8WOT | pdb_00008wot

Cryo-EM structure of human SIDT1 protein with C2 symmetry at low pH

PDB DOI: https://doi.org/10.2210/pdb8WOT/pdb
EM Map EMD-37698: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM mpstruc

Deposited: 2023-10-07 Released: 2024-03-20
Deposition Author(s): Liu, W., Tang, M., Wang, J., Zhang, X., Wu, S., Ru, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.18 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8WOT

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

Literature

Structural insights into cholesterol transport and hydrolase activity of a putative human RNA transport protein SIDT1.

Liu, W., Tang, M., Wang, J., Wang, F., Song, G., Zhang, X., Wu, S., Ru, H.

(2024) Cell Discov 10: 21-21

PubMed: 38378654 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41421-024-00647-2
Primary Citation Related Structures:
8WOQ, 8WOR, 8WOS, 8WOT

Organizational Affiliation

Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.

Macromolecule Content

Total Structure Weight: 205.2 kDa
Atom Count: 10,672
Modeled Residue Count: 1,272
Deposited Residue Count: 1,762
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SID1 transmembrane family member 1	A, B	881	Homo sapiens	Mutation(s): 0 Gene Names: SIDT1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXL6 (Homo sapiens) Explore Q9NXL6 Go to UniProtKB: Q9NXL6
PHAROS: Q9NXL6 GTEx: ENSG00000072858
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NXL6
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q9NXL6-1
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, D, E, F	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR (Subject of Investigation/LOI) Query on CLR Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	I [auth A] J [auth A] K [auth A] L [auth A] P [auth B] I [auth A], J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	G [auth A], H [auth A], N [auth B], O [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 N [auth B] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain T [auth B] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] mmCIF format, chain M [auth A] mmCIF format, chain T [auth B]	M [auth A], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain T [auth B] Interactions & Density Focus chain M [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.18 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: 2024-03-20

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371344

Revision History (Full details and data files)

Version 1.0: 2024-03-20
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Structure summary
Version 1.2: 2025-06-25
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.