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- EMDB-27735: Cryo-EM structure of SIVmac239 SOS-2P Env trimer in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-27735
TitleCryo-EM structure of SIVmac239 SOS-2P Env trimer in complex with human bNAb PGT145
Map datasharpened
Sample
  • Complex: SIVmac239 SOS-2P in complex with PGT145
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: PGT145 Heavy
    • Protein or peptide: PGT145 Light
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose
KeywordsCD4 / HIV-1 / SOSIP / Vaccine / IMMUNE SYSTEM / SIV / VIRAL PROTEIN / 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 speciesSimian immunodeficiency virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.12 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 28, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27735.png

Downloads & links

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Map

FileDownload / File: emd_27735.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened
Projections & slices

Image control

Size
Brightness
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: 0.28
Minimum - Maximum-0.55037695 - 1.4746993
Average (Standard dev.)0.003089229 (±0.05557127)
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_27735_msk_1.map
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Additional map: density modified (resolve)

Fileemd_27735_additional_1.map
Annotationdensity modified (resolve)
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Additional map: unsharpened

Fileemd_27735_additional_2.map
Annotationunsharpened
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Half map: half map A

Fileemd_27735_half_map_1.map
Annotationhalf map A
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Half map: half map B

Fileemd_27735_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : SIVmac239 SOS-2P in complex with PGT145

EntireName: SIVmac239 SOS-2P in complex with PGT145
Components
  • Complex: SIVmac239 SOS-2P in complex with PGT145
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: PGT145 Heavy
    • Protein or peptide: PGT145 Light
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: SIVmac239 SOS-2P in complex with PGT145

SupramoleculeName: SIVmac239 SOS-2P in complex with PGT145 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Simian immunodeficiency virus

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Simian immunodeficiency virus
Molecular weightTheoretical: 16.822201 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GVFVLGFLGF LATAGSAMGA ASLTLTAQSR TLLAGIVQQQ QQLLDVPKRQ QELLRLPVWG TKNLQTRVTA IEKYLKDQAQ LNAWGCAFR QVCCTTVPWP NASLTPKWNN ETWQEWERKV DFLEENITAL LEEAQIQQEK NMYELQKLN

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Simian immunodeficiency virus
Molecular weightTheoretical: 57.1955 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TLYVTVFYGV PAWRNATIPL FCATKNRDTW GTTQCLPDNG DYSEVALNVT ESFDAWNNTV TEQAIEDVWQ LFETSIKPCV KLSPLCITM RCNKSETDRW GLTKSITTTA STTSTTASAK VDMVNETSSC IAQDNCTGLE QEQMISCKFN MTGLKRDKTK E YNETWYSA ...String:
TLYVTVFYGV PAWRNATIPL FCATKNRDTW GTTQCLPDNG DYSEVALNVT ESFDAWNNTV TEQAIEDVWQ LFETSIKPCV KLSPLCITM RCNKSETDRW GLTKSITTTA STTSTTASAK VDMVNETSSC IAQDNCTGLE QEQMISCKFN MTGLKRDKTK E YNETWYSA DLVCEQGNNT GNESRCYMNH CNTSVIQESC DKHYWDAIRF RYCAPPGYAL LRCNDTNYSG FMPKCSKVVV SS CTRMMET QTSTWFGFNG TRAENRTYIY WHGRDNRTII SLNKYYNLTM KCRRPGNKTV LPVTIMSGLV FHSQPINDRP KQA WCWFGG KWKDAIKEVK QTIVKHPRYT GTNNTDKINL TAPGGGDPEV TFMWTNCRGE FLYCKMNWFL NWVEDRNTAN QKPK EQHKR NYVPCHIRQI INTWHKVGKN VYLPPREGDL TCNSTVTSLI ANIDWIDGNQ TNITMSAEVA ELYRLELGDY KLVEI TPIG LAPTDCKRYT TGGTSR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: PGT145 Heavy

MacromoleculeName: PGT145 Heavy / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.393357 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKASGNSFS NHDVHWVRQA TGQGLEWMGW MSHEGDKTGL AQKFQGRVTI TRDSGASTVY MELRGLTAD DTAIYYCLTG SKHRLRDYFL (TYS)NE(TYS)GPNYEE WGDYLATLDV WGHGTAVTVS SASTKGPSVF PLA PSSKST ...String:
QVQLVQSGAE VKKPGSSVKV SCKASGNSFS NHDVHWVRQA TGQGLEWMGW MSHEGDKTGL AQKFQGRVTI TRDSGASTVY MELRGLTAD DTAIYYCLTG SKHRLRDYFL (TYS)NE(TYS)GPNYEE WGDYLATLDV WGHGTAVTVS SASTKGPSVF PLA PSSKST SGGTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNT KVDKK VEPKSCD

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Macromolecule #4: PGT145 Light

MacromoleculeName: PGT145 Light / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.95375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVVITQSPLF LPVTPGEAAS LSCKCSHSLQ HSTGANYLAW YLQRPGQTPR LLIHLATHRA SGVPDRFSGS GSGTDFTLKI SRVESDDVG TYYCMQGLHS PWTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
EVVITQSPLF LPVTPGEAAS LSCKCSHSLQ HSTGANYLAW YLQRPGQTPR LLIHLATHRA SGVPDRFSGS GSGTDFTLKI SRVESDDVG TYYCMQGLHS PWTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #15: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 15 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #16: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 16 / Number of copies: 1 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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

Concentration1.0 mg/mL
BufferpH: 7.4 / Details: PBS
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 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) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 51.15 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination 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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 61881
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.12)

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Atomic model buiding 1

Initial modelPDB ID:

6tyb


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8dvd:
Cryo-EM structure of SIVmac239 SOS-2P Env trimer in complex with human bNAb PGT145

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