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- PDB-3fps: The Structure of Sarcoplasmic Reticulum Ca2+-ATPase Bound To Cycl... -

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Basic information

Entry
Database: PDB / ID: 3fps
TitleThe Structure of Sarcoplasmic Reticulum Ca2+-ATPase Bound To Cyclopiazonic and ADP
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / CALCIUM-TRANSPORTING ATPASE SARCOPLASMIC RETICULUM / FAST TWITCH SKELETAL MUSCLE ISOFORM / ENDOPLASMIC RETICULUM
Function / homology
Function and homology information


positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / regulation of striated muscle contraction / negative regulation of striated muscle contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / P-type Ca2+ transporter / P-type calcium transporter activity ...positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / regulation of striated muscle contraction / negative regulation of striated muscle contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / P-type Ca2+ transporter / P-type calcium transporter activity / I band / endoplasmic reticulum-Golgi intermediate compartment / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / calcium ion transport / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / P-type ATPase, subfamily IIA, SERCA-type / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / haloacid dehalogenase-like hydrolase / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus ...Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / P-type ATPase, subfamily IIA, SERCA-type / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / haloacid dehalogenase-like hydrolase / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Distorted Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-CZA / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMoncoq, K. / Morth, J.P. / Bublitz, M. / Laursen, M. / Nissen, P. / Young, H.S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Cyclopiazonic acid is complexed to a divalent metal ion when bound to the sarcoplasmic reticulum Ca2+-ATPase.
Authors: Laursen, M. / Bublitz, M. / Moncoq, K. / Olesen, C. / Moller, J.V. / Young, H.S. / Nissen, P. / Morth, J.P.
History
DepositionJan 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 2, 2014Group: Database references
Revision 1.3Aug 9, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4155
Polymers109,6031
Non-polymers8124
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.340, 96.500, 155.130
Angle α, β, γ (deg.)90.00, 94.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / SERCA1 / CA(2+) ATPASE / Calcium pump 1 / Calcium-transporting ATPase sarcoplasmic reticulum type / ...SERCA1 / CA(2+) ATPASE / Calcium pump 1 / Calcium-transporting ATPase sarcoplasmic reticulum type / fast twitch skeletal muscle isoform / SR Ca(2+)-ATPase 1 / Endoplasmic reticulum class 1/2 Ca(2+) ATPase


Mass: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: twitch skeletal muscle / References: UniProt: P04191, EC: 3.6.3.8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CZA / (6AR,11AS,11BR)-10-ACETYL-9-HYDROXY-7,7-DIMETHYL-2,6,6A,7,11A,11B-HEXAHYDRO-11H-PYRROLO[1',2':2,3]ISOINDOLO[4,5,6-CD]INDOL-11-ONE


Mass: 336.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O3
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDPEDERRK (994-1001) HAVE BEEN REPLACED DURING EXON SPLICING WITH G. UNIPROT P04191 SHOWS THAT ...DPEDERRK (994-1001) HAVE BEEN REPLACED DURING EXON SPLICING WITH G. UNIPROT P04191 SHOWS THAT DPEDERRK (994-1001)-> G IN ISOFORM SERCA1A

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 71.01 %
Crystal growTemperature: 284 K / Method: vapor diffusion / pH: 6.1
Details: 2.75-3% PEG3350, 25% GLYCEROL, 20mM MGCL2, 0.1mM EGTA, 20mM MES, pH 6.1, VAPOR DIFFUSION, temperature 284K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.11587
SYNCHROTRONALS 8.2.221
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMay 26, 2005
ADSC QUANTUM 3152CCDAug 25, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111)SINGLE WAVELENGTHMx-ray1
2SI(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
211
ReflectionResolution: 3.2→40 Å / Num. obs: 30131 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Redundancy: 4 % / Biso Wilson estimate: 93 Å2
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 2653 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OA0

2oa0


Resolution: 3.2→24.891 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 1.99 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 1532 5.09 %
Rwork0.222 28578 -
obs0.223 30110 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.752 Å2 / ksol: 0.252 e/Å3
Displacement parametersBiso max: 433.47 Å2 / Biso mean: 141.139 Å2 / Biso min: 47.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.981 Å20 Å21.355 Å2
2--3.002 Å20 Å2
3----2.021 Å2
Refinement stepCycle: LAST / Resolution: 3.2→24.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 54 10 7735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017871
X-RAY DIFFRACTIONf_angle_d1.25510687
X-RAY DIFFRACTIONf_chiral_restr0.0921235
X-RAY DIFFRACTIONf_plane_restr0.011363
X-RAY DIFFRACTIONf_dihedral_angle_d21.8952932
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.2-3.30310.28861430.32962595
3.3031-3.42090.27341370.29322548
3.4209-3.55750.24761450.25692575
3.5575-3.71890.30971410.2562595
3.7189-3.91420.23171220.2262592
3.9142-4.15840.21281530.20812599
4.1584-4.47780.23091320.1882582
4.4778-4.92520.19931420.18952591
4.9252-5.63070.21641420.19622628
5.6307-7.06710.24031380.23472616
7.0671-24.89180.24521370.19872657
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7547-0.44590.4501-0.5301-0.94311.00080.16950.7659-0.0776-0.68150.01610.00040.33130.2099-0.16881.7602-0.0933-0.03531.3678-0.01760.663424.9515-15.72814.2946
21.27030.23670.40420.29081.50180.6755-0.02560.7655-0.0068-1.3084-0.18940.0859-0.8669-0.40730.22342.64020.2299-0.32791.78890.09670.59910.4573-3.92262.2547
3-0.069-0.80740.58743.40910.12493.79280.07450.09540.23360.11330.026-0.91770.15630.7848-0.09720.53560.00890.05370.80710.03421.008546.5566-20.630959.2032
41.1614-0.3053-0.31212.58991.90043.18420.09310.0240.1494-0.1033-0.0733-0.0214-0.18120.0407-0.01190.5353-0.02050.0040.50360.04590.707223.62731.955667.0641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 45:122 OR RESID 238:359) OR CHAIN A AND (RESID 1001)A45 - 122
2X-RAY DIFFRACTION1CHAIN A AND (RESID 45:122 OR RESID 238:359) OR CHAIN A AND (RESID 1001)A238 - 359
3X-RAY DIFFRACTION2CHAIN A AND (RESID 742:994) OR CHAIN A AND (RESID 995:996)A1 - 994
4X-RAY DIFFRACTION3CHAIN A AND (RESID 1:44 OR RESID 123:237)A1 - 44
5X-RAY DIFFRACTION3CHAIN A AND (RESID 1:44 OR RESID 123:237)A123 - 237
6X-RAY DIFFRACTION4CHAIN A AND (RESID 360:741) OR CHAIN A AND (RESID 1002)A1 - 994

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