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- EMDB-41426: Cryo-EM structure of TRNM-b*01 Fab in complex with HIV-1 Env trim... -

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Basic information

Entry
Database: EMDB / ID: EMD-41426
TitleCryo-EM structure of TRNM-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP
Map data
Sample
  • Complex: TRNM-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP
    • Complex: TRNM-b*01 heavy chain, TRNM-b*01 light chain
      • Protein or peptide: TRNM-b*01 heavy chain
      • Protein or peptide: TRNM-b*01 light chain
    • Complex: Transmembrane protein gp41, BG505 DS-SOSIP Surface protein gp120
      • Protein or peptide: Transmembrane protein gp41
      • Protein or peptide: BG505 DS-SOSIP Surface protein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / Vaccination / VIRAL PROTEIN / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / 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 speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsRoark RS / Morano NC / Shapiro LS / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell / Year: 2024
Title: Potent and broad HIV-1 neutralization in fusion peptide-primed SHIV-infected macaques.
Authors: Hua Wang / Cheng Cheng / James L Dal Santo / Chen-Hsiang Shen / Tatsiana Bylund / Amy R Henry / Colin A Howe / Juyun Hwang / Nicholas C Morano / Daniel J Morris / Sergei Pletnev / Ryan S ...Authors: Hua Wang / Cheng Cheng / James L Dal Santo / Chen-Hsiang Shen / Tatsiana Bylund / Amy R Henry / Colin A Howe / Juyun Hwang / Nicholas C Morano / Daniel J Morris / Sergei Pletnev / Ryan S Roark / Tongqing Zhou / Bryan T Hansen / Forrest H Hoyt / Timothy S Johnston / Shuyi Wang / Baoshan Zhang / David R Ambrozak / Jordan E Becker / Michael F Bender / Anita Changela / Ridhi Chaudhary / Martin Corcoran / Angela R Corrigan / Kathryn E Foulds / Yicheng Guo / Myungjin Lee / Yingying Li / Bob C Lin / Tracy Liu / Mark K Louder / Marco Mandolesi / Rosemarie D Mason / Krisha McKee / Vinod Nair / Sijy O'Dell / Adam S Olia / Li Ou / Amarendra Pegu / Nagarajan Raju / Reda Rawi / Jesmine Roberts-Torres / Edward K Sarfo / Mallika Sastry / Andrew J Schaub / Stephen D Schmidt / Chaim A Schramm / Cindi L Schwartz / Sarah C Smith / Tyler Stephens / Jonathan Stuckey / I-Ting Teng / John-Paul Todd / Yaroslav Tsybovsky / David J Van Wazer / Shuishu Wang / Nicole A Doria-Rose / Elizabeth R Fischer / Ivelin S Georgiev / Gunilla B Karlsson Hedestam / Zizhang Sheng / Ruth A Woodward / Daniel C Douek / Richard A Koup / Theodore C Pierson / Lawrence Shapiro / George M Shaw / John R Mascola / Peter D Kwong /
Abstract: An antibody-based HIV-1 vaccine will require the induction of potent cross-reactive HIV-1-neutralizing responses. To demonstrate feasibility toward this goal, we combined vaccination targeting the ...An antibody-based HIV-1 vaccine will require the induction of potent cross-reactive HIV-1-neutralizing responses. To demonstrate feasibility toward this goal, we combined vaccination targeting the fusion-peptide site of vulnerability with infection by simian-human immunodeficiency virus (SHIV). In four macaques with vaccine-induced neutralizing responses, SHIV infection boosted plasma neutralization to 45%-77% breadth (geometric mean 50% inhibitory dilution [ID] ∼100) on a 208-strain panel. Molecular dissection of these responses by antibody isolation and cryo-electron microscopy (cryo-EM) structure determination revealed 15 of 16 antibody lineages with cross-clade neutralization to be directed toward the fusion-peptide site of vulnerability. In each macaque, isolated antibodies from memory B cells recapitulated the plasma-neutralizing response, with fusion-peptide-binding antibodies reaching breadths of 40%-60% (50% inhibitory concentration [IC] < 50 μg/mL) and total lineage-concentrations estimates of 50-200 μg/mL. Longitudinal mapping indicated that these responses arose prior to SHIV infection. Collectively, these results provide in vivo molecular examples for one to a few B cell lineages affording potent, broadly neutralizing plasma responses.
History
DepositionAug 2, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41426.png

Downloads & links

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Map

FileDownload / File: emd_41426.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.16678819 - 0.41247106
Average (Standard dev.)0.0011970823 (±0.013072655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41426_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_41426_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 : TRNM-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP

EntireName: TRNM-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP
Components
  • Complex: TRNM-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP
    • Complex: TRNM-b*01 heavy chain, TRNM-b*01 light chain
      • Protein or peptide: TRNM-b*01 heavy chain
      • Protein or peptide: TRNM-b*01 light chain
    • Complex: Transmembrane protein gp41, BG505 DS-SOSIP Surface protein gp120
      • Protein or peptide: Transmembrane protein gp41
      • Protein or peptide: BG505 DS-SOSIP Surface protein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: TRNM-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP

SupramoleculeName: TRNM-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: TRNM-b*01 heavy chain, TRNM-b*01 light chain

SupramoleculeName: TRNM-b*01 heavy chain, TRNM-b*01 light chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #3: Transmembrane protein gp41, BG505 DS-SOSIP Surface protein gp120

SupramoleculeName: Transmembrane protein gp41, BG505 DS-SOSIP Surface protein gp120
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: TRNM-b*01 heavy chain

MacromoleculeName: TRNM-b*01 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.706627 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VQLQESGPGV VKPSETLSLT CEVSLHASRV GSYYWSWIRQ SQGQRPEWMG GLYSDTGNTD YNPSLKSRVS LSRDMSKKQF FLNLRSVTA TDTAVYFCVS RYVDHWTNRR FDVWGPGAQV TVTSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS ...String:
VQLQESGPGV VKPSETLSLT CEVSLHASRV GSYYWSWIRQ SQGQRPEWMG GLYSDTGNTD YNPSLKSRVS LSRDMSKKQF FLNLRSVTA TDTAVYFCVS RYVDHWTNRR FDVWGPGAQV TVTSASTKGP SVFPLAPSSR STSESTAALG CLVKDYFPEP V TVSWNSGS LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYVCNV NHKPSNTKVD KRVEIKTC

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Macromolecule #2: TRNM-b*01 light chain

MacromoleculeName: TRNM-b*01 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.050588 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT VTCRASLDIN KDLNWYQQKP GKAPALLIYA ASTLQTGVSS RFSGSGSGTQ FTLTISSLQP EDFATYYCL QDYSFPLTFG GGTKIDLKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT VTCRASLDIN KDLNWYQQKP GKAPALLIYA ASTLQTGVSS RFSGSGSGTQ FTLTISSLQP EDFATYYCL QDYSFPLTFG GGTKIDLKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRAA

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Macromolecule #3: Transmembrane protein gp41

MacromoleculeName: Transmembrane protein 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: BG505 DS-SOSIP Surface protein gp120

MacromoleculeName: BG505 DS-SOSIP Surface protein gp120 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.086324 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 R

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: 37 / 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: 7.5 / Details: PBS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xrt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124954
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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