[English] 日本語
Yorodumi- EMDB-40622: Chlorella virus Hyaluronan Synthase bound to GlcA extended GlcNAc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40622 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Chlorella virus Hyaluronan Synthase bound to GlcA extended GlcNAc primer | |||||||||
Map data | Chlorella virus Hyaluronan Synthase bound to GlcA extended GlcNAc primer | |||||||||
Sample |
| |||||||||
Keywords | hyaluronic acid / hyaluronan / HA / HAS / glycosyltransferase / GT / membrane protein / nanobody / n-acetylglucosamine / glucuronic acid / TRANSFERASE | |||||||||
Function / homology | hyaluronan synthase activity / Glycosyltransferase like family 2 / extracellular matrix assembly / hyaluronan biosynthetic process / extracellular polysaccharide biosynthetic process / Nucleotide-diphospho-sugar transferases / membrane / Hyaluronan synthase Function and homology information | |||||||||
Biological species | Paramecium bursaria Chlorella virus 1 / Paramecium bursaria Chlorella virus CZ-2 / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Stephens Z / Zimmer J | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: To Be Published Title: Molecular insights into hyaluronan synthesis, secretion, and length control Authors: Gorniak I / Stephens Z / Erramilli SK / Gawda T / Kossiakoff AA / Zimmer J | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_40622.map.gz | 59.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-40622-v30.xml emd-40622.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
Images | emd_40622.png | 34.9 KB | ||
Filedesc metadata | emd-40622.cif.gz | 6.3 KB | ||
Others | emd_40622_half_map_1.map.gz emd_40622_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40622 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40622 | HTTPS FTP |
-Validation report
Summary document | emd_40622_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_40622_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_40622_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_40622_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40622 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40622 | HTTPS FTP |
-Related structure data
Related structure data | 8sncMC 8sndC 8sneC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_40622.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Chlorella virus Hyaluronan Synthase bound to GlcA extended GlcNAc primer | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Half Map A
File | emd_40622_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map B
File | emd_40622_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Ternary complex of Chlorella virus hyaluronan synthase bound to n...
Entire | Name: Ternary complex of Chlorella virus hyaluronan synthase bound to nanobodies 872 and 886 |
---|---|
Components |
|
-Supramolecule #1: Ternary complex of Chlorella virus hyaluronan synthase bound to n...
Supramolecule | Name: Ternary complex of Chlorella virus hyaluronan synthase bound to nanobodies 872 and 886 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
Source (natural) | Organism: Paramecium bursaria Chlorella virus 1 |
Molecular weight | Theoretical: 95.3 kDa/nm |
-Macromolecule #1: Hyaluronan synthase
Macromolecule | Name: Hyaluronan synthase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Paramecium bursaria Chlorella virus CZ-2 |
Molecular weight | Theoretical: 65.890062 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGTSWRTIVS ANLFAVGGAL LMLAPAIVGY VFQWNIGVSA VWGISVYGVF VLGFYIAQIV FSEFNRMRLS DWISLRPDNW NATRVAVII AGYREDPFMF KKCLESVRDS EYGNVARLIC VIDGDEEEDL KMAEIYKQVY NDNVKKPGVV LCESENKNGS T IDSDVSKN ...String: MGTSWRTIVS ANLFAVGGAL LMLAPAIVGY VFQWNIGVSA VWGISVYGVF VLGFYIAQIV FSEFNRMRLS DWISLRPDNW NATRVAVII AGYREDPFMF KKCLESVRDS EYGNVARLIC VIDGDEEEDL KMAEIYKQVY NDNVKKPGVV LCESENKNGS T IDSDVSKN ICILQPHRGK RESLYTGFQL ASMDPSVHAV VLIDSDTVLE KNAILEVVYP LSCDPNIKAV AGECKIWNTD TI LSMLVSW RYFSAFNVER GAQSLWKTVQ CVGGPLGAYT IDIINEIKDP WITQTFLGNK CTYGDDRRLT NEVLMRGKKI VYT PFAVGW SDSPTNVMRY IVQQTRWSKS WCREIWYTLG SAWKHGFSGI YLAFECMYQI MYFFLVMYLF SYIAIKADIR AQTA TVLVS TLVTIIKSSY LALRAKNLKA FYFVLYTYVY FFCMIPARIT AMFTMFDIAW GTRGGNAKMT IGARVWLWAK QFLIT YMWW AGVLAAGVYS IVDNWYFDWA DIQYRFALVG ICSYLVFVSI VLVIYLIGKI TTWNYTPLQK ELIEERYLHN ASENAP EVL EHHHHHHHHH H UniProtKB: Hyaluronan synthase |
-Macromolecule #2: Nanobody 872
Macromolecule | Name: Nanobody 872 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 14.783248 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: QVQLVESGGG LVQAGGSLKV SCAASGRAFK TYRMAWFRQA PGKEREFVSG ISALETTYYA DSVKGRFTIS RDNTKNTVSL QMDSLKPED TAVYYCAARR YGGTDYTTTG SYDYWGQGTQ VTVSSHHHHH HEPEA |
-Macromolecule #3: Nanobody 881
Macromolecule | Name: Nanobody 881 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 15.184657 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: QVQLVESGGG LVQAGGSLRL ACAASGRIFS SDTLAWFRRA PGKEREFVAA SRWSGGGTDY DSVKGRFTFS RDNTFNTMCL EMNSLKPED TAVYYCALRT ARDSYYYTRN PTGYDYWGQG TQVTVSSHHH HHHEPEA |
-Macromolecule #5: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: Y01 |
---|---|
Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Macromolecule #6: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MN |
---|---|
Molecular weight | Theoretical: 54.938 Da |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 1 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115974 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |