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- EMDB-41838: Cryo-EM structure of vaccine-elicited CD4 binding site antibody D... -

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Basic information

Entry
Database: EMDB / ID: EMD-41838
TitleCryo-EM structure of vaccine-elicited CD4 binding site antibody DH1285 bound to partially open HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env
Map dataCryo-EM map of rhesus macaque vaccine elicited CD4 binding site antibody DH1285 Fab bound to partially open CH505M5chimer.6R.SOSIP.664v4.1 Env at all three CD4 binding sites.
Sample
  • Organelle or cellular component: A Complex of ectodomain of HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env with CD4 binding site antibody Dh1285 Fab in 1:3 ratio
KeywordsHIV-1 / CD4 binding site antibody / Vaccine elicited antibody / neutralizing antibody / IgG / Fab / DH1285 / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 6.78 Å
AuthorsThakur B / Stalls VD / Acharya P
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 A1145687 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 A1144371 United States
CitationJournal: To Be Published
Title: Cryo-EM map of rhesus macaque vaccine elicited CD4 binding site antibody DH1285 Fab bound to partially open CH505M5chimer.6R.SOSIP.664v4.1 Env at all three CD4 binding sites.
Authors: Thakur B / Stalls VD / Acharya P
History
DepositionSep 5, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41838.png

Downloads & links

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Map

FileDownload / File: emd_41838.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of rhesus macaque vaccine elicited CD4 binding site antibody DH1285 Fab bound to partially open CH505M5chimer.6R.SOSIP.664v4.1 Env at all three CD4 binding sites.
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.41713125 - 0.752537
Average (Standard dev.)0.00045557518 (±0.021077763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41838_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41838_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A Complex of ectodomain of HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env...

EntireName: A Complex of ectodomain of HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env with CD4 binding site antibody Dh1285 Fab in 1:3 ratio
Components
  • Organelle or cellular component: A Complex of ectodomain of HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env with CD4 binding site antibody Dh1285 Fab in 1:3 ratio

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Supramolecule #1: A Complex of ectodomain of HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env...

SupramoleculeName: A Complex of ectodomain of HIV-1 CH505TFchim.6R.SOSIP.664v4.1 Env with CD4 binding site antibody Dh1285 Fab in 1:3 ratio
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 300 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: LEICA EM CPC

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 14427340
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54659

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Atomic model buiding 1

RefinementSpace: REAL

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