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- EMDB-47000: Rhesus RHA10.01 Fab in complex with HIV-1 Env BG505 DS-SOSIP trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-47000
TitleRhesus RHA10.01 Fab in complex with HIV-1 Env BG505 DS-SOSIP trimer
Map datasharpened map
Sample
  • Complex: Rhesus RHA10.01 Fab in complex with HIV-1 Env BG505 DS-SOSIP trimer
    • Protein or peptide: RHA10.01 Light chain
    • Protein or peptide: RHA10.01 Heavy chain
    • Protein or peptide: BG505 DS-SOSIP glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCD4 / HIV-1 / SHIV / T681 / rhesus macaque / IMMUNE SYSTEM
Function / homology
Function and homology information


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 ...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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.27 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
Other privateSimons Foundation (SF349247) United States
CitationJournal: Cell Rep / Year: 2025
Title: Transient glycan shield reduction induces CD4-binding site broadly neutralizing antibodies in SHIV-infected macaques.
Authors: Daniel J Morris / Jason Gorman / Tongqing Zhou / Jinery Lora / Andrew J Connell / Hui Li / Weimin Liu / Ryan S Roark / Mary S Campion / John W Carey / Rumi Habib / Yingying Li / Christian L ...Authors: Daniel J Morris / Jason Gorman / Tongqing Zhou / Jinery Lora / Andrew J Connell / Hui Li / Weimin Liu / Ryan S Roark / Mary S Campion / John W Carey / Rumi Habib / Yingying Li / Christian L Martella / Younghoon Park / Ajay Singh / Kirsten J Sowers / I-Ting Teng / Shuyi Wang / Neha Chohan / Wenge Ding / Craig Lauer / Emily Lewis / Rosemarie D Mason / Juliette M Rando / Lowrey Peyton / Chaim A Schramm / Kshitij Wagh / Bette Korber / Michael S Seaman / Daniel C Douek / Barton F Haynes / Daniel W Kulp / Mario Roederer / Beatrice H Hahn / Peter D Kwong / George M Shaw /
Abstract: Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 CD4-binding site (CD4bs) occur infrequently in macaques and humans and have not been reproducibly elicited in any outbred animal model. To ...Broadly neutralizing antibodies (bNAbs) targeting the HIV-1 CD4-binding site (CD4bs) occur infrequently in macaques and humans and have not been reproducibly elicited in any outbred animal model. To address this challenge, we first isolated RHA10, an infection-induced rhesus bNAb with 51% breadth. The cryoelectron microscopy (cryo-EM) structure of RHA10 with the HIV-1 envelope (Env) resembled prototypic human CD4bs bNAbs with CDR-H3-dominated binding. Env-antibody co-evolution revealed transient elimination of two Env CD4bs-proximal glycans near the time of RHA10-lineage initiation, and these glycan-deficient Envs bound preferentially to early RHA10 intermediates, suggesting that glycan deletions in infecting SHIVs could induce CD4bs bNAbs. To test this hypothesis, we constructed SHIV.CH505 variants with CD4bs-proximal glycan deletions. Infection of 11 macaques resulted in accelerated CD4bs bNAb responses in 9 compared with 1 of 115 control macaques. Glycan hole-based immunofocusing coupled to Env-Ab co-evolution can consistently induce broad CD4bs responses in macaques and serve as a model for HIV vaccine design.
History
DepositionSep 12, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47000.png

Downloads & links

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Map

FileDownload / File: emd_47000.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 420 pix.
= 454.65 Å		1.08 Å/pix.
x 420 pix.
= 454.65 Å		1.08 Å/pix.
x 420 pix.
= 454.65 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-0.3924822 - 2.4779634
Average (Standard dev.)0.009626951 (±0.08285283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 454.65 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47000_msk_1.map
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Additional map: #2

Fileemd_47000_additional_1.map
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Additional map: #1

Fileemd_47000_additional_2.map
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Half map: half map A

Fileemd_47000_half_map_1.map
Annotationhalf map A
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Half map: half map B

Fileemd_47000_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : Rhesus RHA10.01 Fab in complex with HIV-1 Env BG505 DS-SOSIP trimer

EntireName: Rhesus RHA10.01 Fab in complex with HIV-1 Env BG505 DS-SOSIP trimer
Components
  • Complex: Rhesus RHA10.01 Fab in complex with HIV-1 Env BG505 DS-SOSIP trimer
    • Protein or peptide: RHA10.01 Light chain
    • Protein or peptide: RHA10.01 Heavy chain
    • Protein or peptide: BG505 DS-SOSIP glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Rhesus RHA10.01 Fab in complex with HIV-1 Env BG505 DS-SOSIP trimer

SupramoleculeName: Rhesus RHA10.01 Fab in complex with HIV-1 Env BG505 DS-SOSIP trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: RHA10.01 Light chain

MacromoleculeName: RHA10.01 Light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.852633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQIPVS LSVTPGEPAS ISCSSSQSLQ HISGYTYLDW YLQKPGQSPQ LLISRVSGRA SGVPDRFSGS GSGTDFMLKI SRVEAEDVG IYYCMQGTQL PFSFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DIVMTQIPVS LSVTPGEPAS ISCSSSQSLQ HISGYTYLDW YLQKPGQSPQ LLISRVSGRA SGVPDRFSGS GSGTDFMLKI SRVEAEDVG IYYCMQGTQL PFSFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #2: RHA10.01 Heavy chain

MacromoleculeName: RHA10.01 Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.059332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LLKPSETLSL TCAVSGVSIT SYPWSWIRQS PGKGLEWIGR IFTVGGHTDL NPSLKSRVTI ARDSSRNQVS LILRSVTAA DTALYYCARV PFYWNNKSWY GGAYQWYALD SWGQGVAVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV ...String:
QVQLQESGPG LLKPSETLSL TCAVSGVSIT SYPWSWIRQS PGKGLEWIGR IFTVGGHTDL NPSLKSRVTI ARDSSRNQVS LILRSVTAA DTALYYCARV PFYWNNKSWY GGAYQWYALD SWGQGVAVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSCDKGL EV LFQ

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Macromolecule #3: BG505 DS-SOSIP glycoprotein gp41

MacromoleculeName: BG505 DS-SOSIP glycoprotein gp41 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #4: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.929129 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SACTQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR

UniProtKB: Envelope glycoprotein gp160

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 27 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.73 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 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: PDB ENTRY
PDB model - PDB ID:

6vi0

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 81730
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9dmb:
Rhesus RHA10.01 Fab in complex with HIV-1 Env BG505 DS-SOSIP trimer

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