1T5T

Structure of the (SR)Ca2+-ATPase Ca2-E1-ADP:AlF4- form

PDB DOI: https://doi.org/10.2210/pdb1T5T/pdb

Classification: HYDROLASE
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2004-05-05 Released: 2004-06-15
Deposition Author(s): Sorensen, T.L.-M., Moller, J.V., Nissen, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.293
R-Value Work: 0.246
R-Value Observed: 0.247

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Phosphoryl transfer and calcium ion occlusion in the calcium pump.

Sorensen, T.L., Moller, J.V., Nissen, P.

(2004) Science 304: 1672-1675

PubMed: 15192230 Search on PubMed
DOI: https://doi.org/10.1126/science.1099366
Primary Citation of Related Structures:
1T5S, 1T5T

PubMed Abstract:
A tight coupling between adenosine triphosphate (ATP) hydrolysis and vectorial ion transport has to be maintained by ATP-consuming ion pumps. We report two crystal structures of Ca2+-bound sarco(endo)plasmic reticulum Ca2+-adenosine triphosphatase (SERCA) at 2.6 and 2.9 angstrom resolution in complex with (i) a nonhydrolyzable ATP analog [adenosine (beta-gamma methylene)-triphosphate] and (ii) adenosine diphosphate plus aluminum fluoride. SERCA reacts with ATP by an associative mechanism mediated by two Mg2+ ions to form an aspartyl-phosphorylated intermediate state (Ca2-E1 approximately P). The conformational changes that accompany the reaction with ATP pull the transmembrane helices 1 and 2 and close a cytosolic entrance for Ca2+, thereby preventing backflow before Ca2+ is released on the other side of the membrane.

Organizational Affiliation

Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.

Macromolecule Content

Total Structure Weight: 110.3 kDa
Atom Count: 7,751
Modelled Residue Count: 994
Deposited Residue Count: 994
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 isoform SERCA1A	A	994	Oryctolagus cuniculus	Mutation(s): 0 EC: 3.6.3.8
UniProt
Find proteins for P04191 (Oryctolagus cuniculus) Go to UniProtKB: P04191
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth A]
ALF Query on ALF Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	TETRAFLUOROALUMINATE ION Al F₄ UYOMQIYKOOHAMK-UHFFFAOYSA-J		Interactions Focus chain B [auth A]
CA Query on CA 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] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.293
R-Value Work: 0.246
R-Value Observed: 0.247
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.477	α = 90
b = 75.617	β = 108.82
c = 151.651	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-06-15

Deposition Author(s):

Sorensen, T.L.-M.

Moller, J.V.

Nissen, P.

Revision History (Full details and data files)

Version 1.0: 2004-06-15
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations