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- EMDB-74063: BG505 MD39.3 Env gp151 MPER nanodisc in complex with DH511.2, BG1... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-74063
TitleBG505 MD39.3 Env gp151 MPER nanodisc in complex with DH511.2, BG18, and VRC01 Fabs
Map datasharpened map
Sample
  • Complex: BG505 MD39.3 Env gp151 MPER nanodisc in complex with DH511.2, BG18 and VRC01 Fabs
KeywordsHIV-1 / broadly neutralizing antibody / bnAb / MPER / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsRantalainen R / Ozorowski G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Structural basis of membrane engagement and polyreactivity control in HIV-1 MPER broadly neutralizing antibodies
Authors: Cho S / Rantalainen K
History
DepositionNov 25, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74063.png

Downloads & links

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Map

FileDownload / File: emd_74063.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 448 pix.
= 430.801 Å		0.96 Å/pix.
x 448 pix.
= 430.801 Å		0.96 Å/pix.
x 448 pix.
= 430.801 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96161 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.10821022 - 0.25507748
Average (Standard dev.)0.00024234911 (±0.009652115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 430.8013 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74063_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_74063_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_74063_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BG505 MD39.3 Env gp151 MPER nanodisc in complex with DH511.2, BG1...

EntireName: BG505 MD39.3 Env gp151 MPER nanodisc in complex with DH511.2, BG18 and VRC01 Fabs
Components
  • Complex: BG505 MD39.3 Env gp151 MPER nanodisc in complex with DH511.2, BG18 and VRC01 Fabs

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Supramolecule #1: BG505 MD39.3 Env gp151 MPER nanodisc in complex with DH511.2, BG1...

SupramoleculeName: BG505 MD39.3 Env gp151 MPER nanodisc in complex with DH511.2, BG18 and VRC01 Fabs
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human immunodeficiency virus 1

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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

Concentration14.4 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMsodium chlorideNaCl
0.075 mMFos-choline-12
GridModel: Quantifoil R2/4 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cryosparc ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 23082
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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