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- EMDB-47885: Cryo-EM local map of dimerized VRC36 Fabs -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-47885
TitleCryo-EM local map of dimerized VRC36 Fabs
Map dataLocal cryo-EM map of dimeric VRC36 Fabs
Sample
  • Complex: Cryo-EM local map of dimerized VRC36 Fabs
KeywordsHIV-1 / N-linked glycan / high mannose / neutralizing antibody / VIRAL PROTEIN / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsCheng J / Cale EM / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS ...Cheng J / Cale EM / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS / Becker JE / Tsybovsky Y / Li N / Shapiro L / Pierson TC / Doria-Rose NA / Zhou T / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM local map of dimerized VRC36 Fabs
Authors: Cheng J / Zhou T / Kwong PD
History
DepositionNov 12, 2024-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47885.png

Downloads & links

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Map

FileDownload / File: emd_47885.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal cryo-EM map of dimeric VRC36 Fabs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0020094954 - 2.2644262
Average (Standard dev.)0.00070004 (±0.018192835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of dimeric VRC36 Fabs

Fileemd_47885_half_map_1.map
AnnotationHalf map A of dimeric VRC36 Fabs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of dimeric VRC36 Fabs

Fileemd_47885_half_map_2.map
AnnotationHalf map B of dimeric VRC36 Fabs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM local map of dimerized VRC36 Fabs

EntireName: Cryo-EM local map of dimerized VRC36 Fabs
Components
  • Complex: Cryo-EM local map of dimerized VRC36 Fabs

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Supramolecule #1: Cryo-EM local map of dimerized VRC36 Fabs

SupramoleculeName: Cryo-EM local map of dimerized VRC36 Fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3ve0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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