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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 dataCON-S ch.DS.SOSIP HIV trimer bound to DH842 Fab
Sample
  • Complex: CON-S ch.DS.SOSIP in complex with DH842 Fab
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21449.png

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)
AnnotationCON-S ch.DS.SOSIP HIV trimer bound to DH842 Fab
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

Histogram

Histogram (log scale)
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
Components
  • Complex: CON-S ch.DS.SOSIP in complex with DH842 Fab

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Supramolecule #1: CON-S ch.DS.SOSIP in complex with DH842 Fab

SupramoleculeName: CON-S ch.DS.SOSIP in complex with DH842 Fab / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293F cells
Molecular weightExperimental: 50 KDa

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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: 8
Component:
ConcentrationFormulaName
10.0 mMTRIStris
500.0 mMNaClsodium Chloride
StainingType: NEGATIVE / Material: Uranyl Formate
Details: grids were glow discharged and using 0.7% UF they were stained.
GridModel: C-flat / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: FEI EAGLE (2k x 2k) / Number grids imaged: 1 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.1 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: OTHER

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Image processing

Particle selectionNumber selected: 8758
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 7568
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 4 / Software - Name: RELION

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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