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Yorodumi- EMDB-33422: structure of a membrane-integrated glycosyltransferase with inhibitor -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33422 | |||||||||
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Title | structure of a membrane-integrated glycosyltransferase with inhibitor | |||||||||
Map data | ||||||||||
Sample |
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Keywords | membrane protein / glycosyltransferase / TRANSFERASE | |||||||||
Function / homology | Function and homology information chitosome / : / chitin synthase / chitin synthase activity / septum digestion after cytokinesis / cell septum / cell periphery / cell wall organization / plasma membrane Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Wu YN / Zhang M / Yang YZ / Ding XY / Liu XT / Zhang MJ / Yu HJ | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: structure of a membrane-integrated glycosyltransferase with inhibitor Authors: Wu YN / Zhang M / Yang YZ / Ding XY / Liu XT / Zhang MJ / Yu HJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33422.map.gz | 49 MB | EMDB map data format | |
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Header (meta data) | emd-33422-v30.xml emd-33422.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33422_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_33422.png | 58.8 KB | ||
Filedesc metadata | emd-33422.cif.gz | 6.1 KB | ||
Others | emd_33422_half_map_1.map.gz emd_33422_half_map_2.map.gz | 39.6 MB 39.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33422 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33422 | HTTPS FTP |
-Validation report
Summary document | emd_33422_validation.pdf.gz | 881.1 KB | Display | EMDB validaton report |
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Full document | emd_33422_full_validation.pdf.gz | 880.7 KB | Display | |
Data in XML | emd_33422_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | emd_33422_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33422 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33422 | HTTPS FTP |
-Related structure data
Related structure data | 7xs6MC 7xs7C 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_33422.map.gz / Format: CCP4 / Size: 52.7 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: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33422_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33422_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : membrane-integrated glycosyltransferase
Entire | Name: membrane-integrated glycosyltransferase |
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Components |
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-Supramolecule #1: membrane-integrated glycosyltransferase
Supramolecule | Name: membrane-integrated glycosyltransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Chitin synthase 1
Macromolecule | Name: Chitin synthase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: chitin synthase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 130.001141 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSDQNNRSRN EYHSNRKNEP SYELQNAHSG LFHSSNEELT NRNQRYTNQN ASMGSFTPVQ SLQFPEQSQQ TNMLYNGDDG NNNTINDNE RDIYGGFVNH HRQRPPPATA EYNDVFNTNS QQLPSEHQYN NVPSYPLPSI NVIQTTPELI HNGSQTMATP I ERPFFNEN ...String: MSDQNNRSRN EYHSNRKNEP SYELQNAHSG LFHSSNEELT NRNQRYTNQN ASMGSFTPVQ SLQFPEQSQQ TNMLYNGDDG NNNTINDNE RDIYGGFVNH HRQRPPPATA EYNDVFNTNS QQLPSEHQYN NVPSYPLPSI NVIQTTPELI HNGSQTMATP I ERPFFNEN DYYYNNRNSR TSPSIASSSD GYADQEARPI LEQPNNNMNS GNIPQYHDQP FGYNNGYHGL QAKDYYDDPE GG YIDQRGD DYQINSYLGR NGEMVDPYDY ENSLRHMTPM ERREYLHDDS RPVNDGKEEL DSVKSGYSHR DLGEYDKDDF SRD DEYDDL NTIDKLQFQA NGVPASSSVS SIGSKESDII VSNDNLTANR ALKRSGTEIR KFKLWNGNFV FDSPISKTLL DQYA TTTEN ANTLPNEFKF MRYQAVTCEP NQLAEKNFTV RQLKYLTPRE TELMLVVTMY NEDHILLGRT LKGIMDNVKY MVKKK NSST WGPDAWKKIV VCIISDGRSK INERSLALLS SLGCYQDGFA KDEINEKKVA MHVYEHTTMI NITNISESEV SLECNQ GTV PIQLLFCLKE QNQKKINSHR WAFEGFAELL RPNIVTLLDA GTMPGKDSIY QLWREFRNPN VGGACGEIRT DLGKRFV KL LNPLVASQNF EYKMSNILDK TTESNFGFIT VLPGAFSAYR FEAVRGQPLQ KYFYGEIMEN EGFHFFSSNM YLAEDRIL C FEVVTKKNCN WILKYCRSSY ASTDVPERVP EFILQRRRWL NGSFFASVYS FCHFYRVWSS GHNIGRKLLL TVEFFYLFF NTLISWFSLS SFFLVFRILT VSIALAYHSA FNVLSVIFLW LYGICTLSTF ILSLGNKPKS TEKFYVLTCV IFAVMMIYMI FCSIFMSVK SFQNILKNDT ISFEGLITTE AFRDIVISLG STYCLYLISS IIYLQPWHML TSFIQYILLS PSYINVLNIY A FCNVHDLS WGTKGAMANP LGKINTTEDG TFKMEVLVSS SEIQANYDKY LKVLNDFDPK SESRPTEPSY DEKKTGYYAN VR SLVIIFW VITNFIIVAV VLETGGIADY IAMKSISTDD TLETAKKAEI PLMTSKASIY FNVILWLVAL SALIRFIGCS IYM IVRFFK KVTFR UniProtKB: Chitin synthase 1 |
-Macromolecule #2: TETRADECANE
Macromolecule | Name: TETRADECANE / type: ligand / ID: 2 / Number of copies: 16 / Formula: C14 |
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Molecular weight | Theoretical: 198.388 Da |
Chemical component information | ChemComp-C14: |
-Macromolecule #3: DODECANE
Macromolecule | Name: DODECANE / type: ligand / ID: 3 / Number of copies: 10 / Formula: D12 |
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Molecular weight | Theoretical: 170.335 Da |
Chemical component information | ChemComp-D12: |
-Macromolecule #4: HEPTANE
Macromolecule | Name: HEPTANE / type: ligand / ID: 4 / Number of copies: 14 / Formula: HP6 |
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Molecular weight | Theoretical: 100.202 Da |
Chemical component information | ChemComp-HP6: |
-Macromolecule #5: (2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-m...
Macromolecule | Name: (2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid (non-preferred name) type: ligand / ID: 5 / Number of copies: 2 / Formula: BGI |
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Molecular weight | Theoretical: 495.44 Da |
Chemical component information | ChemComp-BGI: |
-Macromolecule #6: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22l...
Macromolecule | Name: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9Z)-hexadec-9-enoate type: ligand / ID: 6 / Number of copies: 2 / Formula: 0V9 |
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Molecular weight | Theoretical: 689.943 Da |
Chemical component information | ChemComp-0V9: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |