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- EMDB-44891: Rhesus Fab 40591-a.01 in complex with T250.4 RnS SOSIP Env -

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Basic information

Entry
Database: EMDB / ID: EMD-44891
TitleRhesus Fab 40591-a.01 in complex with T250.4 RnS SOSIP Env
Map datasharpened
Sample
  • Complex: Rhesus Fab 40591-a.01 in complex with T250.4 RnS SOSIP Env
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Fab 40591-a.01 heavy chain
    • Protein or peptide: Fab 40591-a.01 light chain
  • 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
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.14 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_44891.png

Downloads & links

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Map

FileDownload / File: emd_44891.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 344.32 Å		1.08 Å/pix.
x 320 pix.
= 344.32 Å		1.08 Å/pix.
x 320 pix.
= 344.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.3862058 - 2.4663825
Average (Standard dev.)0.0032300681 (±0.06300614)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 344.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44891_msk_1.map
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Additional map: unsharpened

Fileemd_44891_additional_1.map
Annotationunsharpened
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Additional map: resolve map

Fileemd_44891_additional_2.map
Annotationresolve map
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Half map: half map B

Fileemd_44891_half_map_1.map
Annotationhalf map B
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Half map: half map A

Fileemd_44891_half_map_2.map
Annotationhalf map A
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Sample components

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Entire : Rhesus Fab 40591-a.01 in complex with T250.4 RnS SOSIP Env

EntireName: Rhesus Fab 40591-a.01 in complex with T250.4 RnS SOSIP Env
Components
  • Complex: Rhesus Fab 40591-a.01 in complex with T250.4 RnS SOSIP Env
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Fab 40591-a.01 heavy chain
    • Protein or peptide: Fab 40591-a.01 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Rhesus Fab 40591-a.01 in complex with T250.4 RnS SOSIP Env

SupramoleculeName: Rhesus Fab 40591-a.01 in complex with T250.4 RnS SOSIP Env
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 gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.268494 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGLGAVFFG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLLKAPEA QQQLLRLGVW GFKQLQARVL ALERYLEVQQ LLGIWGCSG KLICCTTVPW NSTWSNKNYT DIWDNMTWLQ WDREIGNYTD EIYRLIEESQ FQQEINEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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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: 54.113359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPAENLWVTV YYGVPVWREA DTTLFCASDA KGYDTEAHNV WATHACVPTD PNPQEIYLEN VTENFNMWKN NMVEQMHTDI ISLWDESLK PCVKLTPLCV TLDCQAFNSS SHTNSSIAMQ EMKNCSFNVT TELRDKKKKE YSLFYKLDIV QINKNGRQYR L INCNTSAC ...String:
GPAENLWVTV YYGVPVWREA DTTLFCASDA KGYDTEAHNV WATHACVPTD PNPQEIYLEN VTENFNMWKN NMVEQMHTDI ISLWDESLK PCVKLTPLCV TLDCQAFNSS SHTNSSIAMQ EMKNCSFNVT TELRDKKKKE YSLFYKLDIV QINKNGRQYR L INCNTSAC TQICPKVSFE PIPIHFCAPA GFAILKCNEK HFNGTGPCKN VSTVQCTHGI KPVVSTQLLL NGSLAEEEVV IR SENITDN AKTIIVQLAK PVKINCTRPN NMTRKSIRIG PGQTFYALGD IIGNIRKPYC NVSKREWNNT LQQVAAQLRK SFN NTTIVF EKSSGGDLEV TTHSFNCGGE FFYCNTSGLF NSTWTNSTWT NSTTGSNGTE SNDTITLQCR IKQIINMWQR VGRC MYAPP IPGVIRCESN ITGLLLTRDG GNSTQNETFR PGGGDMRDNW RSELYKYKVV QIEPLGVAPT HCKRRVVERR RRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: Fab 40591-a.01 heavy chain

MacromoleculeName: Fab 40591-a.01 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.200182 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCTFSGRSYH NYGMAWVRQA PGKGLEWVSS ISSGSSYTDY IGSVRGRFTI SRENAMNSLS LHMNSLRAE DTGVYFCASQ GPDPWYEDDF GYHYEVLSNR FDVWGPGVLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE ...String:
EVQLVESGGG LVQPGGSLRL SCTFSGRSYH NYGMAWVRQA PGKGLEWVSS ISSGSSYTDY IGSVRGRFTI SRENAMNSLS LHMNSLRAE DTGVYFCASQ GPDPWYEDDF GYHYEVLSNR FDVWGPGVLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK GL EVLFQ

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Macromolecule #4: Fab 40591-a.01 light chain

MacromoleculeName: Fab 40591-a.01 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.308822 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQTVS SNLAWYQQKP GKAPKFLIYD SSTLATGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QHYSRPVTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQTVS SNLAWYQQKP GKAPKFLIYD SSTLATGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QHYSRPVTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 18 / 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 / 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 K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 56.03 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: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66103
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-9bti:
Rhesus Fab 40591-a.01 in complex with T250.4 RnS SOSIP Env

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