+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36791 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SID1 transmembrane family member 1 | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / TRANSPORT PROTEIN | |||||||||
Function / homology | RNA transmembrane transporter activity / SID1 transmembrane family / dsRNA-gated channel SID-1 / RNA transport / cholesterol binding / double-stranded RNA binding / lysosome / plasma membrane / SID1 transmembrane family member 1 Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.47 Å | |||||||||
Authors | Guo H / Qi C / Lu Y / Yang H / Zhu Y / Sun F / Ji X | |||||||||
Funding support | China, 1 items
| |||||||||
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 |
|
-Structure visualization
-Downloads & links
-EMDB archive
Map data | EMDB map data format | |||
---|---|---|---|---|
Header (meta data) | EMDB header | |||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36791 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36791 | HTTPS FTP |
-Validation report
Summary document | emd_36791_validation.pdf.gz | 818 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_36791_full_validation.pdf.gz | 817.6 KB | Display | |
Data in XML | emd_36791_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | emd_36791_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36791 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36791 | HTTPS FTP |
-Related structure data
Related structure data | 8k1bMC 36782 36783 36784 36785 36792 8k10C 8k11C 8k12C 8k13C 8k1dC 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 |
---|
-Map
File | Download / File: emd_36791.map.gz / Format: CCP4 / Size: 16.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : human SID1 transmembrane family member 1 (SIDT1) homodimer, ECD f...
Entire | Name: human SID1 transmembrane family member 1 (SIDT1) homodimer, ECD focused refinement |
---|---|
Components |
|
-Supramolecule #1: human SID1 transmembrane family member 1 (SIDT1) homodimer, ECD f...
Supramolecule | Name: human SID1 transmembrane family member 1 (SIDT1) homodimer, ECD focused refinement type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: SID1 transmembrane family member 1
Macromolecule | Name: SID1 transmembrane family member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 29.089018 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: DFDHVYSGVV NLSTENIYSF NYTSQPDQVT AVRVYVNSSS ENLNYPVLVV VRQQKEVLSW QVPLLFQGLY QRSYNYQEVS RTLCPSEAT NETGPLQQLI FVDVASMAPL GAQYKLLVTK LKHFQLRTNV AFHFTASPSQ PQYFLYKFPK DVDSVIIKVV S EMAYPCSV ...String: DFDHVYSGVV NLSTENIYSF NYTSQPDQVT AVRVYVNSSS ENLNYPVLVV VRQQKEVLSW QVPLLFQGLY QRSYNYQEVS RTLCPSEAT NETGPLQQLI FVDVASMAPL GAQYKLLVTK LKHFQLRTNV AFHFTASPSQ PQYFLYKFPK DVDSVIIKVV S EMAYPCSV VSVQNIMCPV YDLDHNVEFN GVYQSMTKKA AITLQKKDFP GEQFFVVFVI KPEDYACGGS FFIQEKENQT WN LQRKKNL EVTIVPS UniProtKB: SID1 transmembrane family member 1 |
-Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
---|---|
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 |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94868 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |