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Yorodumi- EMDB-33583: CryoEM structure of Klebsiella phage Kp7 tail complex applied wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33583 | |||||||||
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Title | CryoEM structure of Klebsiella phage Kp7 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 Kp7 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 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_33583.map.gz | 106.7 MB | EMDB map data format | |
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Header (meta data) | emd-33583-v30.xml emd-33583.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33583_fsc.xml | 35.2 KB | Display | FSC data file |
Images | emd_33583.png | 28.2 KB | ||
Others | emd_33583_half_map_1.map.gz emd_33583_half_map_2.map.gz | 3.1 GB 3.1 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33583 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33583 | HTTPS FTP |
-Related structure data
Related structure data | 7y22MC 7xy1C 7xycC 7y1cC 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_33583.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.17 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33583_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33583_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Klebsiella phage Kp7
Entire | Name: Klebsiella phage Kp7 (virus) |
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Components |
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-Supramolecule #1: Klebsiella phage Kp7
Supramolecule | Name: Klebsiella phage Kp7 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2936515 / Sci species name: Klebsiella phage Kp7 / 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 Kp7 (virus) |
Molecular weight | Theoretical: 58.339309 KDa |
Sequence | String: MDIRGGASYS GKKSKIPELW EKLSRKRNEF LDRAKHYARL TLPYLLNEPG NNESAQNGWQ GTGAQATNHL ANKLAQVLFP AQRSFFRVD LTVKGEKALL ERGYQKTKLA TVFAKIETQA MKALDARQFR PAVVEAFKHL LVAGNCMLYK PVKSANDPAG P ISCIPMHH ...String: MDIRGGASYS GKKSKIPELW EKLSRKRNEF LDRAKHYARL TLPYLLNEPG NNESAQNGWQ GTGAQATNHL ANKLAQVLFP AQRSFFRVD LTVKGEKALL ERGYQKTKLA TVFAKIETQA MKALDARQFR PAVVEAFKHL LVAGNCMLYK PVKSANDPAG P ISCIPMHH YAVQRDTNGQ LMDIILLQEK ALRTFEPALR AVIQAARKGK QLKDSDNVKL YTHACYEGDG FWKVQQSADD LP VGKSSRV KADKLPFMVL TWKRSYGEDW GRPLCEDYSG DLFVVQFLSE AVARGAALMA DIKYLIRPGA QTDVEHFVNS GTG EVITGV EEDIHIVQLG KYADLTPIDA VLEKYVRRIG VVFMMESLVR RDAERVTALE IQRDAMEVEQ SLGGAYSLFS VTMQ QPMAI WGLQENAGSF GSEFIDPVII TGIEALGRMA ELDKLAQFSN YMNLPTTWPE WAQDAIKPTE YMDWVRGQIS ADFPF LMSE EEAAAAAEQA QEQQADQTLN EGVAQAIPQV INQGLQEL |
-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 Kp7 (virus) |
Molecular weight | Theoretical: 27.228775 KDa |
Sequence | String: MPIQSDTPSI MAESQFNSLS TKLDAVNLCM RAIGRSGVDN LTSGDLDAED ADTMIDIVSQ RLQYNDGKGW WFNREPRWSF APDSNGEVV LPNNTLQVLQ AYTLNTRKID ITIRAGRLYS TTLHSFDVSP LVGPDGFIWL DLMLMLPFEH MPLNVLQAIA Y QAAAEFIV ...String: MPIQSDTPSI MAESQFNSLS TKLDAVNLCM RAIGRSGVDN LTSGDLDAED ADTMIDIVSQ RLQYNDGKGW WFNREPRWSF APDSNGEVV LPNNTLQVLQ AYTLNTRKID ITIRAGRLYS TTLHSFDVSP LVGPDGFIWL DLMLMLPFEH MPLNVLQAIA Y QAAAEFIV SKDADQTKLQ MHMQMAANLH TGMQVEESKQ NRLNMLVHNP TQRNFGIMAG GPNNTAGFDH SPYDRYPVRP WR W |
-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 Kp7 (virus) |
Molecular weight | Theoretical: 87.904539 KDa |
Sequence | String: MEVQGSLGRQ IQGISQQPAS VRLPGQCTDA INCSMDVVEG TKSRPGTVHI ARLGDLGLIQ DNTNIHHYRR GDDVEEYWMI TNPLGIPDI FDKQGRKCTV TETEGAASYF NSNNPRVDYK FFTVGDTTFV VNRTKIVRAR ADKTPAVGGT ALVFSAYGQY G TNYQIIIN ...String: MEVQGSLGRQ IQGISQQPAS VRLPGQCTDA INCSMDVVEG TKSRPGTVHI ARLGDLGLIQ DNTNIHHYRR GDDVEEYWMI TNPLGIPDI FDKQGRKCTV TETEGAASYF NSNNPRVDYK FFTVGDTTFV VNRTKIVRAR ADKTPAVGGT ALVFSAYGQY G TNYQIIIN GVKAAEYKTA SGGSASDVET IRTEVIAEQL YTNLLTWAGA SDYSISRMGT TIVISSLSGA SFTVDTEDGS KG KDLVAIQ YKVTSTDLLP SKAPVGYLVQ VWPTGSKPES RYWLKAEAAD GNLVTWQETL GADEVLGFDG STMPYIIERT NIV GGIAQF TIKQGYWDDR AVGDELTNPM PSFVDQSLSD IFMVQNRLCL AAGESCIMSR TSYFFQFFRQ TVLSAVDTDP IDVF ADASE VYALKHAKVL DGDTVLFSDN AQFILPGDKP LTKATALLRP TTTFEVDTNV APVVTGEAVM FATKDGAYSN IREFY TDSY SDTKKAQPVT SHVNKLIRGG IYHMASSTNF NRLFALSEDN RSRVFVYDWL WQGTDKVQSA WHKWEFYGAT IGGLYY SGE TLYLIIKRND GVFLEAMYMG DPLLSGSDQV RMDRTVTVSL TWDEATLSWK SSPLPWVPTQ VEMLEAVLTN GDPAYLG GA FLFEYDANTR ILSTKYGLGD TSQIWAAKVG QMYKVEFVPT DVIIRDSQDR VSYQDVPVIG LVHLNLDRYP DFTVEITN R KSGAVRVAKA SNRVGGARNN VVGYVKPTSG TFSFPLRALS TDVEYRIISI SPHTFQLRDI EWSGSYNPTR KRV |
-Macromolecule #4: tail adaptor protein
Macromolecule | Name: tail adaptor protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella phage Kp7 (virus) |
Molecular weight | Theoretical: 36.062914 KDa |
Sequence | String: MSYSYVERTG DGVATTFNFA FTGKGKGYLL ANQIYVERWD GASWQSATGW SLSGTNQITF LTPLANGQVI RIRRIAGKDY PFAQFEPGV MLDMASLNNT FIHLLEITQE LLDGFYPDGF YLKQDLNMGW NKIVNLMPGT DGGHAVNKTQ LDTLSSHVDD V DQKHTIWN ...String: MSYSYVERTG DGVATTFNFA FTGKGKGYLL ANQIYVERWD GASWQSATGW SLSGTNQITF LTPLANGQVI RIRRIAGKDY PFAQFEPGV MLDMASLNNT FIHLLEITQE LLDGFYPDGF YLKQDLNMGW NKIVNLMPGT DGGHAVNKTQ LDTLSSHVDD V DQKHTIWN DRQDQQIDGL LKAFDSNISY RTAPWTYEAA GGETMVFPPF YFASALVWRD GAYQDQQAGA FEIDNNVITL AD PPLRAGE RVSVLVGSYI TPADPGSWEW IHVAANGTTT SVDLGVSVSD IDDVTLDGLS QGRSNYTLTG TVLDFGEVIP ECT VGARVQ LA |
-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 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 47 |
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Output model | PDB-7y22: |