6JP5

Rabbit Cav1.1-Nifedipine Complex

PDB DOI: https://doi.org/10.2210/pdb6JP5/pdb
EM Map EMD-9866: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Oryctolagus cuniculus
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2019-03-25 Released: 2019-06-12
Deposition Author(s): Zhao, Y., Huang, G., Wu, J., Yan, N.
Funding Organization(s): Ministry of Science and Technology (China), National Natural Science Foundation of China, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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 3.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 470.87 kDa
Atom Count: 22,068
Modelled Residue Count: 2,694
Deposited Residue Count: 4,068
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent L-type calcium channel subunit alpha-1S	A	1,873	Oryctolagus cuniculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07293 (Oryctolagus cuniculus) Explore P07293 Go to UniProtKB: P07293
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07293
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent calcium channel gamma-1 subunit	B [auth E]	222	Oryctolagus cuniculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P19518 (Oryctolagus cuniculus) Explore P19518 Go to UniProtKB: P19518
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19518
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent calcium channel subunit alpha-2/delta-1	C [auth F]	1,073	Oryctolagus cuniculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P13806 (Oryctolagus cuniculus) Explore P13806 Go to UniProtKB: P13806
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13806
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent L-type calcium channel subunit beta-1	D [auth B], E [auth C]	450	Oryctolagus cuniculus	Mutation(s): 0 Gene Names: CACNB1, CACNLB1 Membrane Entity: Yes
UniProt
Find proteins for P19517 (Oryctolagus cuniculus) Explore P19517 Go to UniProtKB: P19517
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19517
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D], G, J, K, L	2		N-Glycosylation	Interactions Focus chain F [auth D] Focus chain G Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain F [auth D] Focus chain G Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G79924RM GlyCosmos: G79924RM GlyGen: G79924RM

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, I	3		N-Glycosylation	Interactions Focus chain H Focus chain I Interactions & Density Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PC1 Query on PC1 Download Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A]	X [auth A]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain P [auth A] 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 U [auth A] SDF format, chain V [auth A] SDF format, chain Y [auth A] MOL2 format, chain P [auth A] 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 U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth A]	P [auth A] Q [auth A] R [auth A] S [auth A] T [auth A] P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], Y [auth A]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain Y [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain Y [auth A]
C5U Query on C5U Download Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A]	W [auth A]	dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate C₁₇ H₁₈ N₂ O₆ HYIMSNHJOBLJNT-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain M [auth A] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain M [auth A]	BA [auth F] CA [auth F] DA [auth F] EA [auth F] FA [auth F] BA [auth F], CA [auth F], DA [auth F], EA [auth F], FA [auth F], GA [auth F], HA [auth F], IA [auth F], M [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain M [auth A] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain M [auth A]
ETA Query on ETA Download Ideal Coordinates CCD File SDF format, chain AA [auth F] MOL2 format, chain AA [auth F]	AA [auth F]	ETHANOLAMINE C₂ H₇ N O HZAXFHJVJLSVMW-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Interactions & Density Focus chain AA [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Z [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth A]	N [auth A], O [auth A], Z [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain Z [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain Z [auth A]

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

Released Date: 2019-06-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (China)	China	2016YFA0500402
Ministry of Science and Technology (China)	China	2015CB910101
National Natural Science Foundation of China	China	31621092
National Natural Science Foundation of China	China	31630017
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	China	R01GM130762
National Natural Science Foundation of China	China	81861138009

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
Version 2.1: 2022-03-23
Changes: Author supporting evidence, Database references, Derived calculations, Structure summary
Version 3.0: 2023-11-15
Changes: Atomic model, Data collection

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Deposit Data

Help and Resources

6JP5

Rabbit Cav1.1-Nifedipine Complex

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)