+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38246 | |||||||||
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Title | Closed state of central tail fiber of bacteriophage lambda | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Bacteriophage / caudovirales / siphoviridae / phage lambda / host recognition / LamB / cryo-EM / VIRUS | |||||||||
Function / homology | Function and homology information symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / outer membrane-bounded periplasmic space / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell ...symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / outer membrane-bounded periplasmic space / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / periplasmic space / virion attachment to host cell Similarity search - Function | |||||||||
Biological species | Escherichia phage Lambda (virus) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.75 Å | |||||||||
Authors | Ge XF / Wang JW | |||||||||
Funding support | China, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of lambda tail with LamB Authors: Ge XF / Wang JW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38246.map.gz | 398.3 MB | EMDB map data format | |
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Header (meta data) | emd-38246-v30.xml emd-38246.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38246_fsc.xml | 15.7 KB | Display | FSC data file |
Images | emd_38246.png | 49.1 KB | ||
Filedesc metadata | emd-38246.cif.gz | 5.5 KB | ||
Others | emd_38246_half_map_1.map.gz emd_38246_half_map_2.map.gz | 391.1 MB 391.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38246 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38246 | HTTPS FTP |
-Related structure data
Related structure data | 8xckMC 8xcgC 8xciC 8xcjC M: atomic model generated by this map C: citing same article (ref.) |
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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_38246.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: 1.036 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38246_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38246_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bacteriophage lambda tail with LamB
Entire | Name: Bacteriophage lambda tail with LamB |
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Components |
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-Supramolecule #1: Bacteriophage lambda tail with LamB
Supramolecule | Name: Bacteriophage lambda tail with LamB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: tip attachment protein J
Supramolecule | Name: tip attachment protein J / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
-Supramolecule #3: PPIA
Supramolecule | Name: PPIA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Tip attachment protein J
Macromolecule | Name: Tip attachment protein J / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
Molecular weight | Theoretical: 46.045844 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: APAAPSRIEL TPGYFQITAT PHLAVYDPTV QFEFWFSEKQ IADIRQVETS TRYLGTALYW IAASINIKPG HDYYFYIRSV NTVGKSAFV EAVGRASDDA EGYLDFFKGK ITESHLGKEL LEKVELTEDN ASRLEEFSKE WKDASDKWNA MWAVKIEQTK D GKHYVAGI ...String: APAAPSRIEL TPGYFQITAT PHLAVYDPTV QFEFWFSEKQ IADIRQVETS TRYLGTALYW IAASINIKPG HDYYFYIRSV NTVGKSAFV EAVGRASDDA EGYLDFFKGK ITESHLGKEL LEKVELTEDN ASRLEEFSKE WKDASDKWNA MWAVKIEQTK D GKHYVAGI GLSMEDTEEG KLSQFLVAAN RIAFIDPANG NETPMFVAQG NQIFMNDVFL KRLTAPTITS GGNPPAFSLT PD GKLTAKN ADISGSVNAN SGTLSNVTIA ENCTINGTLR AEKIVGDIVK AASAAFPRQR ESSVDWPSGT RTVTVTDDHP FDR QIVVLP LTFRGSKRTV SGRTTYSMCY LKVLMNGAVI YDGAANEAVQ VFSRIVDMPA GRGNVILTFT LTSTRHSADI PPYT FASDV QVMVIKKQAL GISVV UniProtKB: Tip attachment protein J |
-Macromolecule #2: Peptidyl-prolyl cis-trans isomerase A
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase A / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 20.453277 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MFKSTLAAMA AVFALSALSP AAMAAKGDPH VLLTTSAGNI ELELDKQKAP VSVQNFVDYV NSGFYNNTTF HRVIPGFMIQ GGGFTEQMQ QKKPNPPIKN EADNGLRNTR GTIAMARTAD KDSATSQFFI NVADNAFLDH GQRDFGYAVF GKVVKGMDVA D KISQVPTH DVGPYQNVPS KPVVILSAKV LP UniProtKB: Peptidyl-prolyl cis-trans isomerase A |
-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: ETHANE |
-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: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |