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- EMDB-41440: Cryo-EM structure of TRNM-f*01 Fab in complex with HIV-1 Env trim... -

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Basic information

Entry
Database: EMDB / ID: EMD-41440
TitleCryo-EM structure of TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP
Map data
Sample
  • Complex: TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: TRNM-f*01 heavy chain
    • Protein or peptide: TRNM-f*01 light chain
    • Protein or peptide: Envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / Vaccination / VIRAL PROTEIN / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMacaca mulatta (Rhesus monkey) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.03 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 3, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41440.png

Downloads & links

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Map

FileDownload / File: emd_41440.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.084
Minimum - Maximum-0.11997668 - 0.3399646
Average (Standard dev.)0.0010210935 (±0.012236718)
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_41440_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41440_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP

EntireName: TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP
Components
  • Complex: TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: TRNM-f*01 heavy chain
    • Protein or peptide: TRNM-f*01 light chain
    • Protein or peptide: Envelope glycoprotein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP

SupramoleculeName: TRNM-f*01 Fab in complex with HIV-1 Env trimer ConC SOSIP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.737102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLWVTVYYGV PVWKEAKTTL FCASDAKAYE KEVHNVWATH ACVPTDPNPQ EMVLENVTEN FNMWKNDMVD QMHEDIISLW DQSLKPCVK LTPLCVTLNC TNVNVTNTNN NNMKEEMKNC SFNTTTEIRD KKQKEYALFY RLDIVPLNEN SSEYRLINCN T STITQICP ...String:
NLWVTVYYGV PVWKEAKTTL FCASDAKAYE KEVHNVWATH ACVPTDPNPQ EMVLENVTEN FNMWKNDMVD QMHEDIISLW DQSLKPCVK LTPLCVTLNC TNVNVTNTNN NNMKEEMKNC SFNTTTEIRD KKQKEYALFY RLDIVPLNEN SSEYRLINCN T STITQICP KVSFDPIPIH YCAPAGYAIL KCNNKTFNGT GPCNNVSTVQ CTHGIKPVVS TQLLLNGSLA EEEIIIRSEN LT DNAKTII VHLNESVEIN CTRPNNMTRK SIRIGPGQTF YALGDIIGDI RQPHCNISEA KWNKTLQRVK KKLKEHFPNK TIK FAPSSG GDLEITTHSF NCRGEFFYCN TSKLFNSTYN NTTSNSTITL PCRIKQIINM WQEVGRAMYA PPIAGNITCK SNIT GLLLT RDGGNNNNNT ETFRPGGGDM RDNWRSELYK YKVVEIKPLG IAPTKCKRRV VERRRRRR

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Macromolecule #2: TRNM-f*01 heavy chain

MacromoleculeName: TRNM-f*01 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.923301 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG VVKPSETLSL TCAVSGDSIK SAYQYWNWIR QPRGKGPEWI GGVYSSSDST AYNPSLESRV SISRDTSNNR FSLNLRSVT ATDTATYFCA RSVRDSRGWG RYFLDTWGQG LLVTVSS

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Macromolecule #3: TRNM-f*01 light chain

MacromoleculeName: TRNM-f*01 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.464811 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDTVT ITCRASQSIS TWLAWYQQKP GKAPKVLIYS ASILQSGVPS RFRGSGSGSD FTLTIGSLQI EDFATYFCQ QYTGSPFTFG GGTKVEIK

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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: Homo sapiens (human)
Molecular weightTheoretical: 17.174447 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGLGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLLRAPEA QQHMLQLGVW GFKQLQARVL AIERYLEVQQ LLGIWGCSG KLICCTAVPW NSSWSNKSQE DIWDNMTWMQ WDREIGNYTD TIYRLLEESQ FQQEINEKDL LALD

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 42 / 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

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7tfo

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97698
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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