4YCN | pdb_00004ycn

Crystal structure of the calcium pump with bound marine macrolide BLLB

• PDB DOI: https://doi.org/10.2210/pdb4YCN/pdb

• Classification: HYDROLASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2015-02-20 Released: 2016-01-13 
• Deposition Author(s): Morita, M., Ogawa, H., Ohno, O., Yamori, T., Suenaga, K., Toyoshima, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.247 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Biselyngbyasides, cytotoxic marine macrolides, are novel and potent inhibitors of the Ca(2+) pumps with a unique mode of binding

Morita, M., Ogawa, H., Ohno, O., Yamori, T., Suenaga, K., Toyoshima, C.

(2015) FEBS Lett 589: 1406-1411

• PubMed: 25957767 
• DOI: https://doi.org/10.1016/j.febslet.2015.04.056
• Primary Citation Related Structures: 
  4YCM, 4YCN


• PubMed Abstract: 
  

  Biselyngbyasides (BLSs), macrolides from a marine cyanobacterium, are cytotoxic natural products whose target molecule is unknown. Here we report that BLSs are high affinity (Ki∼10 nM) inhibitors of Ca(2+)-pumps with a unique binding mode. The crystal structures of the Ca(2+)-pump in complex with BLSs at 3.2-3.5 Å-resolution show that BLSs bind to the pump near the cytoplasmic surface of the transmembrane region. The crystal structures and activity measurement of BLS analogs allow us to identify the structural features that confer high potency to BLSs as inhibitors of the pump.

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Organizational Affiliation: 
• Department of Chemistry, Keio University, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan; Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
Department of Chemistry, Keio University, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan.
Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Ariake, Koto-ku, Tokyo 135-8550, Japan.
Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 111.76 kDa 
• Atom Count: 7,754 
• Modeled Residue Count: 994 
• Deposited Residue Count: 994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	A	994	Oryctolagus cuniculus	Mutation(s): 0  EC: 3.6.3.8 (PDB Primary Data), 7.2.2.10 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P04191 (Oryctolagus cuniculus) Explore P04191  Go to UniProtKB:  P04191

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTY	F [auth A], G [auth A]	PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N
7BL	E [auth A]	(4S,5E,8S,9E,11S,13E,15E,18R)-4-hydroxy-8-methoxy-9,11-dimethyl-18-[(1Z,4E)-2-methylhexa-1,4-dien-1-yl]oxacyclooctadeca-5,9,13,15-tetraen-2-one C27 H40 O4 DVYYXLNVAXSASA-BEVCVMOBSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7BL	BindingDB:  4YCN	Ki: min: 17, max: 17 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.247 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.54	α = 90
b = 71.54	β = 90
c = 587.669	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data scaling
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Morita, M., Ogawa, H., Ohno, O., Yamori, T., Suenaga, K., Toyoshima, C.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Database references, Derived calculations
• Version 2.0: 2025-04-09
  Changes: Data collection, Database references, Polymer sequence, Structure summary