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- EMDB-49870: Cryo-EM structure of rhesus antibody CH42-Apex1.01 in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-49870
TitleCryo-EM structure of rhesus antibody CH42-Apex1.01 in complex with HIV Env trimer Q23-APEX-GT2
Map data
Sample
  • Complex: CH42-Apex1.01 Fab in complex with HIV envelope trimer
    • Protein or peptide: CH42-Apex1.01 heavy chain
    • Protein or peptide: CH42-Apex1.01 kappa chain
    • Protein or peptide: HIV envelope gp120
    • Protein or peptide: HIV envelope gp41 ectodomain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsimmune complex / neutralization / V2 apex / germline-targeting / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsRoark RS / 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: To Be Published
Title: Germline-targeting HIV immunogen induces cross-neutralizing antibodies in outbred macaques
Authors: Mishra N / Roark RS / Kwong PD / Shaw GM / Andrabi R
History
DepositionMar 21, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49870.png

Downloads & links

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Map

FileDownload / File: emd_49870.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: 0.11
Minimum - Maximum-0.23068911 - 0.5920677
Average (Standard dev.)0.00047563753 (±0.015133732)
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_49870_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_49870_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 : CH42-Apex1.01 Fab in complex with HIV envelope trimer

EntireName: CH42-Apex1.01 Fab in complex with HIV envelope trimer
Components
  • Complex: CH42-Apex1.01 Fab in complex with HIV envelope trimer
    • Protein or peptide: CH42-Apex1.01 heavy chain
    • Protein or peptide: CH42-Apex1.01 kappa chain
    • Protein or peptide: HIV envelope gp120
    • Protein or peptide: HIV envelope gp41 ectodomain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: CH42-Apex1.01 Fab in complex with HIV envelope trimer

SupramoleculeName: CH42-Apex1.01 Fab in complex with HIV envelope trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: CH42-Apex1.01 heavy chain

MacromoleculeName: CH42-Apex1.01 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.402336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKRPGESLRI SCKTSGYSFT GSWINWVRQM PGKGLEWMGS IYPGGSHTRY NPSFQGHVTI SVDKSISTTY LQWSSLKAS DTATYYCAKE EGELYSEDD(TYS) AYYDGYNRFD VWGPGVLVTV SSASTKGPSV FPLAPSSRST SESTAAL GC LVKDYFPEPV ...String:
QVQLVQSGAE VKRPGESLRI SCKTSGYSFT GSWINWVRQM PGKGLEWMGS IYPGGSHTRY NPSFQGHVTI SVDKSISTTY LQWSSLKAS DTATYYCAKE EGELYSEDD(TYS) AYYDGYNRFD VWGPGVLVTV SSASTKGPSV FPLAPSSRST SESTAAL GC LVKDYFPEPV TVSWNSGSLT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYVCNVNH KPSNTKVDKR VEIKTCGG G LEVLFQ

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Macromolecule #2: CH42-Apex1.01 kappa chain

MacromoleculeName: CH42-Apex1.01 kappa chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.331811 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPSS LSASVGDRVT VTCRASENVN NYLHWYQQQP GKAPKLLIYA AYTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ HSFDTPFTFG PGTKLDIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIVMTQSPSS LSASVGDRVT VTCRASENVN NYLHWYQQQP GKAPKLLIYA AYTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ HSFDTPFTFG PGTKLDIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #3: HIV envelope gp120

MacromoleculeName: HIV envelope gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.550621 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWRDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL HCRNVTSVNT TGDREELKNC TFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSACTQAC ...String:
AENLWVTVYY GVPVWRDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL HCRNVTSVNT TGDREELKNC TFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSACTQAC PKVSFEPIPI HYCAPAGFAI LKCKDEGFNG TGLCKNVSTV QCTHGIKPVV STQLLLNGSL AEKNITIRSE NI TNNAKII IVQLVQPVTI KCIRPNNYTR KSIRIGPGQA FYAMGDIIGD IRQAHCNVSR SRWNKTLQEV AEKLRTYFGN KTI IFANSS GGDLEITTHS FNCGGEFFYC NTSGLFNSTW YVNSTWNDTD STQESNDTIT LPCRIKQIIN MWQRAGQCMY APPI PGVIK CESNITGLLL TRDGGKDNNV NETFRPGGGD MRDNWRSELY KYKVVEIEPL GVAPTRCKRR VVEGGGGSGG GGS

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #4: HIV envelope gp41 ectodomain

MacromoleculeName: HIV envelope gp41 ectodomain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.205666 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVRRG FLGAAGSTMG AASITLTVQA RQLLSGIVQP QNNLLRAPEA QQHLLKLGVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNKSLD EIWNNMTWLQ WDKEIGNYTQ LIYRLIEESQ NQQEKNEKEL LALD

UniProtKB: Envelope glycoprotein gp160

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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: 30 / 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

MicroscopeTFS 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:

7llk

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 362484
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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