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- EMDB-9166: Cryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 anti... -

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Basic information

Entry
Database: EMDB / ID: 9166
TitleCryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 antigen binding fragment
Map dataCryo-EM of BG505.SOSIP.664 in complex with BF520.1-Fab
SampleCryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664:
(Envelope Glycoprotein ...) x 2 / BF520.1 Fab variable region / (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
SourceHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4.8 Å resolution
AuthorsWilliams JA / Lee KK / Overbaugh J
CitationJournal: To Be Published
Title: Rapid development of an infant-derived HIV-1 broadly neutralizing antibody lineage
Authors: Simonich CA / Doepker L / Ralph D / Williams JA / Dhar A / Yaffe Z / Gentles L / Small CT / Oliver B / Vigdorovich V / Mangala Prasad V / Nduati R / Sather DN / Lee KK / Matsen FA / Overbaugh J
Validation ReportPDB-ID: 6mn7

SummaryFull reportAbout validation report
DateDeposition: Oct 1, 2018 / Header (metadata) release: Jan 9, 2019 / Map release: Mar 6, 2019 / Last update: Mar 6, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.102
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.102
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6mn7
  • Surface level: 0.102
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9166.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.2 Å/pix.
= 352. Å
160 pix
2.2 Å/pix.
= 352. Å
160 pix
2.2 Å/pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density
Contour Level:0.102 (by author), 0.102 (movie #1):
Minimum - Maximum-0.20188709 - 0.33509022
Average (Standard dev.)0.0013772685 (0.011176277)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin0.00.00.0
Limit159.0159.0159.0
Spacing160160160
CellA=B=C: 352.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.2020.3350.001

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Supplemental data

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Sample components

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Entire Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664

EntireName: Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664
Number of components: 7

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Component #1: protein, Cryo-EM structure of BF520.1 Fab in complex with BG505.S...

ProteinName: Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664
Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1

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Component #2: protein, Envelope Glycoprotein gp120

ProteinName: Envelope Glycoprotein gp120 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 53.278301 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Envelope Glycoprotein gp41

ProteinName: Envelope Glycoprotein gp41 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 17.146482 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, BF520.1 Fab variable region

ProteinName: BF520.1 Fab variable region / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 25.974941 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 111 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #6: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 30 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #7: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 51 / 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 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: 66 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 67174
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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