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- EMDB-49628: Composite map of three pairs of dimeric VRC36 Fabs bound to HIV-1... -

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Basic information

Entry
Database: EMDB / ID: EMD-49628
TitleComposite map of three pairs of dimeric VRC36 Fabs bound to HIV-1 BG505.T332N DS-SOSIP.664 Env trimer
Map data
Sample
  • Complex: Three pairs of dimeric VRC36 Fabs in complex with HIV-1 BG505.T332N DS-SOSIP.664 Env
    • Protein or peptide: HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp120
    • Protein or peptide: HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp41
    • Protein or peptide: VRC36 Fab heavy chain
    • Protein or peptide: VRC36 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / N-linked glycan / high mannose / broadly neutralizing antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / symbiont-mediated perturbation of host defense response / 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 ...membrane fusion involved in viral entry into host cell / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / symbiont-mediated perturbation of host defense response / 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 / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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 speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsCheng J / Cale EM / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS ...Cheng J / Cale EM / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS / Becker JE / Tsybovsky Y / Li N / Zhang B / Du H / Rubin S / Shapiro L / Pierson TC / Doria-Rose NA / Zhou T / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Composite map of three pairs of dimeric VRC36 Fabs bound to HIV-1 BG505.T332N DS-SOSIP.664 Env trimer
Authors: Cheng J / Cale EM / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS / Becker JE / Tsybovsky Y / Li N / Zhang B / Du H / Rubin S / Shapiro L / Pierson TC / ...Authors: Cheng J / Cale EM / Longo N / Sutton MS / Lei H / Huang R / Morton AJ / Lang ZC / Morano NC / Roark RS / Becker JE / Tsybovsky Y / Li N / Zhang B / Du H / Rubin S / Shapiro L / Pierson TC / Doria-Rose NA / Zhou T / Kwong PD
History
DepositionMar 11, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49628.png

Downloads & links

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Map

FileDownload / File: emd_49628.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.8
Minimum - Maximum-10.531057000000001 - 84.526629999999997
Average (Standard dev.)0.05049178 (±1.458789)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Three pairs of dimeric VRC36 Fabs in complex with HIV-1 BG505.T33...

EntireName: Three pairs of dimeric VRC36 Fabs in complex with HIV-1 BG505.T332N DS-SOSIP.664 Env
Components
  • Complex: Three pairs of dimeric VRC36 Fabs in complex with HIV-1 BG505.T332N DS-SOSIP.664 Env
    • Protein or peptide: HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp120
    • Protein or peptide: HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp41
    • Protein or peptide: VRC36 Fab heavy chain
    • Protein or peptide: VRC36 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Three pairs of dimeric VRC36 Fabs in complex with HIV-1 BG505.T33...

SupramoleculeName: Three pairs of dimeric VRC36 Fabs in complex with HIV-1 BG505.T332N DS-SOSIP.664 Env
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp120

MacromoleculeName: HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.200469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINES NKEYRLINCN T SACTQACP ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINES NKEYRLINCN T SACTQACP KVSFEPIPIH YCAPAGFAIL KCKDKKFNGT GPCPSVSTVQ CTHGIKPVVS TQLLLNGSLA EEEVMIRSEN IT NNAKNIL VQFNTPVQIN CTRPNNNTRK SIRIGPGQAF YATGDIIGDI RQAHCNVSKA TWNETLGKVV KQLRKHFGNN TII RFANSS GGDLEVTTHS FNCGGEFFYC NTSGLFNSTW ISNTSVQGSN STGSNDSITL PCRIKQIINM WQRIGQCMYA PPIQ GVIRC VSNITGLILT RDGGSTNSTT ETFRPGGGDM RDNWRSELYK YKVVKIEPLG VAPTRCKRRV VGRRRRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein gp41

MacromoleculeName: HIV-1 BG505.T332N DS-SOSIP.664 Env glycoprotein 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: VRC36 Fab heavy chain

MacromoleculeName: VRC36 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.125166 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVKLVAYGGA VVRPGGLVRI SCQASGFNFV NAWMSWVRQA PGRGPEWVGR IKSRADGWTV DYNSRVKGRF TISRDDDRDR MYLHTTNLK PEDTGIYYCV HLREKGDDWS SGSQVIVSPA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
DVKLVAYGGA VVRPGGLVRI SCQASGFNFV NAWMSWVRQA PGRGPEWVGR IKSRADGWTV DYNSRVKGRF TISRDDDRDR MYLHTTNLK PEDTGIYYCV HLREKGDDWS SGSQVIVSPA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDK

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Macromolecule #4: VRC36 Fab light chain

MacromoleculeName: VRC36 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.38091 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPAT VCLSAGETVR LTCTASHSVG KSLSWLQQRP GQAPRPLISE VSARPTGTPR RFSGSGSETD FTLTIDSLEA EDSAMYYCQ QRGEWPFTFG QGTKVEINRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPAT VCLSAGETVR LTCTASHSVG KSLSWLQQRP GQAPRPLISE VSARPTGTPR RFSGSGSETD FTLTIDSLEA EDSAMYYCQ QRGEWPFTFG QGTKVEINRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 15 / 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 K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 70.53 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8tl3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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