8WOQ

Cryo-EM structure of human SIDT1 protein with C1 symmetry at neutral pH

PDB DOI: https://doi.org/10.2210/pdb8WOQ/pdb
EM Map EMD-37695: EMDB EMDataResource

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

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: 2.85 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-024-00647-2
Primary Citation of 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: 209.4 kDa
Atom Count: 11,218
Modelled Residue Count: 1,294
Deposited Residue Count: 1,762
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NXL6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPL (Subject of Investigation/LOI) Query on SPL Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain Y [auth B] MOL2 format, chain S [auth A] MOL2 format, chain Y [auth B]	S [auth A], Y [auth B]	OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE C₂₆ H₅₁ N O₃ APDLCSPGWPLYEQ-WUBHUQEYSA-N		Interactions Focus chain S [auth A] Focus chain Y [auth B] Interactions & Density Focus chain S [auth A] Focus chain Y [auth B]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain X [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], X [auth B], Z [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain X [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain X [auth B] Focus chain Z [auth B]
OLA (Subject of Investigation/LOI) Query on OLA Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain R [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain R [auth A]	GA [auth B], R [auth A]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain GA [auth B] Focus chain R [auth A] Interactions & Density Focus chain GA [auth B] Focus chain R [auth A]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	I [auth A], J [auth A], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain V [auth B] Focus chain W [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain T [auth B] MOL2 format, chain G [auth A] MOL2 format, chain T [auth B]	G [auth A], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain T [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain U [auth B] MOL2 format, chain H [auth A] MOL2 format, chain U [auth B]	H [auth A], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain U [auth B]