+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36782 | |||||||||
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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: 3.2 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_36782.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-36782-v30.xml emd-36782.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_36782.png | 41.4 KB | ||
Filedesc metadata | emd-36782.cif.gz | 5.9 KB | ||
Others | emd_36782_half_map_1.map.gz emd_36782_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36782 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36782 | HTTPS FTP |
-Validation report
Summary document | emd_36782_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_36782_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_36782_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_36782_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36782 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36782 | HTTPS FTP |
-Related structure data
Related structure data | 8k10MC 8k11C 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_36782.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_36782_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36782_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
Entire | Name: human SID1 transmembrane family member 2 (SIDT2) homodimer |
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Components |
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-Supramolecule #1: human SID1 transmembrane family member 2 (SIDT2) homodimer
Supramolecule | Name: human SID1 transmembrane family member 2 (SIDT2) homodimer 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: 97.054414 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 TLSVLVSQAV TSEAYVSGML FCLGIFLSFY LLTVLLACWE NWR QKKKTL LVAIDRACPE SGHPRVLADS FPGSSPYEGY NYGSFENVSG STDGLVDSAG TGDLSYGYQG RSFEPVGTRP RVDS MSSVE EDDYDTLTDI DSDKNVIRTK QYLYVADLAR KDKRVLRKKY QIYFWNIATI AVFYALPVVQ LVITYQTVVN VTGNQ DICY YNFLCAHPLG NLSAFNNILS NLGYILLGLL FLLIILQREI NHNRALLRND LCALECGIPK HFGLFYAMGT ALMMEG LLS ACYHVCPNYT NFQFDTSFMY MIAGLCMLKL YQKRHPDINA SAYSAYACLA IVIFFSVLGV VFGKGNTAFW IVFSIIH II ATLLLSTQLY YMGRWKLDSG IFRRILHVLY TDCIRQCSGP LYVDRMVLLV MGNVINWSLA AYGLIMRPND FASYLLAI G ICNLLLYFAF YIIMKLRSGE RIKLIPLLCI VCTSVVWGFA LFFFFQGLST WQKTPAESRE HNRDCILLDF FDDHDIWHF LSSIAMFGSF LVLLTLDDDL DTVQRDKIYV FDYKDHDGDY KDHDIDYKDD DDK 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201729 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |