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- EMDB-8644: BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV a... -

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Basic information

Entry
Database: EMDB / ID: 8644
TitleBG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibody 3BNC117
SampleBG505 SOSIP.664 soluble Env trimer in complex with 3BNC117 Fab
SourceHomo sapiens / human
Map dataBG505 SOSIP.664 trimer in complex with 3BNC117 Fab
Methodsingle particle reconstruction, at 4.4 Å resolution
AuthorsLee JH / Ward AB
CitationImmunity, 2017, 46, 690-702

Immunity, 2017, 46, 690-702 Yorodumi Papers
A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic β-Hairpin Structure.
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

Validation ReportPDB-ID: 5v8m

SummaryFull reportAbout validation report
DateDeposition: Mar 22, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Jul 26, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5v8m
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5v8m
  • Imaged by Jmol
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Supplemental images

Downloads & links

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Map

Fileemd_8644.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.31 Å/pix.
= 335.36 Å
256 pix
1.31 Å/pix.
= 335.36 Å
256 pix
1.31 Å/pix.
= 335.36 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:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.050940588 - 0.11937846
Average (Standard dev.)8.067666E-5 (0.00554209)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 335.36 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z335.360335.360335.360
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0510.1190.000

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Supplemental data

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Sample components

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Entire BG505 SOSIP.664 soluble Env trimer in complex with 3BNC117 Fab

EntireName: BG505 SOSIP.664 soluble Env trimer in complex with 3BNC117 Fab
Number of components: 8
MassTheoretical: 510 kDa

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Component #1: protein, BG505 SOSIP.664 soluble Env trimer in complex with 3BNC1...

ProteinName: BG505 SOSIP.664 soluble Env trimer in complex with 3BNC117 Fab
Recombinant expression: No
MassTheoretical: 510 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Homo sapiens / human / Cell of expression system: HEK293F

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Component #2: protein, gp120

ProteinName: gp120 / Recombinant expression: No
MassTheoretical: 54.064277 kDa
Source (engineered)Expression System: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Strain: BG505

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Component #3: protein, gp41

ProteinName: gp41 / Recombinant expression: No
MassTheoretical: 17.146482 kDa
Source (engineered)Expression System: Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
Strain: BG505

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

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

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Component #5: protein, antibody 3BNC117, light chain

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

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

LigandName: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 99 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #7: ligand, BETA-D-MANNOSE

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

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Component #8: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 39 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
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 processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 22625
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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