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- EMDB-17316: In situ subtomogram average of Prototype Foamy Virus Env trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-17316
TitleIn situ subtomogram average of Prototype Foamy Virus Env trimer
Map data
Sample
  • Virus: Eastern chimpanzee simian foamy virus
    • Protein or peptide: Envelope glycoprotein
Keywordsmembrane fusion / envelope glycoprotein / foamy virus / MPER / transmembrane / MEMBRANE PROTEIN / VIRAL PROTEIN
Biological speciesEastern chimpanzee simian foamy virus
Methodsubtomogram averaging / cryo EM / Resolution: 4.9 Å
AuthorsCalcraft T / Nans A / Rosenthal PB
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: To Be Published
Title: In situ cryoEM structures of PFV
Authors: Calcraft T / Lindemann D / Rosenthal PB
History
DepositionMay 9, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17316.png

Downloads & links

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Map

FileDownload / File: emd_17316.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.0956
Minimum - Maximum-0.20037037 - 0.4774703
Average (Standard dev.)0.00000000000053 (±0.03608827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 276.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17316_msk_1.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 : Eastern chimpanzee simian foamy virus

EntireName: Eastern chimpanzee simian foamy virus
Components
  • Virus: Eastern chimpanzee simian foamy virus
    • Protein or peptide: Envelope glycoprotein

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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: all / 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 / Enantiomer: LEVO
Source (natural)Organism: Eastern chimpanzee simian foamy virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAPPMTLQQW IIWNKMNKAH EALQNTTTVT EQQKEQIILD IQNEEVQPTR RDKFRYLLYT CCATSSRVLA WIFLVCILLI IVLVSCFVTI SRIQWNKDIQ VLGPVIDWNV TQRAVYQPLQ TRRIARSLRM QHPVPKYVEV NMTSIPQGVY YEPHPEPIVV KERVLGLSQI ...String:
MAPPMTLQQW IIWNKMNKAH EALQNTTTVT EQQKEQIILD IQNEEVQPTR RDKFRYLLYT CCATSSRVLA WIFLVCILLI IVLVSCFVTI SRIQWNKDIQ VLGPVIDWNV TQRAVYQPLQ TRRIARSLRM QHPVPKYVEV NMTSIPQGVY YEPHPEPIVV KERVLGLSQI LMINSENIAN NANLTQEVKK LLTEMVNEEM QSLSDVMIDF EIPLGDPRDQ EQYIHRKCYQ EFANCYLVKY KEPKPWPKEG LIADQCPLPG YHAGLTYNRQ SIWDYYIKVE SIRPANWTTK SKYGQARLGS FYIPSSLRQI NVSHVLFCSD QLYSKWYNIE NTIEQNERFL LNKLNNLTSG TSVLKKRALP KDWSSQGKNA LFREINVLDI CSKPESVILL NTSYYSFSLW EGDCNFTKDM ISQLVPECDG FYNNSKWMHM HPYACRFWRS KNEKEETKCR DGETKRCLYY PLWDSPESTY DFGYLAYQKN FPSPICIEQQ KIRDQDYEVY SLYQECKIAS KAYGIDTVLF SLKNFLNYTG TPVNEMPNAR AFVGLIDPKF PPSYPNVTRE HYTSCNNRKR RSVDNNYAKL RSMGYALTGA VQTLSQISDI NDENLQQGIY LLRDHVITLM EATLHDISVM EGMFAVQHLH THLNHLKTML LERRIDWTYM SSTWLQQQLQ KSDDEMKVIK RIARSLVYYV KQTHSSPTAT AWEIGLYYEL VIPKHIYLNN WNVVNIGHLV KSAGQLTHVT IAHPYEIINK ECVETIYLHL EDCTRQDYVI CDVVKIVQPC GNSSDTSDCP VWAEAVKEPF VQVNPLKNGS YLVLASSTDC QIPPYVPSIV TVNETTSCFG LDFKRPLVAE ERLSFEPRLP NLQLRLPHLV GIIAKIKGIK IEVTSSGESI KEQIERAKAE LLRLDIHEGD TPAWIQQLAA ATKDVWPAAA SALQGIGNFL SGTAQGIFGT AFSLLGYLKP ILIGVGVILL VILIFKIVSW IPTKKKNQ

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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) / 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: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 14397
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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