+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36783 | |||||||||
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Title | SID1 transmembrane family member 2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information nucleic acid transmembrane transporter activity / AP-1 adaptor complex binding / RNA transmembrane transporter activity / AP-2 adaptor complex binding / RNA transport / type B pancreatic cell development / regulation of insulin secretion involved in cellular response to glucose stimulus / type B pancreatic cell proliferation / RNA catabolic process / response to glucose ...nucleic acid transmembrane transporter activity / AP-1 adaptor complex binding / RNA transmembrane transporter activity / AP-2 adaptor complex binding / RNA transport / type B pancreatic cell development / regulation of insulin secretion involved in cellular response to glucose stimulus / type B pancreatic cell proliferation / RNA catabolic process / response to glucose / cell morphogenesis / double-stranded RNA binding / glucose homeostasis / lysosome / lysosomal membrane / DNA binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Guo H / Qi C / Lu Y / Yang H / Zhu Y / Sun F / Ji X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2024 Title: Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity. Authors: Le Zheng / Tingting Yang / Hangtian Guo / Chen Qi / Yuchi Lu / Haonan Xiao / Yan Gao / Yue Liu / Yixuan Yang / Mengru Zhou / Henry C Nguyen / Yun Zhu / Fei Sun / Chen-Yu Zhang / Xiaoyun Ji / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36783.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-36783-v30.xml emd-36783.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_36783.png | 42.5 KB | ||
Filedesc metadata | emd-36783.cif.gz | 5.5 KB | ||
Others | emd_36783_half_map_1.map.gz emd_36783_half_map_2.map.gz | 115.7 MB 115.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36783 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36783 | HTTPS FTP |
-Validation report
Summary document | emd_36783_validation.pdf.gz | 914.9 KB | Display | EMDB validaton report |
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Full document | emd_36783_full_validation.pdf.gz | 914.5 KB | Display | |
Data in XML | emd_36783_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_36783_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36783 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36783 | HTTPS FTP |
-Related structure data
Related structure data | 8k11MC 8k10C 8k12C 8k13C 8k1bC 8k1dC 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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-Map
File | Download / File: emd_36783.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36783_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36783_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human SID1 transmembrane family member 2 (SIDT2) homodimer, ECD f...
Entire | Name: human SID1 transmembrane family member 2 (SIDT2) homodimer, ECD focused refinement |
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Components |
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-Supramolecule #1: human SID1 transmembrane family member 2 (SIDT2) homodimer, ECD f...
Supramolecule | Name: human SID1 transmembrane family member 2 (SIDT2) homodimer, ECD focused refinement type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: SID1 transmembrane family member 2
Macromolecule | Name: SID1 transmembrane family member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 32.273844 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MKANLLVLLC ALAAADAHLG VLGPKNVSQK DAEFERTYVD EVNSELVNIY TFNHTVTRNR TEGVRVSVNV LNKQKGAPLL FVVRQKEAV VSFQVPLILR GMFQRKYLYQ KVERTLCQPP TKNESEIQFF YVDVSTLSPV NTTYQLRVSR MDDFVLRTGE Q FSFNTTAA ...String: MKANLLVLLC ALAAADAHLG VLGPKNVSQK DAEFERTYVD EVNSELVNIY TFNHTVTRNR TEGVRVSVNV LNKQKGAPLL FVVRQKEAV VSFQVPLILR GMFQRKYLYQ KVERTLCQPP TKNESEIQFF YVDVSTLSPV NTTYQLRVSR MDDFVLRTGE Q FSFNTTAA QPQYFKYEFP EGVDSVIVKV TSNKAFPCSV ISIQDVLCPV YDLDNNVAFI GMYQTMTKKA AITVQRKDFP SN SFYVVVV VKTEDQACGG SLPFYPFAED EPVDQGHRQK TLSVLVSQA UniProtKB: SID1 transmembrane family member 2 |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 8 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-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 / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
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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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 187510 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |