6GYN

Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel

PDB DOI: https://doi.org/10.2210/pdb6GYN/pdb
EM Map EMD-0093: EMDB EMDataResource

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

Deposited: 2018-06-30 Released: 2019-05-08
Deposition Author(s): Shintre, C.A., Pike, A.C.W., Tessitore, A., Young, M., Bushell, S.R., Strain-Damerell, C., Mukhopadhyay, S., Burgess-Brown, N.A., Huiskonen, J.T., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Carpenter, E.P., Structural Genomics Consortium (SGC)
Funding Organization(s): Wellcome Trust, European Commission

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel

Shintre, C.A., Pike, A.C.W., Tessitore, A., Young, M., Bushell, S.R., Strain-Damerell, C., Mukhopadhyay, S., Burgess-Brown, N.A., Huiskonen, J.T., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Carpenter, E.P.

To be published.

Macromolecule Content

Total Structure Weight: 271.46 kDa
Atom Count: 16,932
Modelled Residue Count: 1,980
Deposited Residue Count: 2,084
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4	A, B, C, D	521	Homo sapiens	Mutation(s): 0 Gene Names: HCN4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3Q4 (Homo sapiens) Explore Q9Y3Q4 Go to UniProtKB: Q9Y3Q4
PHAROS: Q9Y3Q4 GTEx: ENSG00000138622
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y3Q4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] DA [auth C] E [auth A] EA [auth C] F [auth A] AA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth D], G [auth A], GA [auth D], HA [auth D], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], U [auth B], V [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain AA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	BA [auth C] CA [auth C] H [auth A] I [auth A] MA [auth D] BA [auth C], CA [auth C], H [auth A], I [auth A], MA [auth D], NA [auth D], S [auth B], T [auth B]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain H [auth A] Focus chain I [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain S [auth B] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.13
RECONSTRUCTION	cryoSPARC	0.6.5

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-08

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	106169/Z/14/Z
European Commission	United Kingdom	IMI 115766

Revision History (Full details and data files)

Version 1.0: 2019-05-08
Type: Initial release
Version 1.1: 2019-12-11
Changes: Other
Version 1.2: 2024-05-15
Changes: Data collection, Database references, Derived calculations, Structure summary