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- EMDB-33560: CryoEM structure of Klebsiella phage Kp9 tail complex applied wit... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | CryoEM structure of Klebsiella phage Kp9 tail complex applied with C6 symmetry | |||||||||
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![]() | Complex / Podophage / short non-contractile tail / VIRUS | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
![]() | Huang L / Xiang Y | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 128.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.2 KB 18.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 35.2 KB | Display | ![]() |
Images | ![]() | 19.9 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() | 3 GB 3 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 694.5 KB | Display | ![]() |
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Full document | ![]() | 694.1 KB | Display | |
Data in XML | ![]() | 41.8 KB | Display | |
Data in CIF | ![]() | 58.9 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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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 |
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Sample components
-Entire : Klebsiella phage Kp9
Entire | Name: ![]() |
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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: ![]() |
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: ![]() |
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: ![]() |
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: ![]() |
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: ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |
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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: |