[English] 日本語
Yorodumi
- EMDB-72986: AM12-352 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72986
TitleAM12-352 Fab in complex with HIV-1 Env 5MUT-3fill SOSIP
Map data
Sample
  • Complex: HIV-1 Envelope protein
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: AM12-352 Fab heavy chain
    • Protein or peptide: AM12-352 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / Envelope protein / Vaccine / Immunogen / Antibody / bNAb / Viral Protein / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / membrane / identical protein binding
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 speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsGristick HB / Gavor E / Bjorkman PJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HIVRAD P01 AI100148 United States
Bill & Melinda Gates FoundationINV-070086 United States
CitationJournal: Science / Year: 2026
Title: Induction of broadly neutralizing HIV antibodies by a two-step mechanism informs vaccine design.
Authors: Ashwin N Skelly / Harry B Gristick / Hui Li / Edem Gavor / Andrew J Connell / Edward F Kreider / Lorie Marchitto / Michael P Hogarty / Maddy L Newby / Joel D Allen / Weimin Liu / Anthony P ...Authors: Ashwin N Skelly / Harry B Gristick / Hui Li / Edem Gavor / Andrew J Connell / Edward F Kreider / Lorie Marchitto / Michael P Hogarty / Maddy L Newby / Joel D Allen / Weimin Liu / Anthony P West / Kasirajan Ayyanathan / Mary S Campion / Kaitlyn Winters / Colette G Gordon / Rebecca A Osbaldeston / Macy J Akeley / Emily Lewis / Yingying Li / Ajay Singh / Kendra Cruickshank / Younghoon Park / Chengyan Zhao / Xuduo Li / Khaled Amereh / Elizabeth Van Itallie / John W Carey / Amie Albertus / Andrew T DeLaitsch / Jennifer R Keeffe / Melinda G Lituchy / Agnes A Walsh / Daniel J Morris / Rumi Habib / Frederic Bibollet-Ruche / Nitesh Mishra / Gabriel Avillion / Nicholas S Koranda / Samantha J Plante / Christian L Martella / Jinery Lora / Eric J D Wang / Mark G Lewis / Malcolm A Martin / Michel C Nussenzweig / Michael S Seaman / Darrell J Irvine / Kevin J Wiehe / Barton F Haynes / Kshitij Wagh / Bette Korber / Raiees Andrabi / Max Crispin / Drew Weissman / Pamela J Bjorkman / Beatrice H Hahn / George M Shaw /
Abstract: A major obstacle confronting HIV-1 vaccine and cure research is the lack of an outbred animal model for rapid and consistent induction of broadly neutralizing antibodies (bNAbs). We designed an ...A major obstacle confronting HIV-1 vaccine and cure research is the lack of an outbred animal model for rapid and consistent induction of broadly neutralizing antibodies (bNAbs). We designed an epitope-focused simian-human immunodeficiency virus (SHIV.5MUT) that elicited broad and potent V3-glycan-targeted antibodies within a year of infection in 14 of 22 macaques compared with 0 of 14 control animals. SHIV.5MUT elicited bNAbs by a two-step mechanism, inducing an initial wave of V1-directed antibodies that selected for Envs with shortened, hypoglycosylated V1 loops, which in turn primed V3-glycan bNAb precursors. Rhesus bNAbs were immunogenetically and structurally diverse, closely resembling human V3-glycan bNAbs. Env-bNAb coevolution revealed a diverse repertoire of bNAb precursors and the Env variants that matured them, yielding a molecular blueprint for vaccine design.
History
DepositionOct 1, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72986.png

Downloads & links

-
Map

FileDownload / File: emd_72986.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0255
Minimum - Maximum-0.11006566 - 0.22638242
Average (Standard dev.)0.00029842893 (±0.007611684)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 313.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_72986_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_72986_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HIV-1 Envelope protein

EntireName: HIV-1 Envelope protein
Components
  • Complex: HIV-1 Envelope protein
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: AM12-352 Fab heavy chain
    • Protein or peptide: AM12-352 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: HIV-1 Envelope protein

SupramoleculeName: HIV-1 Envelope protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Stabilized, soluble form of heterotrimeric membrane glycoprotein comprising gp120 and gp41 subunits
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 330 KDa

-
Macromolecule #1: Transmembrane protein gp41

MacromoleculeName: Transmembrane protein gp41 / type: protein_or_peptide / ID: 1 / 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

-
Macromolecule #2: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.927047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHEDIISLW DQSLKPCVK LTPLCVTLQC TNYTPNLTND MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA ...String:
NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHEDIISLW DQSLKPCVK LTPLCVTLQC TNYTPNLTND MRGELKNCSF NMTTELRDKK QKVYSLFYRL DVVQINENQG NRSNNSNKEY R LINCNTSA CTQACPKVSF EPIPIHYCAP AGFAILKCKN KTFNGTGPCP NVSTVQCTHG IKPVVSTQLL LNGSLAEEEV II RSENITN NAKNILVQLN TPVQINCTRP NNNTVKSIRI GPGQAFYYTG DIIGDIRQAH CNVSKATWNE TLGNVSKQLR KHF GNNTII RFAQSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQCM YAPPI QGVIRCVSNI TGLILTRDGG STNSTTETFR PGGGDMRDNW RSELYKYKVV KIEPLGVAPT RCKRRVVGRR RRRR

UniProtKB: Envelope glycoprotein gp160

-
Macromolecule #3: AM12-352 Fab heavy chain

MacromoleculeName: AM12-352 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 14.45413 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLQQWGEGR VQPSETLSLP CAVYGGSISD YYWSWIRQPP GEGLEWIAHV DPISPTIDYY NPSFKNRITI SKDTSKNQFS LKLRSVTAA DTAVYYCARA GPLRYYGPWN NQRRFDFWGP GVLVTVSS

-
Macromolecule #4: AM12-352 Fab light chain

MacromoleculeName: AM12-352 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 12.338774 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DVVMTQSPLS LSITPGQPAS ISCRFSQSLV HSDGNTYLSW YQQKPGQPPR LLIYKVSNRD SGVPDRFSGS GAGTDFTLKI SRLEAEDVG VYYCGQATHW PWTFGQGTKV EIK

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 30 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris

Details: 150 mM NaCl, 20 mM Tris-HCl, pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was purified and monodisperse.

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 183947
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 54994
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more