8K10 | pdb_00008k10

SID1 transmembrane family member 2

PDB DOI: https://doi.org/10.2210/pdb8K10/pdb
EM Map EMD-36782: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2023-07-10 Released: 2024-07-10
Deposition Author(s): Guo, H., Qi, C., Lu, Y., Yang, H., Zhu, Y., Sun, F., Ji, X.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8K10

This is version 1.2 of the entry. See complete history.

Literature

Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity.

Zheng, L., Yang, T., Guo, H., Qi, C., Lu, Y., Xiao, H., Gao, Y., Liu, Y., Yang, Y., Zhou, M., Nguyen, H.C., Zhu, Y., Sun, F., Zhang, C.Y., Ji, X.

(2024) Cell Res 34: 80-83

PubMed: 37932445 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-023-00893-1
Primary Citation Related Structures:
8K10, 8K11, 8K12, 8K13, 8K1B, 8K1D

Organizational Affiliation

National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China.

Macromolecule Content

Total Structure Weight: 197.58 kDa
Atom Count: 9,478
Modeled Residue Count: 1,176
Deposited Residue Count: 1,706
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SID1 transmembrane family member 2	A, B	853	Homo sapiens	Mutation(s): 0 Gene Names: SIDT2, CGI-40, PSEC0072, UNQ685/PRO1325 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBJ9 (Homo sapiens) Explore Q8NBJ9 Go to UniProtKB: Q8NBJ9
PHAROS: Q8NBJ9 GTEx: ENSG00000149577
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NBJ9
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q8NBJ9-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth O], D [auth C], E [auth D], F [auth E]	2		N-Glycosylation	Interactions Focus chain C [auth O] Focus chain D [auth C] Focus chain E [auth D] Focus chain F [auth E] Interactions & Density Focus chain C [auth O] Focus chain D [auth C] Focus chain E [auth D] Focus chain F [auth E]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth B] G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	--

Revision History (Full details and data files)

Version 1.0: 2024-07-10
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Structure summary
Version 1.2: 2025-07-23
Changes: Data collection