8ZKR | pdb_00008zkr

Structure of Polycystin-1/Polycystin-2 complex with phosphatidic acid bound

PDB DOI: https://doi.org/10.2210/pdb8ZKR/pdb
EM Map EMD-60206: EMDB EMDataResource

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

Deposited: 2024-05-17 Released: 2025-05-21
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: 2.80 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

Structure of Polycystin-1/Polycystin-2 complex with phosphatidic acid bound

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

To be published.

Macromolecule Content

Total Structure Weight: 481.45 kDa
Atom Count: 17,021
Modeled Residue Count: 2,182
Deposited Residue Count: 4,282
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	1,261	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: 3	Glycosylation Focus chain B Focus chain C Focus chain D	Go to GlyGen: Q13563-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PA8 (Subject of Investigation/LOI) Query on PA8 Download Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE C₁₉ H₃₆ O₈ P XYSBQYUENLDGMI-QGZVFWFLSA-M		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain F [auth B]	E [auth B] F [auth B] G [auth B] I [auth C] J [auth C] E [auth B], F [auth B], G [auth B], I [auth C], J [auth C], K [auth C], N [auth D], O [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth D] Focus chain O [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain H [auth B]	H [auth B], L [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain H [auth B] Focus chain L [auth C]