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- EMDB-48283: 61-12A01 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer an... -

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Basic information

Entry
Database: EMDB / ID: EMD-48283
Title61-12A01 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab
Map datasharpened map
Sample
  • Complex: 61-12A01 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab
    • Protein or peptide: 61_12A01 heavy chain Fv
    • Protein or peptide: 61_12A01 kappa chain Fv
    • Protein or peptide: RM20A3 heavy chain Fv
    • Protein or peptide: RM20A3 light chain Fv
    • Protein or peptide: GT1.1 v4.1 SOSIP gp120
    • Protein or peptide: Envelope glycoprotein gp160
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / SOSIP / germline targeting / VRC01 / clinical trial / human / precursor antibody / VIRAL PROTEIN
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 ...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 / Homo sapiens (human) / Macaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPhulera S / Ozorowski G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Science / Year: 2025
Title: Precise targeting of HIV broadly neutralizing antibody precursors in humans
Authors: Caniels TG / Prabhakaran M / Ozorowski G / MacPhee KJ / Wu W / van der Straten K / Agrawal S / Derking R / Reiss EIMM / Millard K / Turroja M / Desrosiers A / Bethony J / Malkin E / Liesdek ...Authors: Caniels TG / Prabhakaran M / Ozorowski G / MacPhee KJ / Wu W / van der Straten K / Agrawal S / Derking R / Reiss EIMM / Millard K / Turroja M / Desrosiers A / Bethony J / Malkin E / Liesdek MH / van der Veen A / Klouwens M / Phulera S / Wilson IA / Ward AB
History
DepositionDec 12, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48283.png

Downloads & links

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Map

FileDownload / File: emd_48283.map.gz / Format: CCP4 / Size: 244.1 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.)
1.03 Å/pix.
x 400 pix.
= 413.56 Å		1.03 Å/pix.
x 400 pix.
= 413.56 Å		1.03 Å/pix.
x 400 pix.
= 413.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0339 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.6625618 - 2.3412228
Average (Standard dev.)-0.00023393241 (±0.037826315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 413.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48283_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_48283_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_48283_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 : 61-12A01 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer an...

EntireName: 61-12A01 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab
Components
  • Complex: 61-12A01 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab
    • Protein or peptide: 61_12A01 heavy chain Fv
    • Protein or peptide: 61_12A01 kappa chain Fv
    • Protein or peptide: RM20A3 heavy chain Fv
    • Protein or peptide: RM20A3 light chain Fv
    • Protein or peptide: GT1.1 v4.1 SOSIP gp120
    • Protein or peptide: Envelope glycoprotein gp160
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 61-12A01 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer an...

SupramoleculeName: 61-12A01 Fab in complex with HIV-1 GT1.1 v4.1 SOSIP Env trimer and RM20A3 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Human immunodeficiency virus

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Macromolecule #1: 61_12A01 heavy chain Fv

MacromoleculeName: 61_12A01 heavy chain Fv / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.989641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKQPGASVKV SCKASGYTFS DHFMHWVRQA PGQGLEWMGW INPKSGGPNY AQKFQGRVTM TRDRSISTAY MELRGLRSD DTAIYYCARP MHDYDDHDWY FDLWGRGTLV TVSS

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Macromolecule #2: 61_12A01 kappa chain Fv

MacromoleculeName: 61_12A01 kappa chain Fv / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.199423 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VSVLTQSPGT LSLSPGERAT LSCRASQTVG SSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYEAFGQGT KVEIK

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Macromolecule #3: RM20A3 heavy chain Fv

MacromoleculeName: RM20A3 heavy chain Fv / 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 light chain Fv

MacromoleculeName: RM20A3 light chain Fv / 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: GT1.1 v4.1 SOSIP gp120

MacromoleculeName: GT1.1 v4.1 SOSIP gp120 / type: protein_or_peptide / ID: 5 / 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 #6: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 6 / 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 #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 24 / 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

Concentration2.1 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / 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

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 3867 / Average exposure time: 2.57 sec. / Average electron dose: 45.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 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

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio (cryoSPARC)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 165097
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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