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- EMDB-27718: SIV E660.CR54 SOS-2P Env Trimer with ITS92.02 -

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Basic information

Entry
Database: EMDB / ID: EMD-27718
TitleSIV E660.CR54 SOS-2P Env Trimer with ITS92.02
Map datasharpened map
Sample
  • Complex: SIV E660.CR54 SOS-2P with ITS92.02
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: ITS92.02 Heavy Chain
    • Protein or peptide: ITS92.02 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSIV / ITS92 / HIV-1 / quaternary / HIV-2 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
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 speciesInfluenza A virus / Simian immunodeficiency virus / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.32 Å
AuthorsGorman J / Kwong PD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateSimons Foundation (SF349247)
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Cryo-EM structures of prefusion SIV envelope trimer.
Authors: Jason Gorman / Chunyan Wang / Rosemarie D Mason / Alexandra F Nazzari / Hugh C Welles / Tongqing Zhou / Julian W Bess / Tatsiana Bylund / Myungjin Lee / Yaroslav Tsybovsky / Raffaello ...Authors: Jason Gorman / Chunyan Wang / Rosemarie D Mason / Alexandra F Nazzari / Hugh C Welles / Tongqing Zhou / Julian W Bess / Tatsiana Bylund / Myungjin Lee / Yaroslav Tsybovsky / Raffaello Verardi / Shuishu Wang / Yongping Yang / Baoshan Zhang / Reda Rawi / Brandon F Keele / Jeffrey D Lifson / Jun Liu / Mario Roederer / Peter D Kwong /
Abstract: Simian immunodeficiency viruses (SIVs) are lentiviruses that naturally infect non-human primates of African origin and seeded cross-species transmissions of HIV-1 and HIV-2. Here we report prefusion ...Simian immunodeficiency viruses (SIVs) are lentiviruses that naturally infect non-human primates of African origin and seeded cross-species transmissions of HIV-1 and HIV-2. Here we report prefusion stabilization and cryo-EM structures of soluble envelope (Env) trimers from rhesus macaque SIV (SIV) in complex with neutralizing antibodies. These structures provide residue-level definition for SIV-specific disulfide-bonded variable loops (V1 and V2), which we used to delineate variable-loop coverage of the Env trimer. The defined variable loops enabled us to investigate assembled Env-glycan shields throughout SIV, which we found to comprise both N- and O-linked glycans, the latter emanating from V1 inserts, which bound the O-link-specific lectin jacalin. We also investigated in situ SIV-Env trimers on virions, determining cryo-electron tomography structures at subnanometer resolutions for an antibody-bound complex and a ligand-free state. Collectively, these structures define the prefusion-closed structure of the SIV-Env trimer and delineate variable-loop and glycan-shielding mechanisms of immune evasion conserved throughout SIV evolution.
History
DepositionJul 27, 2022-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27718.png

Downloads & links

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Map

FileDownload / File: emd_27718.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 346.56 Å		1.08 Å/pix.
x 320 pix.
= 346.56 Å		1.08 Å/pix.
x 320 pix.
= 346.56 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.06535167 - 0.3748795
Average (Standard dev.)0.0023114954 (±0.014629841)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 346.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27718_msk_1.map
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Additional map: density modified map

Fileemd_27718_additional_1.map
Annotationdensity modified map
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Additional map: unsharpened map

Fileemd_27718_additional_2.map
Annotationunsharpened map
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Half map: #2

Fileemd_27718_half_map_1.map
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Half map: #1

Fileemd_27718_half_map_2.map
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Sample components

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Entire : SIV E660.CR54 SOS-2P with ITS92.02

EntireName: SIV E660.CR54 SOS-2P with ITS92.02
Components
  • Complex: SIV E660.CR54 SOS-2P with ITS92.02
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: ITS92.02 Heavy Chain
    • Protein or peptide: ITS92.02 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SIV E660.CR54 SOS-2P with ITS92.02

SupramoleculeName: SIV E660.CR54 SOS-2P with ITS92.02 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus

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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: Simian immunodeficiency virus
Molecular weightTheoretical: 16.852207 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GVFVLGFLGF LATAGSAMGA ASLTLSAQSR TLLAGIVQQQ QQLLDVPKRQ QELLRLPVWG TKNLQTRVTA IEKYLKDQAQ LNSWGCAFR QVCCTTVPWP NETLVPNWSN MTWQEWERQV DFLEANITQL LEEAQIQQEK NMYELQKLN

UniProtKB: Envelope glycoprotein gp160

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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: Simian immunodeficiency virus
Molecular weightTheoretical: 59.053578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IQYVTVFYGV PAWKNATIPL FCATKNRDTW GTTQCLPDND DYSELAINIT EAFDAWNNTV TEQAIEDVWN LFETSIKPCV KLTPLCIAM RCNKTETDRW GLTRNAGTTT TTTTTTTAAT PSVAENVINE SNPCIKNNSC AGLEQEPMIG CKFNMTGLKR D KRIEYNET ...String:
IQYVTVFYGV PAWKNATIPL FCATKNRDTW GTTQCLPDND DYSELAINIT EAFDAWNNTV TEQAIEDVWN LFETSIKPCV KLTPLCIAM RCNKTETDRW GLTRNAGTTT TTTTTTTAAT PSVAENVINE SNPCIKNNSC AGLEQEPMIG CKFNMTGLKR D KRIEYNET WYSRDLICEQ SANESESKCY MHHCNTSVIQ ESCDKHYWDA IRFRYCAPPG YALLRCNDSN YSGFAPNCSK VV VSSCTRM METQTSTWFG FNGTRAENRT YIYWHGKSNR TIISLNKYYN LTMRCRRPGN KTVLPVTIMS GLVFHSQPIN ERP KQAWCW FGGSWKEAIQ EVKETLVKHP RYTGTNDTRK INLTAPAGGD PEVTFMWTNC RGEFLYCKMN WFLNWVEDRD QKSS RWRQQ NTRERQKKNY VPCHIRQIIN TWHKVGKNVY LPPREGDLTC NSTVTSLIAE IDWTNNNETN ITMSAEVAEL YRLEL GDYK LVEITPIGLA PTSCRRYTTT GASRRRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: ITS92.02 Heavy Chain

MacromoleculeName: ITS92.02 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.275268 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCAVSGGSVS GNWWSWIRQP PGKGLEYIGR ISGSDGTTYY RSSLKVTISR DTSKNQFSLR LNSVTAADT AVYYCARKPT WDWFDVWGPG LLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String:
QVQLQESGPG LVKPSETLSL TCAVSGGSVS GNWWSWIRQP PGKGLEYIGR ISGSDGTTYY RSSLKVTISR DTSKNQFSLR LNSVTAADT AVYYCARKPT WDWFDVWGPG LLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDKGLEVLFQ

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Macromolecule #4: ITS92.02 Light Chain

MacromoleculeName: ITS92.02 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.397963 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQGID NYLNWYQQKP GKAPKRLIFA ASSLHNGVPS RFSGSGSGTK FTLTISSLQP EDLGTYYCL QYYSDPYTFG QGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQGID NYLNWYQQKP GKAPKRLIFA ASSLHNGVPS RFSGSGSGTK FTLTISSLQP EDLGTYYCL QYYSDPYTFG QGTKVEIKRT 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: 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

Concentration2 mg/mL
BufferpH: 7.4 / Details: PBS
VitrificationCryogen name: ETHANE
DetailsSIV E660.CR54 SOS-2P with ITS92.02

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 51.16 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 32347
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

6tyb


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8dua:
SIV E660.CR54 SOS-2P Env Trimer with ITS92.02

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