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- EMDB-41498: HIV-1 BG505 Env SOSIP in complex with bovine Fab Bess4 and non-hu... -

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Basic information

Entry
Database: EMDB / ID: EMD-41498
TitleHIV-1 BG505 Env SOSIP in complex with bovine Fab Bess4 and non-human primate Fab RM20A3
Map datasharpened map
Sample
  • Complex: HIV-1 BG505 SOSIP Env in complex with bovine Bess4 Fab and NHP RM20A3 Fab
    • Protein or peptide: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: NHP RM20A3 Fab heavy chain
    • Protein or peptide: NHP RM20A3 Fab light chain
    • Protein or peptide: Bovine Bess4 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSOSIP / apex / broadly neutralizing antibody / Env / HIV-1 / 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 / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / apoptotic process / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey) / Bos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsOzorowski G / Lee WH / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-034657 United States
CitationJournal: To Be Published
Title: Immunization of cows with HIV Envelope trimers generates broadly neutralizing antibodies to the V2-apex as well as the CD4 binding site from the ultra-long CDRH3 repertoire
Authors: Altman P / Ozorowski G
History
DepositionAug 6, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41498.png

Downloads & links

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Map

FileDownload / File: emd_41498.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 384 pix.
= 401.28 Å		1.05 Å/pix.
x 384 pix.
= 401.28 Å		1.05 Å/pix.
x 384 pix.
= 401.28 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.7577391 - 1.4192308
Average (Standard dev.)-0.0007314934 (±0.031120688)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 401.27997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41498_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_41498_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_41498_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 BG505 SOSIP Env in complex with bovine Bess4 Fab and NHP RM...

EntireName: HIV-1 BG505 SOSIP Env in complex with bovine Bess4 Fab and NHP RM20A3 Fab
Components
  • Complex: HIV-1 BG505 SOSIP Env in complex with bovine Bess4 Fab and NHP RM20A3 Fab
    • Protein or peptide: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: NHP RM20A3 Fab heavy chain
    • Protein or peptide: NHP RM20A3 Fab light chain
    • Protein or peptide: Bovine Bess4 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 BG505 SOSIP Env in complex with bovine Bess4 Fab and NHP RM...

SupramoleculeName: HIV-1 BG505 SOSIP Env in complex with bovine Bess4 Fab and NHP RM20A3 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120

MacromoleculeName: HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 57.945977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKKQK VYSLFYRLDV VQINENQGNR SNNSNKEYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCKDKKF NG TGPCPSV STVQCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QAF YATGDI IGDIRQAHCN VSKATWNETL GKVVKQLRKH FGNNTIIRFA NSSGGDLEVT THSFNCGGEF FYCNTSGLFN STWI SNTSV QGSNSTGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRD NWRS ELYKYKVVKI EPLGVAPTRC KRRVVGRRRR RR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Transmembrane protein gp41

MacromoleculeName: Transmembrane protein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: NHP RM20A3 Fab heavy chain

MacromoleculeName: NHP 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: NHP RM20A3 Fab light chain

MacromoleculeName: NHP 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: Bovine Bess4 Fab heavy chain

MacromoleculeName: Bovine Bess4 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 17.435293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
KVQLRESGPS LVKPSQTLSL TCTASGLTLS DKAVGWVRQA PGKALEWLGS IDTSGNTGYN PGLKSRLTIT KDSSKSQVSL SVSSVTTED SATYYCTTVH QQTRNKVKSC PSGEDCGIGC CYHGCSATDY GCWDGSSYAP YSYTYTYELH VDTWGQGLLV T VSS

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 45 / 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

Concentration2.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: cryosparc Ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: non-uniform refinement / Number images used: 82374
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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