6GYO

Structure of human HCN4 hyperpolarization-activated cyclic nucleotide-gated ion channel in complex with cAMP

PDB DOI: https://doi.org/10.2210/pdb6GYO/pdb
EM Map EMD-0094: 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: 2019-05-01
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: 276.38 kDa
Atom Count: 17,540
Modelled Residue Count: 2,004
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIE Query on PIE Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain KA [auth C] SDF format, chain XA [auth D] SDF format, chain Y [auth B] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B]	J [auth A], KA [auth C], XA [auth D], Y [auth B]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL C₄₃ H₈₀ O₁₃ P PDLAMJKMOKWLAJ-OJERQSHOSA-M		Interactions Focus chain J [auth A] Focus chain KA [auth C] Focus chain XA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain J [auth A] Focus chain KA [auth C] Focus chain XA [auth D] Focus chain Y [auth B]
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain RA [auth D] SDF format, chain S [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B]	BA [auth B] DA [auth C] EA [auth C] F [auth A] G [auth A] BA [auth B], DA [auth C], EA [auth C], F [auth A], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], JA [auth C], M [auth A], N [auth A], NA [auth C], O [auth A], PA [auth D], QA [auth D], R [auth B], RA [auth D], S [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], VA [auth D], W [auth B], WA [auth D], X [auth B]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain BA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Interactions & Density Focus chain BA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain MA [auth C] 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 K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D]	AA [auth B] K [auth A] L [auth A] LA [auth C] MA [auth C] AA [auth B], K [auth A], L [auth A], LA [auth C], MA [auth C], YA [auth D], Z [auth B], ZA [auth D]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain AA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
CMP Query on CMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain FA [auth C] SDF format, chain SA [auth D] SDF format, chain T [auth B] MOL2 format, chain E [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] mmCIF format, chain E [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth B]	E [auth A], FA [auth C], SA [auth D], T [auth B]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C₁₀ H₁₂ N₅ O₆ P IVOMOUWHDPKRLL-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain FA [auth C] Focus chain SA [auth D] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain FA [auth C] Focus chain SA [auth D] Focus chain T [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain Q [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth B]	CA [auth C], OA [auth D], P [auth A], Q [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain CA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Q [auth B] Interactions & Density Focus chain CA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Q [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
RECONSTRUCTION	cryoSPARC	0.6.5
MODEL REFINEMENT	PHENIX	1.13

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-01

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: 2019-05-01
Type: Initial release
Version 1.1: 2019-12-18
Changes: Other
Version 1.2: 2024-05-15
Changes: Data collection, Database references, Derived calculations, Structure summary