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- EMDB-74654: Cryo-EM structure of SHIV-elicited CE79-1571 Fab in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-74654
TitleCryo-EM structure of SHIV-elicited CE79-1571 Fab in complex with HIV Env trimer Q23-SCT27
Map data
Sample
  • Complex: Complex of CE79-1571 Fab with HIV-1 envelope trimer
    • Protein or peptide: CE79-1571 heavy chain
    • Protein or peptide: CE79-1571 light chain
    • Protein or peptide: Envelope gp120
    • Protein or peptide: Envelope gp41 ectodomain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeutralizing antibody / HIV V2 apex / SHIV-elicited / Immune complex / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsRoark RS / Shapiro L / 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: Enhanced Priming Leads to Rapid Induction of Broadly Neutralizing HIV-1 Apex Antibodies
Authors: Roark RS / Shapiro L / Kwong PD
History
DepositionDec 21, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74654.png

Downloads & links

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Map

FileDownload / File: emd_74654.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: 0.09
Minimum - Maximum-0.20798466 - 0.41236442
Average (Standard dev.)0.0005014151 (±0.011300615)
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: #1

Fileemd_74654_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74654_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 : Complex of CE79-1571 Fab with HIV-1 envelope trimer

EntireName: Complex of CE79-1571 Fab with HIV-1 envelope trimer
Components
  • Complex: Complex of CE79-1571 Fab with HIV-1 envelope trimer
    • Protein or peptide: CE79-1571 heavy chain
    • Protein or peptide: CE79-1571 light chain
    • Protein or peptide: Envelope gp120
    • Protein or peptide: Envelope gp41 ectodomain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of CE79-1571 Fab with HIV-1 envelope trimer

SupramoleculeName: Complex of CE79-1571 Fab with HIV-1 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: CE79-1571 heavy chain

MacromoleculeName: CE79-1571 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.698391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVRPSETLSL TCAVSGGSIS ITTWWTWIRQ PPGKGLEWIG GVDGNSESIN YNPSLKSRVT ISKDTSKNQF SLRLSSVTA ADTAVYFCAR DGASHSYYAD D(TYS)GEDYTETY YGLDSWGQGV VVTVSSASTK GPSVFPLAPS SRSTSES TA ALGCLVKDYF ...String:
QVQLQESGPG LVRPSETLSL TCAVSGGSIS ITTWWTWIRQ PPGKGLEWIG GVDGNSESIN YNPSLKSRVT ISKDTSKNQF SLRLSSVTA ADTAVYFCAR DGASHSYYAD D(TYS)GEDYTETY YGLDSWGQGV VVTVSSASTK GPSVFPLAPS SRSTSES TA ALGCLVKDYF PEPVTVSWNS GSLTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYVC NVNHKPSNTK VDKRVEIK T CGGHHHHHHH H

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Macromolecule #2: CE79-1571 light chain

MacromoleculeName: CE79-1571 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.096879 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVVMTQSPLS LPVTPGQPAS ISCSSSQSLV HSDGRTYLNW LQQKPGQPPR RLIYKVSNRD SGVPDRFSGS GAGTHFTLKI SRVEAEDVG VYYCVQGTHW PLTFGGGTKV EIKRTRTVAA PSVFIFPPSE DQVKSGTVSV VCLLNNFYPR EASVKWKVDG A LKTGNSQE ...String:
DVVMTQSPLS LPVTPGQPAS ISCSSSQSLV HSDGRTYLNW LQQKPGQPPR RLIYKVSNRD SGVPDRFSGS GAGTHFTLKI SRVEAEDVG VYYCVQGTHW PLTFGGGTKV EIKRTRTVAA PSVFIFPPSE DQVKSGTVSV VCLLNNFYPR EASVKWKVDG A LKTGNSQE SVTEQDSKDN TYSLSSTLTL SSTEYQSHKV YACEVTHQGL SSPVTKSFNR GEC

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Macromolecule #3: Envelope gp120

MacromoleculeName: Envelope gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus
Molecular weightTheoretical: 56.731629 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW RDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLDNVTEKFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLHCTNV TSVNTTGDRE ELKNCSFNMT T ELRDKRQK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW RDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLDNVTEKFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLHCTNV TSVNTTGDRE ELKNCSFNMT T ELRDKRQK VYSLFYRLDI VPINENQGSE YRLINCNTSA CTQACPKVSF EPIPIHYCAP AGFAILKCKD EGFNGTGLCK NV STVQCTH GIKPVVSTQL LLNGSLAEKN ITIRSENITN NAKIIIVQLV QPVTIKCIRP NNYTRKSIRI GPGQAFYAMG DII GDIRQA HCNVSRSRWN KTLQEVAEKL RTYFGNKTII FANSSGGDLE ITTHSFNCGG EFFYCNTSGL FNSTWYVNST WNDT DSTQE SNDTITLPCR IKQIINMWQR AGQCMYAPPI PGVIKCESNI TGLLLTRDGG KDNNVNETFR PGGGDMRDNW RSELY KYKV VEIEPLGVAP TRCKRRVVE

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #4: Envelope gp41 ectodomain

MacromoleculeName: Envelope gp41 ectodomain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus
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: 31 / 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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9nvv

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 204457
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9nvv

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 204457
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9zrx:
Cryo-EM structure of SHIV-elicited CE79-1571 Fab in complex with HIV Env trimer Q23-SCT27

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