8ZL8 | pdb_00008zl8

Structure of Polycystin-1/Polycystin-2 complex with 7b,27-DHC

PDB DOI: https://doi.org/10.2210/pdb8ZL8/pdb
EM Map EMD-60222: EMDB EMDataResource

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

Deposited: 2024-05-17 Released: 2025-11-26
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: 3.38 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 7b,27-DHC

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

To be published.

Macromolecule Content

Total Structure Weight: 480.93 kDa
Atom Count: 16,682
Modeled Residue Count: 2,176
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: 2	Glycosylation Focus chain B Focus chain C	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
A1EQ3 Query on A1EQ3 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]	(3~{S},7~{R},8~{S},9~{S},10~{R},13~{R},14~{S},17~{R})-10,13-dimethyl-17-[(2~{R},6~{R})-6-methyl-7-oxidanyl-heptan-2-yl]-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthrene-3,7-diol C₂₇ H₄₆ O₃ RXMHNAKZMGJANZ-BMOLSTJGSA-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 C] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B] G [auth B] H [auth B] I [auth C] J [auth C] F [auth B], G [auth B], H [auth B], I [auth C], J [auth C], K [auth C]	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 B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C]