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- EMDB-44728: Cryo-EM structure of rhesus antibody V031-a.01 in complex with HI... -

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Basic information

Entry
Database: EMDB / ID: EMD-44728
TitleCryo-EM structure of rhesus antibody V031-a.01 in complex with HIV-1 Env BG505 DS-SOSIP
Map data
Sample
  • Complex: Complex of V031-a.01 with HIV-1 BG505 envelope trimer
    • Protein or peptide: V031-a.01 heavy chain
    • Protein or peptide: V031-a.01 light chain
    • Protein or peptide: Human immunodeficiency virus 1 envelope glycoprotein Gp120
    • Protein or peptide: Envelope glycoprotein Gp41
  • 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 speciesHomo sapiens (human) / Macaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44728.png

Downloads & links

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Map

FileDownload / File: emd_44728.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-0.18708393 - 0.5349725
Average (Standard dev.)0.00079051754 (±0.015283529)
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_44728_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_44728_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 V031-a.01 with HIV-1 BG505 envelope trimer

EntireName: Complex of V031-a.01 with HIV-1 BG505 envelope trimer
Components
  • Complex: Complex of V031-a.01 with HIV-1 BG505 envelope trimer
    • Protein or peptide: V031-a.01 heavy chain
    • Protein or peptide: V031-a.01 light chain
    • Protein or peptide: Human immunodeficiency virus 1 envelope glycoprotein Gp120
    • Protein or peptide: Envelope glycoprotein Gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of V031-a.01 with HIV-1 BG505 envelope trimer

SupramoleculeName: Complex of V031-a.01 with HIV-1 BG505 envelope trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: V031-a.01 heavy chain

MacromoleculeName: V031-a.01 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 27.095355 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LVTLKESGPA LVTPTQTLTL TCTLSGFSLT TTGMRVNWIR QAPGKALEWL ARIDYNEARF YSSSLKTRLS ISTDASKNQV VLRMTNMAP VDTGTYYCAR SQQHYYEDA(TYS) TFDWYYFHSR DNGLDSWGQG VVVTVSSAST KGPSVFPLAP SSRSTSE ST AALGCLVKDY ...String:
LVTLKESGPA LVTPTQTLTL TCTLSGFSLT TTGMRVNWIR QAPGKALEWL ARIDYNEARF YSSSLKTRLS ISTDASKNQV VLRMTNMAP VDTGTYYCAR SQQHYYEDA(TYS) TFDWYYFHSR DNGLDSWGQG VVVTVSSAST KGPSVFPLAP SSRSTSE ST AALGCLVKDY FPEPVTVSWN SGSLTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYV CNVNHKPSNT KVDKRVEI K TCGGGLEVLF Q

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Macromolecule #2: V031-a.01 light chain

MacromoleculeName: V031-a.01 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.802484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQTPLS LPVTPGEPAS ISCRSSQSLL DSDGYTHLSW YLQKPGQSPQ LLISLVSNRA SGVPDRFSGS GSGTDFTLKL NRVEAEDVG LYYCMQGLQT PYTFGQGTKV EIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV ...String:
DIVMTQTPLS LPVTPGEPAS ISCRSSQSLL DSDGYTHLSW YLQKPGQSPQ LLISLVSNRA SGVPDRFSGS GSGTDFTLKL NRVEAEDVG LYYCMQGLQT PYTFGQGTKV EIKRTVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGAL K TGNSQESV TEQDSKDNTY SLSSTLTLSS TEYQSHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #3: Human immunodeficiency virus 1 envelope glycoprotein Gp120

MacromoleculeName: Human immunodeficiency virus 1 envelope glycoprotein Gp120
type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.01502 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ENLWVTVYYG VPVWKDAETT LFCASDAKAY ETEKHNVWAT HACVPTDPNP QEIHLENVTE EFNMWKNNMV EQMHTDIISL WDQSLKPCV KLTPLCVTLQ CTNVTNNITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE Y RLINCNTS ...String:
ENLWVTVYYG VPVWKDAETT LFCASDAKAY ETEKHNVWAT HACVPTDPNP QEIHLENVTE EFNMWKNNMV EQMHTDIISL WDQSLKPCV KLTPLCVTLQ CTNVTNNITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE Y RLINCNTS ACTQACPKVS FEPIPIHYCA PAGFAILKCK DKKFNGTGPC PSVSTVQCTH GIKPVVSTQL LLNGSLAEEE VM IRSENIT NNAKNILVQF NTPVQINCTR PNNNTRKSIR IGPGQAFYAT GDIIGDIRQA HCNVSKATWN ETLGKVVKQL RKH FGNNTI IRFANSSGGD LEVTTHSFNC GGEFFYCNTS GLFNSTWISN TSVQGSNSTG SNDSITLPCR IKQIINMWQR IGQC MYAPP IQGVIRCVSN ITGLILTRDG GSTNSTTETF RPGGGDMRDN WRSELYKYKV VKIEPLGVAP TRCKRRVV

UniProtKB: Envelope glycoprotein gp160

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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: 16.693975 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VFLGFLGAAG STMGAASMTL TVQARNLLSG IVQQQSNLLR AIEAQQHLLK LTVWGIKQLQ ARVLAVERYL RDQQLLGIWG CSGKLICCT NVPWNSSWSN RNLSEIWDNM TWLQWDKEIS NYTQIIYGLL EESQNQQEKN EQDLLALD

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: 39 / 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 353856
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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