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- EMDB-40797: BG505 GT1.1 SOSIP in complex with NHP Fabs 21N13, 21M20 and RM20A3 -

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Basic information

Entry
Database: EMDB / ID: EMD-40797
TitleBG505 GT1.1 SOSIP in complex with NHP Fabs 21N13, 21M20 and RM20A3
Map datasharpened map
Sample
  • Complex: BG505 GT1.1 SOSIP in complex with 21N13 Fab, 21M20 Fab and RM20A3 Fab
    • Protein or peptide: 21M20 heavy chain variable region
    • Protein or peptide: 21M20 light chain variable region
    • Protein or peptide: BG505 GT1.1 SOSIP gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: RM20A3 heavy chain variable region
    • Protein or peptide: RM20A3 light chain variable region
    • Protein or peptide: 21N13 heavy chain variable region
    • Protein or peptide: 21N13 light chain variable region
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsgermline targeting / HIV-1 Env / neutralizing antibody / non-human primate antibody / CD4 binding site / fusion peptide / VIRAL PROTEIN
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 / virion attachment to host cell / apoptotic process / 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
Similarity search - Component
Biological speciesMacaca (macaques) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsOzorowski G / Torres JL / Zhang S / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: To Be Published
Title: Neutralizing antibodies induced in non-human primates by germline targeting Env trimer
Authors: Caniels T / Ozorowski G / Ward AB / Sanders RW
History
DepositionMay 17, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40797.png

Downloads & links

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Map

FileDownload / File: emd_40797.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 1.044 Å
Density
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.1151115 - 1.9512358
Average (Standard dev.)-0.00077392225 (±0.034971155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 417.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40797_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_40797_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_40797_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BG505 GT1.1 SOSIP in complex with 21N13 Fab, 21M20 Fab and RM20A3 Fab

EntireName: BG505 GT1.1 SOSIP in complex with 21N13 Fab, 21M20 Fab and RM20A3 Fab
Components
  • Complex: BG505 GT1.1 SOSIP in complex with 21N13 Fab, 21M20 Fab and RM20A3 Fab
    • Protein or peptide: 21M20 heavy chain variable region
    • Protein or peptide: 21M20 light chain variable region
    • Protein or peptide: BG505 GT1.1 SOSIP gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: RM20A3 heavy chain variable region
    • Protein or peptide: RM20A3 light chain variable region
    • Protein or peptide: 21N13 heavy chain variable region
    • Protein or peptide: 21N13 light chain variable region
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505 GT1.1 SOSIP in complex with 21N13 Fab, 21M20 Fab and RM20A3 Fab

SupramoleculeName: BG505 GT1.1 SOSIP in complex with 21N13 Fab, 21M20 Fab and RM20A3 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 770 KDa

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Macromolecule #1: 21M20 heavy chain variable region

MacromoleculeName: 21M20 heavy chain variable region / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 13.737351 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LAKPGGSLRL SCAASGFTFS RSIMHWVRQA PGKGLEWVST INYAGSTYYA DSVRGRFVIS RDNSKNTLSL QMNSVRPED RAVYHCAKDK EGYYSGGYPL WYFDLWGPGT PVTISS

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Macromolecule #2: 21M20 light chain variable region

MacromoleculeName: 21M20 light chain variable region / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 11.358563 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DVQMTQSPSS LSASVGDKVS ITCRASQGIA DALAWYQQKP GKAPKLLIYG ASNLESGVPS RFSGSGSGTD FSLTISSLQA EDFAVYYCQ QRNSHPPTFG QGTRVEVK

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Macromolecule #3: BG505 GT1.1 SOSIP gp120

MacromoleculeName: BG505 GT1.1 SOSIP gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 57.27548 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETKK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKRQK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETKK HNVWATHACV PTDPNPQEI HLENVTEEFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLQCTNV TNNITDDMRG ELKNCSFNMT T ELRDKRQK VHALFYKLDI VPINENQNTS YRLINCNTAA ITQACPKVSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SV STVQCTH GIKPVVSTQL LLNGSLAEEE VMIRSKDIRN NAKNILVQFN TPVQINCTRP NNNTRKSIRI GPGQWFYATG DII GDIRQA HCNVSKATWN ETLGKVVKQL RKHFGNNTII RFANSSGGDL EVTTHSFNCG GEFFYCDTSG LFNSTWISNT SVQG SNSTG SNDSITLPCR IKQIINMWQR IGQAMYAPPI QGVIRCVSNI TGLILTRDGG STDSTTETFR PSGGDMRDNW RSELY KYKV VKIEPLGVAP TRCKRRVVGR RRRRR

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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: 17.146482 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 #5: RM20A3 heavy chain variable region

MacromoleculeName: RM20A3 heavy chain variable region / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 13.424034 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVETGGG LVQPGGSLKL SCRASGYTFS SFAMSWVRQA PGKGLEWVSL INDRGGLTFY VDSVKGRFTI SRDNSKNTLS LQMHSLRDG DTAVYYCATG GMSSALQSSK YYFDFWGQGA LVTVS

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Macromolecule #6: RM20A3 light chain variable region

MacromoleculeName: RM20A3 light chain variable region / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 11.755821 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPPSV SGSPGQSVTI SCTGTSSDIG SYNYVSWYQQ HPGKAPKLMI YDVTQRPSGV SDRFSGSKSG NTASLTISGL QADDEADYY CSAYAGRQTF YIFGGGTRLT VL

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Macromolecule #7: 21N13 heavy chain variable region

MacromoleculeName: 21N13 heavy chain variable region / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 14.476926 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG RVKPSETLSL TCAVSDDSFG SSYFYWSWIR QAPGKGLEWI GYIAYSGGVR YNPSLSSRVT ISRNIHERQF YLRLTSMTA ADTAVYYCAR HCEDDYGYYS AAQSYGLDSW GQGIAVTVSP S

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Macromolecule #8: 21N13 light chain variable region

MacromoleculeName: 21N13 light chain variable region / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 11.757068 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRTSENVN NCLNWYQQKP GKAPKLLIYR TSTLQRGVPS RFSGTGSGTD YTLTISSLQS EDFGTYYCQ HYYGTPLTFG GGTMVDIK

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 33 / 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

Concentration6 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMSodium chlorideNaCl
0.06 mMn-Dodecyl-B-D-Maltopyranoside

Details: Detergent added shortly before freezing
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 48.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Software - details: Non-uniform refinement / Number images used: 242098
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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