8Z6H | pdb_00008z6h

Structure of Polycystin-1/Polycystin-2 complex with Phosphatidylglycerol-bound

PDB DOI: https://doi.org/10.2210/pdb8Z6H/pdb
EM Map EMD-39799: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-04-19 Released: 2025-04-23
Deposition Author(s): Chen, M.Y., Su, Q., Shi, Y.G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of Polycystin-1/Polycystin-2 complex with Phosphatidylglycerol-bound

Chen, M., Su, Q., Shi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 481.37 kDa
Atom Count: 17,589
Modeled Residue Count: 2,196
Deposited Residue Count: 4,283
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycystin-1	A	1,262	Homo sapiens	Mutation(s): 0 Gene Names: PKD1
UniProt & NIH Common Fund Data Resources
Find proteins for P98161 (Homo sapiens) Explore P98161 Go to UniProtKB: P98161
PHAROS: P98161 GTEx: ENSG00000008710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P98161
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycystin-2	B, C, D	1,007	Homo sapiens	Mutation(s): 0 Gene Names: PKD2, TRPP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13563 (Homo sapiens) Explore Q13563 Go to UniProtKB: Q13563
PHAROS: Q13563 GTEx: ENSG00000118762
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13563
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q13563-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGW (Subject of Investigation/LOI) Query on PGW Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C₄₀ H₇₇ O₁₀ P PAZGBAOHGQRCBP-HGWHEPCSSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B] G [auth B] H [auth C] I [auth C] J [auth D] F [auth B], G [auth B], H [auth C], I [auth C], J [auth D], K [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D]