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- EMDB-49239: AMC008 v4.2 SOSIP Env trimer in complex with b12 Fab -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49239
TitleAMC008 v4.2 SOSIP Env trimer in complex with b12 Fab
Map dataAMC008 v4.2 SOSIP Env trimer in complex with b12 Fab
Sample
  • Complex: AMC008 v4.2 SOSIP Env trimer in complex with b12 Fab
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: b12 Fab heavy chain
    • Protein or peptide: b12 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


host cell endosome / clathrin-dependent endocytosis of virus by host cell / 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: 3.88 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: To Be Published
Title: Conformational Landscape of HIV-1 Env from Closed to Fully Open
Authors: Cui J / Du J / Lin Z / Pallesen J
History
DepositionFeb 14, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49239.png

Downloads & links

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Map

FileDownload / File: emd_49239.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 b12 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.4208304 - 2.0341809
Average (Standard dev.)-0.0014025155 (±0.029686749)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49239_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49239_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 b12 Fab

EntireName: AMC008 v4.2 SOSIP Env trimer in complex with b12 Fab
Components
  • Complex: AMC008 v4.2 SOSIP Env trimer in complex with b12 Fab
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: b12 Fab heavy chain
    • Protein or peptide: b12 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 b12 Fab

SupramoleculeName: AMC008 v4.2 SOSIP Env trimer in complex with b12 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: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / 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: b12 Fab heavy chain

MacromoleculeName: b12 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.910846 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCQASGYRFS NFVIHWVRQA PGQRFEWMGW INPYNGNKEF SAKFQDRVTF TADTSANTAY MELRSLRSA DTAVYYCARV GPYSWDDSPQ DNYYMDVWGK GTTVIVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QVQLVQSGAE VKKPGASVKV SCQASGYRFS NFVIHWVRQA PGQRFEWMGW INPYNGNKEF SAKFQDRVTF TADTSANTAY MELRSLRSA DTAVYYCARV GPYSWDDSPQ DNYYMDVWGK GTTVIVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKAEPK SC

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Macromolecule #4: b12 Fab light chain

MacromoleculeName: b12 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.707354 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT FSCRSSHSIR SRRVAWYQHK PGQAPRLVIH GVSNRASGIS DRFSGSGSGT DFTLTITRVE PEDFALYYC QVYGASSYTF GQGTKLERKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVLTQSPGT LSLSPGERAT FSCRSSHSIR SRRVAWYQHK PGQAPRLVIH GVSNRASGIS DRFSGSGSGT DFTLTITRVE PEDFALYYC QVYGASSYTF GQGTKLERKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLRSPVTK SFNRGEC

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Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 14 / Number of copies: 15 / 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: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 151769
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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