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- EMDB-44730: Cryo-EM structure of rhesus antibody 44715-a.01 in complex with H... -

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Basic information

Entry
Database: EMDB / ID: EMD-44730
TitleCryo-EM structure of rhesus antibody 44715-a.01 in complex with HIV-1 Env BG505 DS-SOSIP
Map data
Sample
  • Complex: Complex of 44715-a.01 and HIV-1 BG505 envelope trimer
    • Protein or peptide: Envelope glycoprotein Gp120
    • Protein or peptide: Envelope glycoprotein Gp41
    • Protein or peptide: 47715-a.01 heavy chain
    • Protein or peptide: 44715-a.01 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeutralizing antibody / HIV-1 V2 apex / SHIV-elicited / 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 / 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
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 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: HIV-1 neutralizing antibodies in SHIV-infected macaques recapitulate structurally divergent modes of human V2 apex recognition with a single D gene
Authors: Roark RS / Shapiro L / Kwong PD
History
DepositionMay 2, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44730.png

Downloads & links

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Map

FileDownload / File: emd_44730.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: 0.1
Minimum - Maximum-0.31063098 - 0.5184518
Average (Standard dev.)0.0012335541 (±0.017204836)
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_44730_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_44730_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 44715-a.01 and HIV-1 BG505 envelope trimer

EntireName: Complex of 44715-a.01 and HIV-1 BG505 envelope trimer
Components
  • Complex: Complex of 44715-a.01 and HIV-1 BG505 envelope trimer
    • Protein or peptide: Envelope glycoprotein Gp120
    • Protein or peptide: Envelope glycoprotein Gp41
    • Protein or peptide: 47715-a.01 heavy chain
    • Protein or peptide: 44715-a.01 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of 44715-a.01 and HIV-1 BG505 envelope trimer

SupramoleculeName: Complex of 44715-a.01 and HIV-1 BG505 envelope trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #4, #2-#3
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: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.300348 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 R

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: 47715-a.01 heavy chain

MacromoleculeName: 47715-a.01 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.143355 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQVVESGGG LVQPGGSLRL SCAASGFTFS HVWMNWVRQA PGKGLEWVAR IKTKGEGGAH YAASVKDRFS VSRDEAKNTA YLQMNSLKI EDTAVYHCKV DGSIVVDEGF D(TYS)YIDAIEKG FVVWGPGVQV TVSSASTKGP SVFPLAPSSR STSESTA AL GCLVKDYFPE ...String:
EVQVVESGGG LVQPGGSLRL SCAASGFTFS HVWMNWVRQA PGKGLEWVAR IKTKGEGGAH YAASVKDRFS VSRDEAKNTA YLQMNSLKI EDTAVYHCKV DGSIVVDEGF D(TYS)YIDAIEKG FVVWGPGVQV TVSSASTKGP SVFPLAPSSR STSESTA AL GCLVKDYFPE PVTVSWNSGS LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYVCNV NHKPSNTKVD KRVEIKTC G GGLEVLFQ

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Macromolecule #3: 44715-a.01 light chain

MacromoleculeName: 44715-a.01 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.939674 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVVMTQSPLS LSITPGQPAS ISCRSIQSLL DSNGKTFLSW YQQKPGRPPR RLIYEVSNRD SGVPDRISGS GAGTDFTLKI SRVEAEDVG IYYCGQDSFF PFTFGPGTKL DIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV ...String:
DVVMTQSPLS LSITPGQPAS ISCRSIQSLL DSNGKTFLSW YQQKPGRPPR RLIYEVSNRD SGVPDRISGS GAGTDFTLKI SRVEAEDVG IYYCGQDSFF PFTFGPGTKL DIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV TEQDSKDNTY SLSSTLTLSS TEYQSHKVYA CEVTHQGLSS PVTKSFNRGE C

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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: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.075406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VGIGAVFLGF LGAAGSTMGA ASMTLTVQAR NLLSGIVQQQ SNLLRAPEAQ QHLLKLTVWG IKQLQARVLA VERYLRDQQL LGIWGCSGK LICCTNVPWN SSWSNRNLSE IWDNMTWLQW DKEISNYTQI IYGLLEESQN QQEKNEQDLL ALD

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: 19 / 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

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Electron microscopy

MicroscopeFEI TITAN 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: 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:

6xrt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48722
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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