6JPB

Rabbit Cav1.1-Diltiazem Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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


Literature

Molecular Basis for Ligand Modulation of a Mammalian Voltage-Gated Ca2+Channel.

Zhao, Y.Huang, G.Wu, J.Wu, Q.Gao, S.Yan, Z.Lei, J.Yan, N.

(2019) Cell 177: 1495-1506.e12

  • DOI: 10.1016/j.cell.2019.04.043
  • Primary Citation of Related Structures:  
    6JP5, 6JP8, 6JPA, 6JPB

  • PubMed Abstract: 
  • The L-type voltage-gated Ca 2+ (Ca v ) channels are modulated by various compounds exemplified by 1,4-dihydropyridines (DHP), benzothiazepines (BTZ), and phenylalkylamines (PAA), many of which have been used for characterizing channel properties and for treatment of hypertension and other disorders ...

    The L-type voltage-gated Ca 2+ (Ca v ) channels are modulated by various compounds exemplified by 1,4-dihydropyridines (DHP), benzothiazepines (BTZ), and phenylalkylamines (PAA), many of which have been used for characterizing channel properties and for treatment of hypertension and other disorders. Here, we report the cryoelectron microscopy (cryo-EM) structures of Ca v 1.1 in complex with archetypal antagonistic drugs, nifedipine, diltiazem, and verapamil, at resolutions of 2.9 Å, 3.0 Å, and 2.7 Å, respectively, and with a DHP agonist Bay K 8644 at 2.8 Å. Diltiazem and verapamil traverse the central cavity of the pore domain, directly blocking ion permeation. Although nifedipine and Bay K 8644 occupy the same fenestration site at the interface of repeats III and IV, the coordination details support previous functional observations that Bay K 8644 is less favored in the inactivated state. These structures elucidate the modes of action of different Ca v ligands and establish a framework for structure-guided drug discovery.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. Electronic address: nyan@princeton.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit alpha-1SA1873Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNA1SCACH1CACNL1A3
Membrane Entity: Yes 
UniProt
Find proteins for P07293 (Oryctolagus cuniculus)
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Go to UniProtKB:  P07293
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent calcium channel gamma-1 subunitB [auth E]222Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNG1CACNLG
Membrane Entity: Yes 
UniProt
Find proteins for P19518 (Oryctolagus cuniculus)
Explore P19518 
Go to UniProtKB:  P19518
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit beta-1C [auth B]450Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNB1CACNLB1
Membrane Entity: Yes 
UniProt
Find proteins for P19517 (Oryctolagus cuniculus)
Explore P19517 
Go to UniProtKB:  P19517
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent L-type calcium channel subunit beta-1D [auth C]524Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNB1CACNLB1
Membrane Entity: Yes 
UniProt
Find proteins for P19517 (Oryctolagus cuniculus)
Explore P19517 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Voltage-dependent calcium channel subunit alpha-2/delta-1E [auth F]1046Oryctolagus cuniculusMutation(s): 0 
Gene Names: CACNA2D1CACNL2ACCHL2A
Membrane Entity: Yes 
UniProt
Find proteins for P13806 (Oryctolagus cuniculus)
Explore P13806 
Go to UniProtKB:  P13806
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D], G, J, K2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G79924RM
GlyCosmos:  G79924RM
GlyGen:  G79924RM
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH, I3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G11411VI
GlyCosmos:  G11411VI
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1 (Subject of Investigation/LOI)
Query on PC1

Download Ideal Coordinates CCD File 
Q [auth A]1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
3PE (Subject of Investigation/LOI)
Query on 3PE

Download Ideal Coordinates CCD File 
P [auth A], R [auth A], S [auth A], T [auth A]1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
C9F (Subject of Investigation/LOI)
Query on C9F

Download Ideal Coordinates CCD File 
U [auth A][(2~{S},3~{S})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate
C22 H26 N2 O4 S
HSUGRBWQSSZJOP-RTWAWAEBSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth F], BA [auth F], CA [auth F], DA [auth F], M [auth A], X [auth F], Y [auth F], Z [auth F]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ETA
Query on ETA

Download Ideal Coordinates CCD File 
W [auth F]ETHANOLAMINE
C2 H7 N O
HZAXFHJVJLSVMW-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
N [auth A], O [auth A], V [auth F]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
C9F BindingDB:  6JPB Ki: min: 16, max: 380 (nM) from 3 assay(s)
IC50: min: 42, max: 2600 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2016YFA0500402
Ministry of Science and Technology (China)China2015CB910101
National Natural Science Foundation of ChinaChina31621092
National Natural Science Foundation of ChinaChina31630017
National Institutes of Health/National Institute of General Medical SciencesChinaR01GM130762
National Natural Science Foundation of ChinaChina81861138009

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    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