4YCN

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.247
R-Value Work: 0.210
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2015.04.056
Primary Citation of 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.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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 Membrane Entity: Yes
UniProt
Find proteins for P04191 (Oryctolagus cuniculus) Explore P04191 Go to UniProtKB: P04191
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04191
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	F [auth A], G [auth A]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
7BL Query on 7BL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	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		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]