARC / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Correlation Coefficient / Refinement space: REAL / Overall bvalue: 142
Output model

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