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- EMDB-44892: Rhesus Fab 6561-a.01 in complex with HIV-1 Ce1176.A3 RnS SOSIP Env -

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Basic information

Entry
Database: EMDB / ID: EMD-44892
TitleRhesus Fab 6561-a.01 in complex with HIV-1 Ce1176.A3 RnS SOSIP Env
Map datasharpened map
Sample
  • Complex: Rhesus Fab 6561-a.01 in complex with HIV-1 Ce1176.A3 RnS SOSIP Env
    • Protein or peptide: Fab 6561-a.01 light chain
    • Protein or peptide: Fab 6561-a.01 heavy chain
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / SOSIP / Vaccine / VIRAL PROTEIN-IMMUNE SYSTEM complex / V2-Apex / multi-donor / SHIV / IMMUNE SYSTEM
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
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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsGorman J / Kwong PD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Simons FoundationSF349247 United States
CitationJournal: J Exp Med / Year: 2025
Title: Structural and genetic basis of HIV-1 envelope V2 apex recognition by rhesus broadly neutralizing antibodies.
Authors: Ryan S Roark / Rumi Habib / Jason Gorman / Hui Li / Andrew Jesse Connell / Mattia Bonsignori / Yicheng Guo / Michael P Hogarty / Adam S Olia / Kirsten J Sowers / Baoshan Zhang / Frederic ...Authors: Ryan S Roark / Rumi Habib / Jason Gorman / Hui Li / Andrew Jesse Connell / Mattia Bonsignori / Yicheng Guo / Michael P Hogarty / Adam S Olia / Kirsten J Sowers / Baoshan Zhang / Frederic Bibollet-Ruche / Tatsiana Bylund / Sean Callaghan / John W Carey / Gabriele Cerutti / Darcy R Harris / Wanting He / Emily Lewis / Tracy Liu / Rosemarie D Mason / Yujie Qiao / Younghoon Park / Juliette M Rando / Ajay Singh / Jeremy J Wolff / Q Paula Lei / Mark K Louder / Raiees Andrabi / Nicole A Doria-Rose / Kevin O Saunders / Michael S Seaman / Barton F Haynes / Daniel W Kulp / John R Mascola / Mario Roederer / Theodore C Pierson / Zizhang Sheng / Beatrice H Hahn / George M Shaw / Peter D Kwong / Lawrence Shapiro /
Abstract: Broadly neutralizing antibodies targeting the V2 apex of HIV-1 envelope are desired as vaccine design templates, but few have been described. Here, we report 11 lineages of V2 apex-neutralizing ...Broadly neutralizing antibodies targeting the V2 apex of HIV-1 envelope are desired as vaccine design templates, but few have been described. Here, we report 11 lineages of V2 apex-neutralizing antibodies from simian-human immunodeficiency virus (SHIV)-infected rhesus macaques and determine cryo-EM structures for 9. A single V2 apex-neutralizing lineage accounted for cross-clade breadth in most macaques, and somatic hypermutation relative to breadth was generally low, exemplified by antibody V033-a.01 with <5% nucleotide mutation and 37% breadth (208-strain panel). Envelope complex structures revealed eight different antibody classes (one multi-donor) and the complete repertoire of all five possible recognition topologies, recapitulating canonical human modes of apex insertion and C-strand hydrogen bonding. Despite this diversity in recognition, all rhesus-V2 apex antibodies were derived from reading frame two of the DH3-15*01 gene. Collectively, these results define-in rhesus-the structural and genetic basis of HIV-1 V2 apex recognition and demonstrate unprecedented structural plasticity of a highly selected immunogenetic element.
History
DepositionMay 15, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44892.png

Downloads & links

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Map

FileDownload / File: emd_44892.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 288 pix.
= 309.11 Å		1.07 Å/pix.
x 288 pix.
= 309.11 Å		1.07 Å/pix.
x 288 pix.
= 309.11 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0733 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.22796337 - 1.2950952
Average (Standard dev.)0.009472055 (±0.052754413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 309.1104 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44892_msk_1.map
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Additional map: deepemhancer map

Fileemd_44892_additional_1.map
Annotationdeepemhancer map
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Additional map: resolve map

Fileemd_44892_additional_2.map
Annotationresolve map
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Additional map: unsharpened

Fileemd_44892_additional_3.map
Annotationunsharpened
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Half map: half map B

Fileemd_44892_half_map_1.map
Annotationhalf map B
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Half map: half map A

Fileemd_44892_half_map_2.map
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Sample components

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Entire : Rhesus Fab 6561-a.01 in complex with HIV-1 Ce1176.A3 RnS SOSIP Env

EntireName: Rhesus Fab 6561-a.01 in complex with HIV-1 Ce1176.A3 RnS SOSIP Env
Components
  • Complex: Rhesus Fab 6561-a.01 in complex with HIV-1 Ce1176.A3 RnS SOSIP Env
    • Protein or peptide: Fab 6561-a.01 light chain
    • Protein or peptide: Fab 6561-a.01 heavy chain
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Rhesus Fab 6561-a.01 in complex with HIV-1 Ce1176.A3 RnS SOSIP Env

SupramoleculeName: Rhesus Fab 6561-a.01 in complex with HIV-1 Ce1176.A3 RnS SOSIP Env
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4, #3
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Fab 6561-a.01 light chain

MacromoleculeName: Fab 6561-a.01 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.076508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QPVVTQSPSA SASLGASVKL TCTLGSGNTN YAIAWHQQQE GKAPRFLMRV ESGGSHSKGD GIPHRFSGSS SGAERYLTIS NLQSEDEAD YFCQTWTTGT HVFGVGTKLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QPVVTQSPSA SASLGASVKL TCTLGSGNTN YAIAWHQQQE GKAPRFLMRV ESGGSHSKGD GIPHRFSGSS SGAERYLTIS NLQSEDEAD YFCQTWTTGT HVFGVGTKLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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Macromolecule #2: Fab 6561-a.01 heavy chain

MacromoleculeName: Fab 6561-a.01 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 27.288469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVRPSETLSL TCTVSGGSIS DRYYWNWIRQ RPGKPLEWLG NIYGFSERTY HNPSFKSRVT ISKDTSKNQF FLSLSSVTA ADTAVYYCVR DRLLEEY(TYS)EE D(TYS)DNWYRVFD ALEVWGRGLL VTVSSASTKG PSVFPLAPSS KST SGGTAA ...String:
QVQLQESGPG LVRPSETLSL TCTVSGGSIS DRYYWNWIRQ RPGKPLEWLG NIYGFSERTY HNPSFKSRVT ISKDTSKNQF FLSLSSVTA ADTAVYYCVR DRLLEEY(TYS)EE D(TYS)DNWYRVFD ALEVWGRGLL VTVSSASTKG PSVFPLAPSS KST SGGTAA LGCLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKV EPKSC DKGLEVLFQ

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Macromolecule #3: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.648887 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPAENLWVTV YYGVPVWKEA KTTLFCASDA KAYEKEVHNV WATHACVPTD PNPQEMVLEN VTENFNMWKN DMVDQMHEDV ISLWDQSLK PCVKLTPLCV TLNCTNTTVS NGSSNSNANF EEMKNCSFNA TTEIKDKKKN EYALFYKLDI VPLNNSSGKY R LINCNTSA ...String:
GPAENLWVTV YYGVPVWKEA KTTLFCASDA KAYEKEVHNV WATHACVPTD PNPQEMVLEN VTENFNMWKN DMVDQMHEDV ISLWDQSLK PCVKLTPLCV TLNCTNTTVS NGSSNSNANF EEMKNCSFNA TTEIKDKKKN EYALFYKLDI VPLNNSSGKY R LINCNTSA CTQICPKVTF EPIPIHYCAP AGYAILKCNN KTFNGTGPCN NVSTVQCTHG IKPVVSTQLL LNGSLAEKEI II RSENLTN NAKTIIVHLN ESVGIVCTRP SNMTRKSIRI GPGQTFYALG DIIGDIRQPH CNISKQNWNR TLQQVGRKLA EHF PNRNIT FNHSSGGDLE ITTHSFNCRG EFFYCNTSGL FNGTYHPNGT YNETAVNSSD TITLQCRIKQ IINMWQEVGR CMYA PPIAG NITCNSNITG LLLTRDGGIN QTGEEIFRPG GGDMRDNWRS ELYKYKVVEI KPLGIAPTKC KRRVVERRRR RR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #4: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.24051 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLLRAPEA QQHMLQLGVW GFKQLQARVL AIERYLEVQQ LLGIWGCSG KLICCTNVPW NSTWSNRTQE DIWNNMTWME WEREIGNYTH TIYSLLEESQ FQQEINEKDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 51 / 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

Concentration2 mg/mL
BufferpH: 7.4 / Details: PBS
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 69.48 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 150641
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelPDB ID:

6vtt


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9btj:
Rhesus Fab 6561-a.01 in complex with HIV-1 Ce1176.A3 RnS SOSIP Env

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