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- EMDB-49242: AMC008 v4.2 SOSIP Env trimer in complex with one 3BC315 Fab -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-49242
TitleAMC008 v4.2 SOSIP Env trimer in complex with one 3BC315 Fab
Map dataAMC008 v4.2 SOSIP Env trimer in complex with one 3BC315 Fab
Sample
  • Complex: AMC008 v4.2 SOSIP Env trimer in complex with one 3BC315 Fab
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Env polyprotein
    • Protein or peptide: 3BC315 Fab heavy chain
    • Protein or peptide: 3BC315 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 Envelope glycoprotein / broadly neutralizing antibodies / IMMUNE SYSTEM
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell endosome / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Retroviral envelope protein / Retroviral envelope protein GP41-like
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsCui J / Du J / Lin Z / Pallesen J
Funding support United States, 2 items
OrganizationGrant numberCountry
Other privateW.W.Smith Charitable Trust #A2404 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI166916-01A1 United States
CitationJournal: Nat Commun / Year: 2026
Title: Conformational landscape of HIV-1 Env from closed to fully open.
Authors: Jiayan Cui / Zi Jie Lin / Sukanya Ghosh / Jianqiu Du / Roopak Sadeesh / David B Weiner / Jesper Pallesen /
Abstract: The molecular mechanism of HIV-1 entry into host cells is governed by dynamic conformational changes to its envelope glycoprotein (Env), which are triggered by the engagement of the host receptor CD4 ...The molecular mechanism of HIV-1 entry into host cells is governed by dynamic conformational changes to its envelope glycoprotein (Env), which are triggered by the engagement of the host receptor CD4 and coreceptors. Structural insights into these transitions have been advanced by cryo-electron tomography (cryo-ET), resolving Env structures in closed and multifarious open states within native membranes, and by cryo-electron microscopy (cryo-EM), which has provided atomic details of these states. In this study, we determine cryo-EM structures of soluble native-like Env in complex with antibody 3BC315, antibody b12, CD4, or a combination of 3BC315 and b12, capturing previously uncharacterized conformational states. Observing enhanced 3BC315 binding occupancy in the presence of b12, we investigate the cooperativity of these antibodies using mass photometry and neutralization assays. Integrating these states with the literature, we establish a classification framework for symmetric and asymmetric Env states, categorizing by their degree of openness and stepwise structural rearrangements. Our findings refine the mechanistic understanding of HIV-1 Env dynamics and provide a structural roadmap for targeting dynamic Env states to develop more potent vaccines and immunotherapies.
History
DepositionFeb 14, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49242.png

Downloads & links

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Map

FileDownload / File: emd_49242.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAMC008 v4.2 SOSIP Env trimer in complex with one 3BC315 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 421.6 Å		1.05 Å/pix.
x 400 pix.
= 421.6 Å		1.05 Å/pix.
x 400 pix.
= 421.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.1006682 - 2.010445
Average (Standard dev.)-0.0010573427 (±0.029775206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 421.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49242_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_49242_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 : AMC008 v4.2 SOSIP Env trimer in complex with one 3BC315 Fab

EntireName: AMC008 v4.2 SOSIP Env trimer in complex with one 3BC315 Fab
Components
  • Complex: AMC008 v4.2 SOSIP Env trimer in complex with one 3BC315 Fab
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Env polyprotein
    • Protein or peptide: 3BC315 Fab heavy chain
    • Protein or peptide: 3BC315 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: AMC008 v4.2 SOSIP Env trimer in complex with one 3BC315 Fab

SupramoleculeName: AMC008 v4.2 SOSIP Env trimer in complex with one 3BC315 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 55.212527 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDWTWILFLV AAATRVHSTE KLWVTVYYGV PVWKEATTTL FCASDAKAYD TEVRNVWATH ACVPTDPSPQ EVILENVTEN FNMWTNNMV EQMHEDIISL WDQSLKPCVK LTPLCVTLNC TNELKNTTKT NNSSWGGEMK NCSFNVTTSI RDKVQKEYAL F YKLDIVPI ...String:
MDWTWILFLV AAATRVHSTE KLWVTVYYGV PVWKEATTTL FCASDAKAYD TEVRNVWATH ACVPTDPSPQ EVILENVTEN FNMWTNNMV EQMHEDIISL WDQSLKPCVK LTPLCVTLNC TNELKNTTKT NNSSWGGEMK NCSFNVTTSI RDKVQKEYAL F YKLDIVPI DDDNNTSNYR LINCNTSVIT QACPKITFEP IPIQFCTPAG FAILKCNNKK FNGKGPCTNV STVQCTHGIR PV VSTQLLL NGSLAEEEVI IRSDNFTDNA KTIIVQLNES VVINCTRPNN NTRKSINIGP GRWFYTTGEI IGDIRQAHCN LSR TQWNNT LKQIAIKLRE QFENKTIVFN QSSGGDPEIV MHSFNCGGEF FYCNTTKLFN STWNDTDIRG NNTEGNDTIT IPCR IKQIV NMWQEVGKAM YAPPIRGQIR CSSNITGLLL TRDGGSESNT TEIFRPGGGD MRDNWRSELY KYKVVRIEPL GVAPT KCKR RVVQ

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Macromolecule #2: Env polyprotein

MacromoleculeName: Env polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.428814 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGTIGAMFL GFLGAAGSTM GAASMTLTVQ ARNLLSGIVQ QQNNLLRAPE AQQHLLQLTV WGIKQLQARV LAVERYLRDQ QLLGIWGCS GKLICCTSVP WNTSWSNKSL DKIWNNMTWM EWEREIDNYT SLIYTLLEES QNQQEKNEQE LLELD

UniProtKB: Env polyprotein

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Macromolecule #3: 3BC315 Fab heavy chain

MacromoleculeName: 3BC315 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.99924 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE MKDPGASVKV SCRASGYKFT DYYMHWVRQA PGQGLEWVGW VNTNGGFTKY GAKFQGRVTV TRDTSTNTVF LELSRLTFG DTAMYFCARP MRPVSHGIDY SGLFVFQFWG RGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
QVQLVQSGAE MKDPGASVKV SCRASGYKFT DYYMHWVRQA PGQGLEWVGW VNTNGGFTKY GAKFQGRVTV TRDTSTNTVF LELSRLTFG DTAMYFCARP MRPVSHGIDY SGLFVFQFWG RGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCD

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Macromolecule #4: 3BC315 Fab light chain

MacromoleculeName: 3BC315 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.009605 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPASV SASPGQSITI SCSGTRSDVG GYDFVSWYQQ HPGKVPKLII YEVTKRPSGI PQRFSGSKSG NTASLTISGL QADDEADYY CCSYANYDKL ILGGGTKLTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADGSPV K AGVETTKP ...String:
QSALTQPASV SASPGQSITI SCSGTRSDVG GYDFVSWYQQ HPGKVPKLII YEVTKRPSGI PQRFSGSKSG NTASLTISGL QADDEADYY CCSYANYDKL ILGGGTKLTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADGSPV K AGVETTKP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 36 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76962
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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