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Yorodumi- EMDB-33560: CryoEM structure of Klebsiella phage Kp9 tail complex applied wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33560 | |||||||||
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Title | CryoEM structure of Klebsiella phage Kp9 tail complex applied with C6 symmetry | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / Podophage / short non-contractile tail / VIRUS | |||||||||
Biological species | Klebsiella phage Kp9 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
Authors | Huang L / Xiang Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Structure and assembly of the Klebsiella pneumoniae phage tail fibers Authors: Huang L / Xiang Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33560.map.gz | 128.7 MB | EMDB map data format | |
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Header (meta data) | emd-33560-v30.xml emd-33560.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33560_fsc.xml | 35.2 KB | Display | FSC data file |
Images | emd_33560.png | 19.9 KB | ||
Filedesc metadata | emd-33560.cif.gz | 6.7 KB | ||
Others | emd_33560_half_map_1.map.gz emd_33560_half_map_2.map.gz | 3 GB 3 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33560 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33560 | HTTPS FTP |
-Validation report
Summary document | emd_33560_validation.pdf.gz | 694.5 KB | Display | EMDB validaton report |
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Full document | emd_33560_full_validation.pdf.gz | 694.1 KB | Display | |
Data in XML | emd_33560_validation.xml.gz | 41.8 KB | Display | |
Data in CIF | emd_33560_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33560 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33560 | HTTPS FTP |
-Related structure data
Related structure data | 7y1cMC 7xy1C 7xycC 7y22C 7y23C 7y3tC 7y5sC 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_33560.map.gz / Format: CCP4 / Size: 3.7 GB / 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: 1.0742 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33560_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33560_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Klebsiella phage Kp9
Entire | Name: Klebsiella phage Kp9 (virus) |
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Components |
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-Supramolecule #1: Klebsiella phage Kp9
Supramolecule | Name: Klebsiella phage Kp9 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2936516 / Sci species name: Klebsiella phage Kp9 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Klebsiella pneumoniae ATCC 43816 (bacteria) |
Virus shell | Shell ID: 1 / Diameter: 600.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: phage connector protein
Macromolecule | Name: phage connector protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella phage Kp9 (virus) |
Molecular weight | Theoretical: 58.661219 KDa |
Sequence | String: MAEVKLEGFA EEGAKAVYDR LKNDRQPYET RAESCAQYTI PSLFPKDSDN ASTDYTTPWQ SVGARGLNNL ASKLMLALFP MQSWMKLTI SEYEAKNLLG DAEGLAKVDE GLSMVERIIM NYIESNSYRV TLFECLKQLC VAGNALLYLP EPEGYTPMKL Y RLNSYVVQ ...String: MAEVKLEGFA EEGAKAVYDR LKNDRQPYET RAESCAQYTI PSLFPKDSDN ASTDYTTPWQ SVGARGLNNL ASKLMLALFP MQSWMKLTI SEYEAKNLLG DAEGLAKVDE GLSMVERIIM NYIESNSYRV TLFECLKQLC VAGNALLYLP EPEGYTPMKL Y RLNSYVVQ RDAFGNVLQI VTLDKIAFNA LPEDVRSQVE AAQGEQKEDA EIDVYTHVYL NEAGDGYSKY EEVAEEVVPG SE AEYPLEE CPYIPVRMVR IDGESYGRSY VEEYLGDLKS LENLQESIVK MAMITAKVIG LVDPAGITQV RRLTAAQSGA FVP GRKQDI EFLQLEKSGD FTVAKNVSDT IEARLSYAFM LNSAVQRTGE RVTAEEIRYV ASELEDTLGG VYSILSQELQ LPLV RVLLK QLQATQQIPE LPKEAVEPTI STGLEAIGRG QDLDKLERCI AAWSALKALE GDDDLNLANL KLRIANAIGL DTAGM LLTQ EQKNALMAQQ GAQIATQQGA AALGQGMAAQ ATASPEAMAA AADSVGMQPG M |
-Macromolecule #2: phage tail tubular protein A
Macromolecule | Name: phage tail tubular protein A / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella phage Kp9 (virus) |
Molecular weight | Theoretical: 21.374646 KDa |
Sequence | String: MNMQDAYFGS AAELDAVNEM LAAIGESPVT TLDEDGSADV ANARRILNRI NRQIQSKGWA FNINESATLT PDASTGLIPF RPAYLSILG GQYINRGGWV YDKSTGTDTF SGPITVTLIT LQDYDEMPEC FRQWIVTKAS RQFNSRFFGA EDVENSLAQE E MEARMACN ...String: MNMQDAYFGS AAELDAVNEM LAAIGESPVT TLDEDGSADV ANARRILNRI NRQIQSKGWA FNINESATLT PDASTGLIPF RPAYLSILG GQYINRGGWV YDKSTGTDTF SGPITVTLIT LQDYDEMPEC FRQWIVTKAS RQFNSRFFGA EDVENSLAQE E MEARMACN EYEMDFGQYN MLDGDAYVQG LIGR |
-Macromolecule #3: phage tail tubular protein B
Macromolecule | Name: phage tail tubular protein B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella phage Kp9 (virus) |
Molecular weight | Theoretical: 89.081969 KDa |
Sequence | String: MALVSQSIKN LKGGISQQPE ILRYPEQGTL QVNGWSSETE GLQKRPPMVF IKSLGPRGYL GEDPYIHLIN RDEYEQYYAV FTGNDVRVF DLSGYEYQVR GDRSYVTVNN PKDNLRMVTV ADYTFIVNRT RQVRENQNRT NGGTFRDNVD AIINVRGGQY G RKLEVNIN ...String: MALVSQSIKN LKGGISQQPE ILRYPEQGTL QVNGWSSETE GLQKRPPMVF IKSLGPRGYL GEDPYIHLIN RDEYEQYYAV FTGNDVRVF DLSGYEYQVR GDRSYVTVNN PKDNLRMVTV ADYTFIVNRT RQVRENQNRT NGGTFRDNVD AIINVRGGQY G RKLEVNIN GVWVSHQLPP GDNAKEDPPK VDAQAIAEAI ATLLRTAHPT WTFNVGTGFI HCIAPADTTI DILETKDGYA DQ LINPVTH YVQSFSKLPL NAPDGYMVKI VGDTSKTADQ YYVKYDKSQK VWKETVGWNI SVGLEYHTMP WTLVRAADGN FDL GYHEWK DRRAGDDDTN PQPSFVNSTI TDVFFFRNRL GFISGENIVM SRTSKYFEFY PPSVANYTDD DPLDVAVSHN RVSV LKYAV SFAEELLLWS DEAQFVLSAN GVLSAKTAQL DLTTQFDVSD RARPYGIGRN IYYASPRSSF TSIMRYYAVQ DVSSV KNAE DMTAHVPNYI PNGVYSINGS GTENFACVLT KGAPSKVFIY KFLYMDENIR QQSWSHWDFG DGVEVMAANC INSTMY MLM RNGYNVWIAA VDFKKESTDF PFEPYRFHVD AKRSYHISET AYDIETNQTV VNVKDIYGAS FAKGTVAICE SDGKITE YE PTGNSWDSTP DIRISGDVSG KNIVIGFLYD FQYVFSRFLI KQEQNDGTTS TEDSGRLQLR RAWVNYQNTG AFTVSVDN G SREFNYLVNA RVGSTGLRLG QKATTTGQYR FPVTGNALYQ KVSLSSFNAS PVSIIGCGWE GNYSRRANGI |
-Macromolecule #4: phage type I tail fiber
Macromolecule | Name: phage type I tail fiber / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella phage Kp9 (virus) |
Molecular weight | Theoretical: 84.120445 KDa |
Sequence | String: MDQDIKTVIQ YPVGTTEFDI PFDYLSRKFV RVSLVSDDNR RLLSNITEYR YVSKTRVKLL VATTGFDRVE IRRFTSASER IVDFSDGSV LRANDLNVSQ LQSAHIAEEA RDAALLAMPE DDAGNLDARN RKIVRLAPGE AGTDAINKNQ LDTTLGEAGG I LSEVKDLQ ...String: MDQDIKTVIQ YPVGTTEFDI PFDYLSRKFV RVSLVSDDNR RLLSNITEYR YVSKTRVKLL VATTGFDRVE IRRFTSASER IVDFSDGSV LRANDLNVSQ LQSAHIAEEA RDAALLAMPE DDAGNLDARN RKIVRLAPGE AGTDAINKNQ LDTTLGEAGG I LSEVKDLQ KDMEDYLQNW GDDTTAIRGV LWVYNQGSAV GGETSFVITK EGPVLAVPYI EINGSRQYRG WHYEYDLGSK TI TLAKPLS AGDLVVCTTA ETTLPLADSL AGPTGASQIG TANGLNVQIA LDNLRSGVNV LDFMTFAERA AVLNYTGTND NSE AFRKAF ATGSRQIIVP PGRYHVKDVE IPSKVKLFGT YSYKPYNVTS DASFGTDGTI IRKVAGADNM FLWNTACAAE GVMF DGRDR TSPAIQSKSG GKISVGFFKC GFYRFDRVGN RRGAYIGCSF QFCNFNQNNI GIYNTVDGNH IGCTINANKS HGVML ETGA NSNTFTNCRN EWNEGDNWNF YGATSIQVIN ELCDRAFGYG FRISNSSVTL INVNIRRSAR TAASGAASAQ IYFESS TLK MIGVNSSVGG DDTGGSITEP SPDYFFRMAG TSEGRLEISD SRLTGYTVGL ISGTARPSVI RVINSPGWED TINEGVA RI SGGRPYIGTM PTATGPANVS PAVLGLSCGG VNTYDNDMFD IHLTIRNTNN GGHNGAILTV LLYREGGAAR ATIVRVDS R SNAVGEGDVN STSADPQQVY QVSVEVTSND ASTFNLLVST KSDNSASYRF RAKVKP |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 63 |
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Output model | PDB-7y1c: |