+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36784 | |||||||||
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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_36784.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-36784-v30.xml emd-36784.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_36784.png | 39.7 KB | ||
Filedesc metadata | emd-36784.cif.gz | 5.5 KB | ||
Others | emd_36784_half_map_1.map.gz emd_36784_half_map_2.map.gz | 115.7 MB 115.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36784 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36784 | HTTPS FTP |
-Validation report
Summary document | emd_36784_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_36784_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_36784_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_36784_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36784 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36784 | HTTPS FTP |
-Related structure data
Related structure data | 8k12MC 8k10C 8k11C 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_36784.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_36784_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36784_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, TMD f...
Entire | Name: human SID1 transmembrane family member 2 (SIDT2) homodimer, TMD focused refinement |
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Components |
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-Supramolecule #1: human SID1 transmembrane family member 2 (SIDT2) homodimer, TMD f...
Supramolecule | Name: human SID1 transmembrane family member 2 (SIDT2) homodimer, TMD focused refinement type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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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: 60.065715 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: VTSEAYVSGM LFCLGIFLSF YLLTVLLACW ENWRQKKKTL LVAIDRACPE SGHPRVLADS FPGSSPYEGY NYGSFENVDT LTDIDSDKN VIRTKQYLYV ADLARKDKRV LRKKYQIYFW NIATIAVFYA LPVVQLVITY QTVVNVTGNQ DICYYNFLCA H PLGNLSAF ...String: VTSEAYVSGM LFCLGIFLSF YLLTVLLACW ENWRQKKKTL LVAIDRACPE SGHPRVLADS FPGSSPYEGY NYGSFENVDT LTDIDSDKN VIRTKQYLYV ADLARKDKRV LRKKYQIYFW NIATIAVFYA LPVVQLVITY QTVVNVTGNQ DICYYNFLCA H PLGNLSAF NNILSNLGYI LLGLLFLLII LQREINHNRA LLRNDLCALE CGIPKHFGLF YAMGTALMME GLLSACYHVC PN YTNFQFD TSFMYMIAGL CMLKLYQKRH PDINASAYSA YACLAIVIFF SVLGVVFGKG NTAFWIVFSI IHIIATLLLS TQL YYMGRW KLDSGIFRRI LHVLYTDCIR QCSGPLYVDR MVLLVMGNVI NWSLAAYGLI MRPNDFASYL LAIGICNLLL YFAF YIIMK LRSGERIKLI PLLCIVCTSV VWGFALFFFF QGLSTWQKTP AESREHNRDC ILLDFFDDHD IWHFLSSIAM FGSFL VLLT LDDDLDTVQR DKIYVFDYKD HDGDYKDHDI DYKDDDDK UniProtKB: SID1 transmembrane family member 2 |
-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: 67365 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |