5MKE

cryoEM Structure of Polycystin-2 in complex with cations and lipids

PDB DOI: https://doi.org/10.2210/pdb5MKE/pdb
EM Map EMD-3523: EMDB EMDataResource

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

Deposited: 2016-12-04 Released: 2017-01-18
Deposition Author(s): Wilkes, M., Madej, M.G., Ziegler, C.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.30 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: 450.24 kDa
Atom Count: 16,426
Modelled Residue Count: 1,900
Deposited Residue Count: 3,872
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycystin-2	A, B, C, D	968	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

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PX6 Query on PX6 Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain L [auth A] SDF format, chain NA [auth D] SDF format, chain V [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain V [auth B]	DA [auth C], L [auth A], NA [auth D], V [auth B]	1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE C₃₅ H₆₈ O₈ P PORPENFLTBBHSG-MGBGTMOVSA-M		Interactions Focus chain DA [auth C] Focus chain L [auth A] Focus chain NA [auth D] Focus chain V [auth B] Interactions & Density Focus chain DA [auth C] Focus chain L [auth A] Focus chain NA [auth D] Focus chain V [auth B]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	EA [auth C] FA [auth C] GA [auth C] M [auth A] N [auth A] EA [auth C], FA [auth C], GA [auth C], M [auth A], N [auth A], O [auth A], OA [auth D], PA [auth D], QA [auth D], W [auth B], X [auth B], Y [auth B]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Z [auth C]	AA [auth C] H [auth A] HA [auth D] I [auth A] IA [auth D] AA [auth C], H [auth A], HA [auth D], I [auth A], IA [auth D], JA [auth D], KA [auth D], R [auth B], S [auth B], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth C]
CHS Query on CHS Download Ideal Coordinates CCD File SDF format, chain MA [auth D] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain LA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	BA [auth C] CA [auth C] J [auth A] K [auth A] LA [auth D] BA [auth C], CA [auth C], J [auth A], K [auth A], LA [auth D], MA [auth D], T [auth B], U [auth B]	4-AMINO-5-CYCLOHEXYL-3-HYDROXY-PENTANOIC ACID C₁₁ H₂₁ N O₃ UQWNNUPJBDWRHC-UWVGGRQHSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain T [auth B] Focus chain U [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	P [auth A], Q [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-01-18

Deposition Author(s):

Wilkes, M.

Madej, M.G.

Ziegler, C.

Revision History (Full details and data files)

Version 1.0: 2017-01-18
Type: Initial release
Version 1.1: 2017-01-25
Changes: Database references, Source and taxonomy
Version 1.2: 2017-02-15
Changes: Database references
Version 1.3: 2019-12-11
Changes: Data collection, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary