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- EMDB-25755: ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs -

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Basic information

Entry
Database: EMDB / ID: EMD-25755
TitleApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs
Map data
Sample
  • Complex: HIV-1 Envelope ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs
    • Protein or peptide: HIV-1 Envelope ApexGT5 gp120
    • Protein or peptide: HIV-1 Envelope ApexGT5 gp41
    • Protein or peptide: RM20A3 Fab Heavy Chain
    • Protein or peptide: RM20A3 Fab Light Chain
    • Protein or peptide: GT5-d42.16 Fab Heavy Chain
    • Protein or peptide: GT5-d42.16 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV / germline targeting vaccine / VIRAL PROTEIN / 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 speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsBerndsen ZT / Ward AB
Funding support United States, 4 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1084519 United States
Bill & Melinda Gates FoundationOPP1196345 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 Al100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: Immunity / Year: 2022
Title: Priming HIV Envelope V2 Apex-directed broadly neutralizing antibody responses with protein or mRNA immunogens
Authors: Melzi E / Willis J / Ma K / Lin Y / Kratochvil S / Berndsen ZT / Nair U / Warner J / Steichen J / Pecetta S / Perez M / Kirsch K / Ward AB / Schief W / Batista FD
History
DepositionDec 18, 2021-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25755.png

Downloads & links

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Map

FileDownload / File: emd_25755.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 300 pix.
= 345. Å		1.15 Å/pix.
x 300 pix.
= 345. Å		1.15 Å/pix.
x 300 pix.
= 345. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.293
Minimum - Maximum-0.47683078 - 1.3099647
Average (Standard dev.)0.0017004884 (±0.039037075)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 345.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25755_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_25755_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_25755_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 : HIV-1 Envelope ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs

EntireName: HIV-1 Envelope ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs
Components
  • Complex: HIV-1 Envelope ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs
    • Protein or peptide: HIV-1 Envelope ApexGT5 gp120
    • Protein or peptide: HIV-1 Envelope ApexGT5 gp41
    • Protein or peptide: RM20A3 Fab Heavy Chain
    • Protein or peptide: RM20A3 Fab Light Chain
    • Protein or peptide: GT5-d42.16 Fab Heavy Chain
    • Protein or peptide: GT5-d42.16 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Envelope ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs

SupramoleculeName: HIV-1 Envelope ApexGT5 in complex with GT5-d42.16 and RM20A3 Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 Envelope ApexGT5 gp120

MacromoleculeName: HIV-1 Envelope ApexGT5 gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.196496 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNATTELRN KRQKVYSLFY RLDIVPMVDL WTNYRLINCN T SAITQACP ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNATTELRN KRQKVYSLFY RLDIVPMVDL WTNYRLINCN T SAITQACP KVSFEPIPIH YCAPAGFAIL KCKDKKFNGT GPCPSVSTVQ CTHGIKPVVS TQLLLNGSLA EEEVIIRSEN IT NNAKNIL VQLNTPVQIN CTRPNNNTVK SIRIGPGQAF YYTGDIIGDI RQAHCNVSKA TWNETLGKVV KQLRKHFGNN TII RFAQSS GGDLEVTTHS FNCGGEFFYC NTSGLFNSTW ISNTSVQGSN STGSNDSITL PCRIKQIINM WQRIGQAMYA PPIQ GVIRC VSNITGLILT RDGGSTNSTT ETFRPGGGDM RDNWRSELYK YKVVKIEPLG VAPTRCKRRV VGRRRRRR

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Macromolecule #2: HIV-1 Envelope ApexGT5 gp41

MacromoleculeName: HIV-1 Envelope ApexGT5 gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.134324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVSLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: RM20A3 Fab Heavy Chain

MacromoleculeName: RM20A3 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.511111 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVETGGG LVQPGGSLKL SCRASGYTFS SFAMSWVRQA PGKGLEWVSL INDRGGLTFY VDSVKGRFTI SRDNSKNTLS LQMHSLRDG DTAVYYCATG GMSSALQSSK YYFDFWGQGA LVTVSS

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Macromolecule #4: RM20A3 Fab Light Chain

MacromoleculeName: RM20A3 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.5088 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ALTQPPSVSG SPGQSVTISC TGTSSDIGSY NYVSWYQQHP GKAPKLMIYD VTQRPSGVSD RFSGSKSGNT ASLTISGLQA DDEADYYCS AYAGRQTFYI FGGGTRLTVL GQPKASPTVT LFPPSSEEL

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Macromolecule #5: GT5-d42.16 Fab Heavy Chain

MacromoleculeName: GT5-d42.16 Fab Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 15.126627 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVKPGGSLRL SCTASGFTFS NAWMSWVRQA PGKGLEWVGR IKSKTEGGTT DYATPVKGRF TISRDDSKDT LFLQMNSLK TEDTAVYYCN TGVETYDFWS G(TYS)DDH(TYS)YDYY FRDVWGKGTT VTVSS

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Macromolecule #6: GT5-d42.16 Fab Light Chain

MacromoleculeName: GT5-d42.16 Fab Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.605943 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASQIIS SIYFAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSFTFG PGTKVDIK

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Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 41 / 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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35763
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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