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- EMDB-41346: CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41346
TitleCRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO DJ85-b.01 FAB
Map data
Sample
  • Complex: BG505 DS-SOSIP DJ85-b.01 FAB COMPLEX
    • Complex: BG505 DS-SOSIP
      • Protein or peptide: BG505 DS-SOSIP Surface protein gp120
      • Protein or peptide: BG505 DS-SOSIP Transmembrane protein gp41
    • Complex: DJ85-b.01 FAB
      • Protein or peptide: DJ85-b.01 FAB HEAVY CHAIN
      • Protein or peptide: DJ85-b.01 FAB LIGHT CHAIN
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsbroadly neutralizing antibody / fusion peptide / HIV-1 / glycoprotein / viral protein / FP-targeting vaccines / 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 / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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 speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsPletnev S / Hoyt F / Fischer E / Kwong P
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: Broad and potent HIV-1 neutralization in fusion peptide-primed SHIV-boosted macaques.
Authors: Wang H
History
DepositionJul 25, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41346.png

Downloads & links

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Map

FileDownload / File: emd_41346.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 440 pix.
= 380.028 Å		0.86 Å/pix.
x 440 pix.
= 380.028 Å		0.86 Å/pix.
x 440 pix.
= 380.028 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8637 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-1.9816291 - 2.7513974
Average (Standard dev.)0.00013991699 (±0.0406417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 380.02798 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41346_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41346_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41346_half_map_2.map
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 DS-SOSIP DJ85-b.01 FAB COMPLEX

EntireName: BG505 DS-SOSIP DJ85-b.01 FAB COMPLEX
Components
  • Complex: BG505 DS-SOSIP DJ85-b.01 FAB COMPLEX
    • Complex: BG505 DS-SOSIP
      • Protein or peptide: BG505 DS-SOSIP Surface protein gp120
      • Protein or peptide: BG505 DS-SOSIP Transmembrane protein gp41
    • Complex: DJ85-b.01 FAB
      • Protein or peptide: DJ85-b.01 FAB HEAVY CHAIN
      • Protein or peptide: DJ85-b.01 FAB LIGHT CHAIN
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505 DS-SOSIP DJ85-b.01 FAB COMPLEX

SupramoleculeName: BG505 DS-SOSIP DJ85-b.01 FAB COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: BG505 DS-SOSIP

SupramoleculeName: BG505 DS-SOSIP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: DJ85-b.01 FAB

SupramoleculeName: DJ85-b.01 FAB / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BG505 DS-SOSIP Surface protein gp120

MacromoleculeName: BG505 DS-SOSIP Surface protein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.086324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SACTQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRR R

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: BG505 DS-SOSIP Transmembrane protein gp41

MacromoleculeName: BG505 DS-SOSIP 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: DJ85-b.01 FAB HEAVY CHAIN

MacromoleculeName: DJ85-b.01 FAB HEAVY CHAIN / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.501328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKASETLSL TCAVSGASVS GNYYWNWIRQ SPGKELEWIG NIHGNSGTTT YNPSLESRVT ISTDTSKNQF SLKLTSVTG ADTATYFCAT QFKKYWGLSV SSPFSFSDSW GQGVLVSVSS ASTKGPSVFP LAPSSRSTSE STAALGCLVK D YFPEPVTV ...String:
QVQLQESGPG LVKASETLSL TCAVSGASVS GNYYWNWIRQ SPGKELEWIG NIHGNSGTTT YNPSLESRVT ISTDTSKNQF SLKLTSVTG ADTATYFCAT QFKKYWGLSV SSPFSFSDSW GQGVLVSVSS ASTKGPSVFP LAPSSRSTSE STAALGCLVK D YFPEPVTV SWNSGSLTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYVCNVNHKP SNTKVDKRVE IKTCGGLEVL FQ

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Macromolecule #4: DJ85-b.01 FAB LIGHT CHAIN

MacromoleculeName: DJ85-b.01 FAB LIGHT CHAIN / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.429877 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPRS LSASVGDRVT ITCRASQDIS PDLNWYQQKP GGPLKLLIYD ASNLQGGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCL QYNGYPWTFG QGTKVDHKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIQMTQSPRS LSASVGDRVT ITCRASQDIS PDLNWYQQKP GGPLKLLIYD ASNLQGGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCL QYNGYPWTFG QGTKVDHKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / 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

Concentration5.2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9614 / Average electron dose: 46.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1183403
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8euv

Final reconstructionNumber classes used: 68 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 534557
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final 3D classificationNumber classes: 68 / Software - Name: cryoSPARC (ver. 3.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8tkc:
CRYO-EM STRUCTURE OF HIV-1 BG505DS-SOSIP.664 ENV TRIMER BOUND TO DJ85-b.01 FAB

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