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- EMDB-21449: CON-S ch.DS.SOSIP HIV trimer bound to DH842 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-21449
TitleCON-S ch.DS.SOSIP HIV trimer bound to DH842 Fab
Map data
SampleCON-S ch.DS.SOSIP in complex with DH842 Fab
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 17 Å
AuthorsCai F / Chen WH / Wu W / Jones J / Misook C / Gohain N / Shen X / LaBranche C / Eaton A / Sutherland L ...Cai F / Chen WH / Wu W / Jones J / Misook C / Gohain N / Shen X / LaBranche C / Eaton A / Sutherland L / Hernandez G / Nelson RW / Scearce R / Seaman M / Moody MA / Santra S / Wiehe KJ / Tomaras GD / Wagh K / Korber B / Bonsignori M / Montefiori DC / Haynes BF / de Val N / Joyce GM / Saunders KO
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI120801 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100645 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001 United States
CitationJournal: To Be Published
Title: HIV-1 vaccination elicits structurally and genetically-convergent neutralizing antibodies in non-human primates
Authors: Cai F / Chen WH / Wu W / Jones J / Misook C / Gohain N / Shen X / LaBranche C / Eaton A / Sutherland L / Hernandez G / Nelson RW / Scearce R / Seaman M / Moody MA / Santra S / Wiehe KJ / ...Authors: Cai F / Chen WH / Wu W / Jones J / Misook C / Gohain N / Shen X / LaBranche C / Eaton A / Sutherland L / Hernandez G / Nelson RW / Scearce R / Seaman M / Moody MA / Santra S / Wiehe KJ / Tomaras GD / Wagh K / Korber B / Bonsignori M / Montefiori DC / Haynes BF / de Val N / Joyce GM / Saunders KO
History
DepositionFeb 24, 2020-
Header (metadata) releaseMar 4, 2020-
Map releaseMar 3, 2021-
UpdateMar 3, 2021-
Current statusMar 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.033
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.033
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21449.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.19 Å/pix.
x 160 pix.
= 350.4 Å
2.19 Å/pix.
x 160 pix.
= 350.4 Å
2.19 Å/pix.
x 160 pix.
= 350.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.19 Å
Density
Contour LevelBy AUTHOR: 0.033 / Movie #1: 0.033
Minimum - Maximum-0.07375774 - 0.1523277
Average (Standard dev.)0.00013209872 (±0.0076074265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 350.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.192.192.19
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z350.400350.400350.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0740.1520.000

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Supplemental data

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Sample components

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Entire CON-S ch.DS.SOSIP in complex with DH842 Fab

EntireName: CON-S ch.DS.SOSIP in complex with DH842 Fab / Number of components: 1

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Component #1: protein, CON-S ch.DS.SOSIP in complex with DH842 Fab

ProteinName: CON-S ch.DS.SOSIP in complex with DH842 Fab / Recombinant expression: No
MassExperimental: 50 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK 293F cells

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: negative staining
Sample solutionSpecimen conc.: 0.01 mg/mL / pH: 8
Staininggrids were glow discharged and using 0.7% UF they were stained.
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 40 e/Å2 / Illumination mode: OTHER
LensMagnification: 100000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 1100.0 nm
Specimen HolderModel: OTHER
CameraDetector: FEI EAGLE (2k x 2k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 7568
3D reconstructionSoftware: RELION / Resolution: 17 Å / Resolution method: FSC 0.5 CUT-OFF

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