+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41861 | ||||||||||||
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Title | Structure of NAAG-bound Sialin | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Transporter / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information sialic acid:proton symporter activity / D-glucuronate transmembrane transporter activity / Defective SLC17A5 causes Salla disease (SD) and ISSD / sialic acid transport / Organic anion transporters / sialic acid transmembrane transporter activity / carbohydrate:proton symporter activity / Sialic acid metabolism / monoatomic anion transport / amino acid transport ...sialic acid:proton symporter activity / D-glucuronate transmembrane transporter activity / Defective SLC17A5 causes Salla disease (SD) and ISSD / sialic acid transport / Organic anion transporters / sialic acid transmembrane transporter activity / carbohydrate:proton symporter activity / Sialic acid metabolism / monoatomic anion transport / amino acid transport / monoatomic ion transport / response to bacterium / synaptic vesicle membrane / basolateral plasma membrane / lysosome / lysosomal membrane / membrane / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.42 Å | ||||||||||||
Authors | Schmiege P / Li X | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: To Be Published Title: Structure of NAAG-bound Sialin Authors: Schmiege P / Li X | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41861.map.gz | 97 MB | EMDB map data format | |
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Header (meta data) | emd-41861-v30.xml emd-41861.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
Images | emd_41861.png | 22.6 KB | ||
Filedesc metadata | emd-41861.cif.gz | 5.4 KB | ||
Others | emd_41861_half_map_1.map.gz emd_41861_half_map_2.map.gz | 95.6 MB 95.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41861 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41861 | HTTPS FTP |
-Validation report
Summary document | emd_41861_validation.pdf.gz | 884.7 KB | Display | EMDB validaton report |
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Full document | emd_41861_full_validation.pdf.gz | 884.3 KB | Display | |
Data in XML | emd_41861_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_41861_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41861 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41861 | HTTPS FTP |
-Related structure data
Related structure data | 8u3gMC 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_41861.map.gz / Format: CCP4 / Size: 103 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: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41861_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41861_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structure of NAAG-bound Sialin
Entire | Name: Structure of NAAG-bound Sialin |
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Components |
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-Supramolecule #1: Structure of NAAG-bound Sialin
Supramolecule | Name: Structure of NAAG-bound Sialin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Sialin
Macromolecule | Name: Sialin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.681137 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MDYKDDDDKR SPVRDLARND GEESTDRTPL LPGAPRAEAA PVCCSARYNL AILAFFGFFI VYALRVNLSV ALVDMVDSNT TLEDNRTSK ACPEHSAPIK VHHNQTGKKY QWDAETQGWI LGSFFYGYII TQIPGGYVAS KIGGKMLLGF GILGTAVLTL F TPIAADLG ...String: MDYKDDDDKR SPVRDLARND GEESTDRTPL LPGAPRAEAA PVCCSARYNL AILAFFGFFI VYALRVNLSV ALVDMVDSNT TLEDNRTSK ACPEHSAPIK VHHNQTGKKY QWDAETQGWI LGSFFYGYII TQIPGGYVAS KIGGKMLLGF GILGTAVLTL F TPIAADLG VGPLIVLRAL EGLGEGVTFP AMHAMWSSWA PPLERSKLLS ISYAGAQLGT VISLPLSGII CYYMNWTYVF YF FGTIGIF WFLLWIWLVS DTPQKHKRIS HYEKEYILSS LRNQLSSQKS VPWVPILKSL PLWAIVVAHF SYNWTFYTLL TLL PTYMKE ILRFNVQENG FLSSLPYLGS WLCMILSGQA ADNLRAKWNF STLCVRRIFS LIGMIGPAVF LVAAGFIGCD YSLA VAFLT ISTTLGGFCS SGFSINHLDI APSYAGILLG ITNTFATIPG MVGPVIAKSL TPDNTVGEWQ TVFYIAAAIN VFGAI FFTL FAKGEVQNWA LNDHHGHRH UniProtKB: Sialin |
-Macromolecule #2: ACETYL GROUP
Macromolecule | Name: ACETYL GROUP / type: ligand / ID: 2 / Number of copies: 1 / Formula: ACE |
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Molecular weight | Theoretical: 44.053 Da |
Chemical component information | ChemComp-ACE: |
-Macromolecule #3: ASPARTIC ACID
Macromolecule | Name: ASPARTIC ACID / type: ligand / ID: 3 / Number of copies: 1 / Formula: ASP |
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Molecular weight | Theoretical: 133.103 Da |
Chemical component information | ChemComp-ASP: |
-Macromolecule #4: GLUTAMIC ACID
Macromolecule | Name: GLUTAMIC ACID / type: ligand / ID: 4 / Number of copies: 1 / Formula: GLU |
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Molecular weight | Theoretical: 147.129 Da |
Chemical component information | ChemComp-GLU: |
-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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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: 60.0 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: 2.2 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272923 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |