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Open data
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Basic information
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Title | In situ cryoEM structure of Prototype Foamy Virus Env trimer | |||||||||
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![]() | membrane fusion / envelope glycoprotein / foamy virus / MPER / transmembrane / MEMBRANE PROTEIN / VIRAL PROTEIN | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.91 Å | |||||||||
![]() | Calcraft T / Nans A / Rosenthal PB | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 393.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.1 KB 20.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.9 KB | Display | ![]() |
Images | ![]() | 59.4 KB | ||
Masks | ![]() | 421.9 MB | ![]() | |
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() | 331.1 MB 331.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 801.5 KB | Display | ![]() |
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Full document | ![]() | 801.1 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 32.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ozhMC ![]() 8ozjC ![]() 8ozkC ![]() 8ozlC ![]() 8ozmC ![]() 8oznC ![]() 8ozpC ![]() 8ozqC C: citing same article ( M: atomic model generated by this map |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #2
File | emd_17309_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : Eastern chimpanzee simian foamy virus
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Eastern chimpanzee simian foamy virus
Supramolecule | Name: 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
Macromolecule | Name: Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 113.804594 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 9 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #9: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 9 / Number of copies: 3 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ![]() ChemComp-CLR: |
-Macromolecule #10: PHOSPHATIDYLETHANOLAMINE
Macromolecule | Name: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 10 / Number of copies: 3 / Formula: PTY |
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Molecular weight | Theoretical: 734.039 Da |
Chemical component information | ![]() ChemComp-PTY: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film 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: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-8ozh: |