+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38541 | |||||||||
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Title | Prohead portal vertex of bacteriophage lambda | |||||||||
Map data | ||||||||||
Sample |
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Keywords | caudovirales / siphoviridae / portal vertex / portal / capsid / connector/neck / tail / delivery device / B-DNA / phage lambda / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral portal complex / T=7 icosahedral viral capsid / virion assembly / viral capsid / host cell cytoplasm / structural molecule activity / DNA binding Similarity search - Function | |||||||||
Biological species | Escherichia phage Lambda (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.58 Å | |||||||||
Authors | Wang JW / Gu ZW | |||||||||
Funding support | China, 2 items
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Citation | Journal: To Be Published Title: Structural morphing in the viral portal vertex of bacteriophage lambda Authors: Wang JW / Gu ZW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38541.map.gz | 31 MB | EMDB map data format | |
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Header (meta data) | emd-38541-v30.xml emd-38541.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38541_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_38541.png | 67.3 KB | ||
Filedesc metadata | emd-38541.cif.gz | 5.4 KB | ||
Others | emd_38541_half_map_1.map.gz emd_38541_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38541 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38541 | HTTPS FTP |
-Related structure data
Related structure data | 8xouMC 8xotC 8xowC 8xpmC 8xqbC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38541.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.30654 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_38541_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38541_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Escherichia phage Lambda
Entire | Name: Escherichia phage Lambda (virus) |
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Components |
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-Supramolecule #1: Escherichia phage Lambda
Supramolecule | Name: Escherichia phage Lambda / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2681611 / Sci species name: Escherichia phage Lambda / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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-Macromolecule #1: Portal protein B
Macromolecule | Name: Portal protein B / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
Molecular weight | Theoretical: 59.529609 KDa |
Recombinant expression | Organism: Escherichia phage Lambda (virus) |
Sequence | String: MKTPTIPTLL GPDGMTSLRE YAGYHGGGSG FGGQLRSWNP PSESVDAALL PNFTRGNARA DDLVRNNGYA ANAIQLHQDH IVGSFFRLS HRPSWRYLGI GEEEARAFSR EVEAAWKEFA EDDCCCIDVE RKRTFTMMIR EGVAMHAFNG ELFVQATWDT S SSRLFRTQ ...String: MKTPTIPTLL GPDGMTSLRE YAGYHGGGSG FGGQLRSWNP PSESVDAALL PNFTRGNARA DDLVRNNGYA ANAIQLHQDH IVGSFFRLS HRPSWRYLGI GEEEARAFSR EVEAAWKEFA EDDCCCIDVE RKRTFTMMIR EGVAMHAFNG ELFVQATWDT S SSRLFRTQ FRMVSPKRIS NPNNTGDSRN CRAGVQINDS GAALGYYVSE DGYPGWMPQK WTWIPRELPG GRASFIHVFE PV EDGQTRG ANVFYSVMEQ MKMLDTLQNT QLQSAIVKAM YAATIESELD TQSAMDFILG ANSQEQRERL TGWIGEIAAY YAA APVRLG GAKVPHLMPG DSLNLQTAQD TDNGYSVFEQ SLLRYIAAGL GVSYEQLSRN YAQMSYSTAR ASANESWAYF MGRR KFVAS RQASQMFLCW LEEAIVRRVV TLPSKARFSF QEARSAWGNC DWIGSGRMAI DGLKEVQEAV MLIEAGLSTY EKECA KRGD DYQEIFAQQV RETMERRAAG LKPPAWAAAA FESGLRQSTE EEKSDSRAA UniProtKB: Portal protein B |
-Macromolecule #2: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 30 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
Molecular weight | Theoretical: 38.22916 KDa |
Recombinant expression | Organism: Escherichia phage Lambda (virus) |
Sequence | String: MSMYTTAQLL AANEQKFKFD PLFLRLFFRE SYPFTTEKVY LSQIPGLVNM ALYVSPIVSG EVIRSRGGST SEFTPGYVKP KHEVNPQMT LRRLPDEDPQ NLADPAYRRR RIIMQNMRDE ELAIAQVEEM QAVSAVLKGK YTMTGEAFDP VEVDMGRSEE N NITQSGGT ...String: MSMYTTAQLL AANEQKFKFD PLFLRLFFRE SYPFTTEKVY LSQIPGLVNM ALYVSPIVSG EVIRSRGGST SEFTPGYVKP KHEVNPQMT LRRLPDEDPQ NLADPAYRRR RIIMQNMRDE ELAIAQVEEM QAVSAVLKGK YTMTGEAFDP VEVDMGRSEE N NITQSGGT EWSKRDKSTY DPTDDIEAYA LNASGVVNII VFDPKGWALF RSFKAVKEKL DTRRGSNSEL ETAVKDLGKA VS YKGMYGD VAIVVYSGQY VENGVKKNFL PDNTMVLGNT QARGLRTYGC IQDADAQREG INASARYPKN WVTTGDPARE FTM IQSAPL MLLADPDEFV SVQLA UniProtKB: Major capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |