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Yorodumi- EMDB-17311: In situ cryoEM structure of Prototype Foamy Virus Env dimer of trimers -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17311 | |||||||||
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Title | In situ cryoEM structure of Prototype Foamy Virus Env dimer of trimers | |||||||||
Map data | ||||||||||
Sample |
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Keywords | membrane fusion / envelope glycoprotein / foamy virus / MPER / transmembrane / MEMBRANE PROTEIN / VIRAL PROTEIN | |||||||||
Biological species | Eastern chimpanzee simian foamy virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Calcraft T / Nans A / Rosenthal PB | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: To Be Published Title: In situ cryoEM structures of PFV Authors: Calcraft T / Lindemann D / Rosenthal PB | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17311.map.gz | 386.7 MB | EMDB map data format | |
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Header (meta data) | emd-17311-v30.xml emd-17311.xml | 16.5 KB 16.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17311_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_17311.png | 99.4 KB | ||
Masks | emd_17311_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-17311.cif.gz | 6.7 KB | ||
Others | emd_17311_half_map_1.map.gz emd_17311_half_map_2.map.gz | 330.1 MB 330.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17311 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17311 | HTTPS FTP |
-Validation report
Summary document | emd_17311_validation.pdf.gz | 1003.9 KB | Display | EMDB validaton report |
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Full document | emd_17311_full_validation.pdf.gz | 1003.5 KB | Display | |
Data in XML | emd_17311_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | emd_17311_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17311 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17311 | HTTPS FTP |
-Related structure data
Related structure data | 8ozjMC 17309 17312 17313 17314 17315 17316 17317 17318 17319 17320 17321 17322 8ozhC 8ozkC 8ozlC 8ozmC 8oznC 8ozpC 8ozqC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17311.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_17311_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Eastern chimpanzee simian foamy virus
Entire | Name: Eastern chimpanzee simian foamy virus |
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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: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: Eastern chimpanzee simian foamy virus |
Molecular weight | Theoretical: 113.804594 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 8 / Number of copies: 3 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Macromolecule #9: PHOSPHATIDYLETHANOLAMINE
Macromolecule | Name: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 9 / Number of copies: 3 / Formula: PTY |
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Molecular weight | Theoretical: 734.039 Da |
Chemical component information | ChemComp-PTY: |
-Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 9 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: FIELD EMISSION GUN |
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 |