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- EMDB-50020: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in com... -

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Basic information

Entry
Database: EMDB / ID: EMD-50020
TitleHIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody.
Map dataFinal map filtered with DeepEMhancer. Suitable for illustration purposes.
Sample
  • Complex: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: ELC07 heavy chain
    • Protein or peptide: ELC07 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / envelope glycoprotein / gp140 / neutralizing antibody / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsHope J / Alguel Y / Nans A / Cherepanov P
Funding support United States, United Kingdom, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170791 United States
The Francis Crick InstituteCC2058 United Kingdom
Wellcome TrustCC2058 United Kingdom
Medical Research Council (MRC, United Kingdom)CC2058 United Kingdom
Cancer Research UKCC2058 United Kingdom
CitationJournal: To Be Published
Title: TITLE: Preservation of memory B cell homeostasis in an individual producing broadly neutralizing antibodies against HIV-1
Authors: Griffith S / Muir L / Suchanek O / Hope J / Pade C / Gibbons G / Tuong K / Fung A / Touizer E / Rees-Spear C / Nans A / Roustan C / Alguel Y / Fink D / Orkin C / Deayton J / Anderson J / ...Authors: Griffith S / Muir L / Suchanek O / Hope J / Pade C / Gibbons G / Tuong K / Fung A / Touizer E / Rees-Spear C / Nans A / Roustan C / Alguel Y / Fink D / Orkin C / Deayton J / Anderson J / Gupta RK / Doores KJ / Cherepanov P / McKnight A / Clatworthy M / McCoy LE
History
DepositionApr 2, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50020.png

Downloads & links

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Map

FileDownload / File: emd_50020.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map filtered with DeepEMhancer. Suitable for illustration purposes.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.022710493 - 1.6258967
Average (Standard dev.)0.0009700964 (±0.020539772)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50020_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Mask #2

Fileemd_50020_msk_2.map
Projections & Slices
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Additional map: Locally filtered sharpened map. Used for real-space refinement.

Fileemd_50020_additional_1.map
AnnotationLocally filtered sharpened map. Used for real-space refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A.

Fileemd_50020_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_50020_half_map_2.map
AnnotationHalf-map B.
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in com...

EntireName: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody
Components
  • Complex: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: ELC07 heavy chain
    • Protein or peptide: ELC07 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in com...

SupramoleculeName: HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505 SOSIP.664
Molecular weightTheoretical: 19.10359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALDGSGLND I FEAQKIEW HE

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Macromolecule #2: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505 SOSIP.664
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

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Macromolecule #3: ELC07 heavy chain

MacromoleculeName: ELC07 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.586055 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG EVQLVQSGAE LKKAGSSVKL SCQAYGVAFS TYSFHWVRQA PGQGLEWLGG FIPLVGKPNY TNKFRGRLT ITADESARTT YMELRSLRSD DTAIYYCAGG GAYSSGGGRF HYFGMAVWGQ GSTVTVSSAS TKGPSVFPLA P SSKSTSGG ...String:
METDTLLLWV LLLWVPGSTG EVQLVQSGAE LKKAGSSVKL SCQAYGVAFS TYSFHWVRQA PGQGLEWLGG FIPLVGKPNY TNKFRGRLT ITADESARTT YMELRSLRSD DTAIYYCAGG GAYSSGGGRF HYFGMAVWGQ GSTVTVSSAS TKGPSVFPLA P SSKSTSGG TAALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TK VDKRVEP KSCGSGENLY FQSAGHHHHH H

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Macromolecule #4: ELC07 light chain

MacromoleculeName: ELC07 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.599775 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTQTPASLLF LLLLWLPGAK CDIQLTQSPS TLSAPVGAGV TITCQASQSI SNGLAWYQQK PGRAPKMLIT EGSSLKSGVP DRFRGSGSG THFILTISDL QPDDSATYFC QQYNTFPWTF GRGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ ...String:
MTQTPASLLF LLLLWLPGAK CDIQLTQSPS TLSAPVGAGV TITCQASQSI SNGLAWYQQK PGRAPKMLIT EGSSLKSGVP DRFRGSGSG THFILTISDL QPDDSATYFC QQYNTFPWTF GRGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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: 27 / 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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTristris

Details: 150 mM NaCl, 50 mM Tris-HCl, pH 7.5
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 275291
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8fr6

chain_id: A, source_name: PDB, initial_model_type: experimental model

8fr6

chain_id: C, source_name: PDB, initial_model_type: experimental model
chain_id: H, source_name: AlphaFold, initial_model_type: in silico model
chain_id: L, source_name: AlphaFold, initial_model_type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9evz:
HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody.

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