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- EMDB-17318: In situ subtomogram average of Prototype Foamy Virus Env hexamer ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17318
TitleIn situ subtomogram average of Prototype Foamy Virus Env hexamer of trimers
Map data
Sample
  • Virus: Eastern chimpanzee simian foamy virus
    • Protein or peptide: Envelope glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: PHOSPHATIDYLETHANOLAMINE
Keywordsmembrane fusion / envelope glycoprotein / foamy virus / MPER / transmembrane / MEMBRANE PROTEIN / VIRAL PROTEIN
Biological speciesEastern chimpanzee simian foamy virus
Methodsubtomogram averaging / cryo EM / Resolution: 10.0 Å
AuthorsCalcraft T / Nans A / Rosenthal PB
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: Cell / Year: 2024
Title: Integrated cryoEM structure of a spumaretrovirus reveals cross-kingdom evolutionary relationships and the molecular basis for assembly and virus entry.
Authors: Thomas Calcraft / Nicole Stanke-Scheffler / Andrea Nans / Dirk Lindemann / Ian A Taylor / Peter B Rosenthal /
Abstract: Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates ...Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates for gene and oncolytic therapies. Structural studies of PFV contribute to the understanding of the mechanisms of FV replication, cell entry and infection, and retroviral evolution. Here we combine cryoEM and cryoET to determine high-resolution in situ structures of the PFV icosahedral capsid (CA) and envelope glycoprotein (Env), including its type III transmembrane anchor and membrane-proximal external region (MPER), and show how they are organized in an integrated structure of assembled PFV particles. The atomic models reveal an ancient retroviral capsid architecture and an unexpected relationship between Env and other class 1 fusion proteins of the Mononegavirales. Our results represent the de novo structure determination of an assembled retrovirus particle.
History
DepositionMay 9, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17318.png

Downloads & links

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Map

FileDownload / File: emd_17318.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.76 Å/pix.
x 160 pix.
= 441.6 Å		2.76 Å/pix.
x 160 pix.
= 441.6 Å		2.76 Å/pix.
x 160 pix.
= 441.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0702
Minimum - Maximum-0.11117784 - 0.19826221
Average (Standard dev.)0.000000000002462 (±0.030950662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 441.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17318_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_17318_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_17318_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Eastern chimpanzee simian foamy virus

EntireName: Eastern chimpanzee simian foamy virus
Components
  • Virus: Eastern chimpanzee simian foamy virus
    • Protein or peptide: Envelope glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: PHOSPHATIDYLETHANOLAMINE

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Supramolecule #1: Eastern chimpanzee simian foamy virus

SupramoleculeName: Eastern chimpanzee simian foamy virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2170195 / Sci species name: Eastern chimpanzee simian foamy virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Envelope glycoprotein

MacromoleculeName: Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Eastern chimpanzee simian foamy virus
Molecular weightTheoretical: 113.804594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPPMTLQQW IIWNKMNKAH EALQNTTTVT EQQKEQIILD IQNEEVQPTR RDKFRYLLYT CCATSSRVLA WIFLVCILLI IVLVSCFVT ISRIQWNKDI QVLGPVIDWN VTQRAVYQPL QTRRIARSLR MQHPVPKYVE VNMTSIPQGV YYEPHPEPIV V KERVLGLS ...String:
MAPPMTLQQW IIWNKMNKAH EALQNTTTVT EQQKEQIILD IQNEEVQPTR RDKFRYLLYT CCATSSRVLA WIFLVCILLI IVLVSCFVT ISRIQWNKDI QVLGPVIDWN VTQRAVYQPL QTRRIARSLR MQHPVPKYVE VNMTSIPQGV YYEPHPEPIV V KERVLGLS QILMINSENI ANNANLTQEV KKLLTEMVNE EMQSLSDVMI DFEIPLGDPR DQEQYIHRKC YQEFANCYLV KY KEPKPWP KEGLIADQCP LPGYHAGLTY NRQSIWDYYI KVESIRPANW TTKSKYGQAR LGSFYIPSSL RQINVSHVLF CSD QLYSKW YNIENTIEQN ERFLLNKLNN LTSGTSVLKK RALPKDWSSQ GKNALFREIN VLDICSKPES VILLNTSYYS FSLW EGDCN FTKDMISQLV PECDGFYNNS KWMHMHPYAC RFWRSKNEKE ETKCRDGETK RCLYYPLWDS PESTYDFGYL AYQKN FPSP ICIEQQKIRD QDYEVYSLYQ ECKIASKAYG IDTVLFSLKN FLNYTGTPVN EMPNARAFVG LIDPKFPPSY PNVTRE HYT SCNNRKRRSV DNNYAKLRSM GYALTGAVQT LSQISDINDE NLQQGIYLLR DHVITLMEAT LHDISVMEGM FAVQHLH TH LNHLKTMLLE RRIDWTYMSS TWLQQQLQKS DDEMKVIKRI ARSLVYYVKQ THSSPTATAW EIGLYYELVI PKHIYLNN W NVVNIGHLVK SAGQLTHVTI AHPYEIINKE CVETIYLHLE DCTRQDYVIC DVVKIVQPCG NSSDTSDCPV WAEAVKEPF VQVNPLKNGS YLVLASSTDC QIPPYVPSIV TVNETTSCFG LDFKRPLVAE ERLSFEPRLP NLQLRLPHLV GIIAKIKGIK IEVTSSGES IKEQIERAKA ELLRLDIHEG DTPAWIQQLA AATKDVWPAA ASALQGIGNF LSGTAQGIFG TAFSLLGYLK P ILIGVGVI LLVILIFKIV SWIPTKKKNQ

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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: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #9: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 9 / Number of copies: 3 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #10: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 10 / Number of copies: 3 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 2.62 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: 4.5 µm / Nominal defocus min: 2.0 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

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 5697
ExtractionNumber tomograms: 250 / Number images used: 156183 / Software - Name: Dynamo
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8ozq:
In situ subtomogram average of Prototype Foamy Virus Env hexamer of trimers

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