9NJS | pdb_00009njs

human polycystin-2 with clinical variant D511V

PDB DOI: https://doi.org/10.2210/pdb9NJS/pdb
EM Map EMD-49489: EMDB EMDataResource

Classification: METAL TRANSPORT
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-02-27 Released: 2026-09-09
Deposition Author(s): Wang, Q., Cao, E.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9NJS

This is version 1.0 of the entry. See complete history.

Literature

human polycystin-2 with clinical variant D511V

Wang, Q., Cao, E.

To be published.

Macromolecule Content

Total Structure Weight: 344.39 kDa
Atom Count: 15,636
Modeled Residue Count: 1,916
Deposited Residue Count: 2,980
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycystin-2	A [auth a], B [auth b], C [auth c], D [auth d]	745	Homo sapiens	Mutation(s): 1 Gene Names: PKD2, TRPP1, 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13563
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth a] Focus chain B [auth b] Focus chain C [auth c] Focus chain D [auth d]	Go to GlyGen: Q13563-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth d] SDF format, chain O [auth d] SDF format, chain N [auth d] SDF format, chain M [auth c] SDF format, chain L [auth c] SDF format, chain K [auth c] SDF format, chain J [auth b] SDF format, chain I [auth b] SDF format, chain H [auth b] SDF format, chain G [auth a] SDF format, chain F [auth a] SDF format, chain E [auth a] MOL2 format, chain P [auth d] MOL2 format, chain O [auth d] MOL2 format, chain N [auth d] MOL2 format, chain M [auth c] MOL2 format, chain L [auth c] MOL2 format, chain K [auth c] MOL2 format, chain J [auth b] MOL2 format, chain I [auth b] MOL2 format, chain H [auth b] MOL2 format, chain G [auth a] MOL2 format, chain F [auth a] MOL2 format, chain E [auth a] mmCIF format, chain P [auth d] mmCIF format, chain O [auth d] mmCIF format, chain N [auth d] mmCIF format, chain M [auth c] mmCIF format, chain L [auth c] mmCIF format, chain K [auth c] mmCIF format, chain J [auth b] mmCIF format, chain I [auth b] mmCIF format, chain H [auth b] mmCIF format, chain G [auth a] mmCIF format, chain F [auth a] mmCIF format, chain E [auth a]	E [auth a] F [auth a] G [auth a] H [auth b] I [auth b] E [auth a], F [auth a], G [auth a], H [auth b], I [auth b], J [auth b], K [auth c], L [auth c], M [auth c], N [auth d], O [auth d], P [auth d]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth a] Focus chain F [auth a] Focus chain G [auth a] Focus chain H [auth b] Focus chain I [auth b] Focus chain J [auth b] Focus chain K [auth c] Focus chain L [auth c] Focus chain M [auth c] Focus chain N [auth d] Focus chain O [auth d] Focus chain P [auth d] Interactions & Density Focus chain E [auth a] Focus chain F [auth a] Focus chain G [auth a] Focus chain H [auth b] Focus chain I [auth b] Focus chain J [auth b] Focus chain K [auth c] Focus chain L [auth c] Focus chain M [auth c] Focus chain N [auth d] Focus chain O [auth d] Focus chain P [auth d]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-09-09
Type: Initial release

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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.