6T9N

CryoEM structure of human polycystin-2/PKD2 in UDM supplemented with PI(4,5)P2

PDB DOI: https://doi.org/10.2210/pdb6T9N/pdb
EM Map EMD-10418: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2019-10-28 Released: 2019-11-20
Deposition Author(s): Wang, Q., Pike, A.C.W., Grieben, M., Baronina, A., Nasrallah, C., Shintre, C., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Carpenter, E.P., Structural Genomics Consortium (SGC)
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.96 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 276.89 kDa
Atom Count: 16,917
Modelled Residue Count: 1,920
Deposited Residue Count: 2,188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycystin-2	A, B, C, D	547	Homo sapiens	Mutation(s): 0 Gene Names: PKD2, TRPP2 Membrane Entity: Yes
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
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	E, F, G, H	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UMQ Query on UMQ Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] 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 IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] 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 IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D]	AA [auth B] AB [auth D] BA [auth B] CA [auth B] DA [auth B] AA [auth B], AB [auth D], BA [auth B], CA [auth B], DA [auth B], EA [auth B], IA [auth C], JA [auth C], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], R [auth A], S [auth A], T [auth A], TA [auth D], UA [auth D], VA [auth D], WA [auth D], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	UNDECYL-MALTOSIDE C₂₃ H₄₄ O₁₁ UYEMNFYVTFDKRG-ZNGNCRBCSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain I [auth A] SDF format, chain QA [auth D] SDF format, chain V [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain V [auth B]	FA [auth C], I [auth A], QA [auth D], V [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain FA [auth C] Focus chain I [auth A] Focus chain QA [auth D] Focus chain V [auth B] Interactions & Density Focus chain FA [auth C] Focus chain I [auth A] Focus chain QA [auth D] Focus chain V [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	GA [auth C] HA [auth C] J [auth A] K [auth A] RA [auth D] GA [auth C], HA [auth C], J [auth A], K [auth A], RA [auth D], SA [auth D], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain W [auth B] Focus chain X [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A]	U [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.96 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.13
RECONSTRUCTION	RELION	3

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-11-20

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	106169/Z/14/Z

Revision History (Full details and data files)

Version 1.0: 2019-11-20
Type: Initial release
Version 1.1: 2019-12-18
Changes: Database references
Version 1.2: 2020-02-12
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary