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- EMDB-70231: Ab1983 in complex with HIV-1 Env variant WIN332 -

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Basic information

Entry
Database: EMDB / ID: EMD-70231
TitleAb1983 in complex with HIV-1 Env variant WIN332
Map data
Sample
  • Complex: Antibody Ab1983 in complex with HIV-1 Env WIN332
    • Protein or peptide: Antibody Ab1983 Heavy Chain variable fragment
    • Protein or peptide: Ab1983 Light Chain variable fragment
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160 of Transmembrane protein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 Env / antibody / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsLin ZJ / Cui J / Du J / Relano-Rodriguez I / Escolano A / Pallesen J
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: To Be Published
Title: Rapid elicitation of a new class of 1 neutralizing N332-glycan independent V3-glycan antibodies against HIV-1 in nonhuman primates
Authors: Relano-Rodriguez I / Du J / Lin ZJ / Kerwin M / Tarquis-Medina M / Urbano E / Cui J / Watkins M / Zhao P / Habib R / Ghosh S / Park J / Boroughs C / Walsh AA / Melo MB / Shaw GM / Hahn BH / ...Authors: Relano-Rodriguez I / Du J / Lin ZJ / Kerwin M / Tarquis-Medina M / Urbano E / Cui J / Watkins M / Zhao P / Habib R / Ghosh S / Park J / Boroughs C / Walsh AA / Melo MB / Shaw GM / Hahn BH / Irvine DJ / Wells L / Weiner DB / Kulp DW / Veazey RS / Pallesen J / Escolano A
History
DepositionApr 16, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70231.png

Downloads & links

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Map

FileDownload / File: emd_70231.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 400 pix.
= 379. Å		0.95 Å/pix.
x 400 pix.
= 379. Å		0.95 Å/pix.
x 400 pix.
= 379. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9475 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.89724046 - 1.3104209
Average (Standard dev.)-0.000018778206 (±0.020692682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 379.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70231_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_70231_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 : Antibody Ab1983 in complex with HIV-1 Env WIN332

EntireName: Antibody Ab1983 in complex with HIV-1 Env WIN332
Components
  • Complex: Antibody Ab1983 in complex with HIV-1 Env WIN332
    • Protein or peptide: Antibody Ab1983 Heavy Chain variable fragment
    • Protein or peptide: Ab1983 Light Chain variable fragment
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160 of Transmembrane protein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Antibody Ab1983 in complex with HIV-1 Env WIN332

SupramoleculeName: Antibody Ab1983 in complex with HIV-1 Env WIN332 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Antibody Ab1983 Heavy Chain variable fragment

MacromoleculeName: Antibody Ab1983 Heavy Chain variable fragment / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.425882 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLQLQESGPG LVKPSETLSL TCAVSGGSIS SDYYYWSWIR QPPGKGLEWI GGIYSISEST NYNPSLKSRV TISKDTSKNQ FSLKLSSVT AADTAVYFCA RKDPYSSGWT PDYWGQGVLV TVSS

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Macromolecule #2: Ab1983 Light Chain variable fragment

MacromoleculeName: Ab1983 Light Chain variable fragment / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.127288 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPSSA SASLGASVTL TCTLSSGYSN YAVDWHQQRP GKGPQFVMRV GTGGIVGSKG DGIPDRFSGS GSGLNRYLTI KNIQEEDES DYHCGADHGT GSSFVWVFGG GTRLTVL

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Macromolecule #3: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.963402 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHEDIISLW DQSLKPCVK LTPLCVTLQC TNYAPNLLSN MRGELKQCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ...String:
NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHEDIISLW DQSLKPCVK LTPLCVTLQC TNYAPNLLSN MRGELKQCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SVSTVQCTHG IKPVVSTQLL LNGSLAEEEV II RSENITN NAKNILVQLN TPVQINCTRP NNNTVKSIRI GPGQAFYYFG DIIGDIRMAH CQVSKATWNE TLGKVVKQLR KHF GNNTII RFAQSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSIVLPCRI KQIINMWQRI GQAM YAPPI QGVIRCVSNI TGLILTRDGG STNSTTETFR PGGGDMRDNW RSELYKYKVV KIEPLGVAPT RCKRRVVGRR RRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #4: Envelope glycoprotein gp160 of Transmembrane protein gp41

MacromoleculeName: Envelope glycoprotein gp160 of Transmembrane protein gp41
type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.134324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVSLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 22 / 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: 7.6
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Software - details: Non-Uniform Refinement / Number images used: 218900
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6orn


Chain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9o8m:
Ab1983 in complex with HIV-1 Env variant WIN332

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