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

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Basic information

Entry
Database: PDB / ID: 3fpb
TitleThe Structure of Sarcoplasmic Reticulum Ca2+-ATPase Bound To Cyclopiazonic acid with ATP
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / CALCIUM PUMP / SERCA / NONHYDROLYZABLE ATP ANALOG / P-TYPE ATPase / CYCLOPIAZONIC ACID / ION TRANSPORT / PHOSPHOPROTEIN / SARCOPLASMIC RETICULUM / TRANSMEMBRANE
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 / negative regulation of striated muscle contraction / 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 / negative regulation of striated muscle contraction / 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 / intracellular calcium ion homeostasis / 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 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / 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'-TRIPHOSPHATE / Chem-CZA / : / TETRAFLUOROMAGNESATE(2-) / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 5, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,6347
Polymers109,6031
Non-polymers1,0326
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.360, 69.870, 143.500
Angle α, β, γ (deg.)90.00, 107.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / SERCA1 / Calcium pump 1 / Calcium-transporting ATPase sarcoplasmic reticulum type / fast twitch ...SERCA1 / 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

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Non-polymers , 6 types, 201 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MF4 / TETRAFLUOROMAGNESATE(2-) / MAGNESIUMTETRAFLUORIDE


Mass: 100.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F4Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: 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
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.83 Å3/Da / Density % sol: 67.9 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 8% PEG 3350, 21% GLYCEROL, 20mM MGCL2, 0.1mM EGTA, 20mM MES, pH 6.10, VAPOR DIFFUSION, HANGING DROP, temperature 284K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.115872 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 2.55→40 Å / Num. all: 54351 / Num. obs: 54351 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 %
Reflection shellResolution: 2.55→2.6 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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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: 2O9J

2o9j


Resolution: 2.55→24.942 Å / Occupancy max: 1 / Occupancy min: 0.75 / SU ML: 0.02 / σ(F): 1.99 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 2773 5.11 %
Rwork0.183 --
obs0.185 54308 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 83.131 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso max: 402.83 Å2 / Biso mean: 99.067 Å2 / Biso min: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.267 Å20 Å2-3.93 Å2
2--1.102 Å2-0 Å2
3---2.165 Å2
Refinement stepCycle: LAST / Resolution: 2.55→24.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 64 195 7930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0297879
X-RAY DIFFRACTIONf_angle_d2.4310700
X-RAY DIFFRACTIONf_dihedral_angle_d21.3722933
X-RAY DIFFRACTIONf_chiral_restr0.1681235
X-RAY DIFFRACTIONf_plane_restr0.0141363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.5940.361220.27192546X-RAY DIFFRACTION100
2.594-2.64110.2711700.232532X-RAY DIFFRACTION100
2.6411-2.69180.25181440.20272561X-RAY DIFFRACTION100
2.6918-2.74670.24911430.18762543X-RAY DIFFRACTION100
2.7467-2.80630.2381590.18672529X-RAY DIFFRACTION100
2.8063-2.87150.2271200.1672584X-RAY DIFFRACTION100
2.8715-2.94320.2371330.16932559X-RAY DIFFRACTION100
2.9432-3.02270.21691580.16342553X-RAY DIFFRACTION100
3.0227-3.11150.21541370.15962543X-RAY DIFFRACTION100
3.1115-3.21170.25051310.17142573X-RAY DIFFRACTION100
3.2117-3.32620.21921160.18022625X-RAY DIFFRACTION100
3.3262-3.45910.25681290.18562561X-RAY DIFFRACTION100
3.4591-3.61610.29631200.1882614X-RAY DIFFRACTION100
3.6161-3.80610.22541500.17762549X-RAY DIFFRACTION100
3.8061-4.04360.19671290.16522575X-RAY DIFFRACTION100
4.0436-4.35430.20651460.15412607X-RAY DIFFRACTION100
4.3543-4.78970.19741600.14922555X-RAY DIFFRACTION100
4.7897-5.47640.20261260.1662635X-RAY DIFFRACTION100
5.4764-6.87560.26381290.19252635X-RAY DIFFRACTION100
6.8756-24.94330.20161510.16622656X-RAY DIFFRACTION99
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)
11.1493-0.30210.02860.1107-0.0908-1.83860.05081.20.0784-0.6434-0.0256-0.09210.15510.24930.01151.1318-0.12360.01181.45960.09330.296833.558310.296512.0252
21.00510.50950.3863-0.21982.2538-0.238-0.38241.00640.2531-0.712-0.01490.264-0.9129-0.44630.26451.3832-0.1395-0.31631.80190.42710.363119.581523.8221.0226
32.6365-1.1242-0.0422.0152-0.05721.1318-0.1650.2032-0.20880.45770.1548-0.88720.2330.11570.01860.3297-0.0013-0.0490.1028-0.07070.584155.0215-1.403955.2733
40.53880.40450.43660.76890.29842.3204-0.1695-0.10130.066-0.02850.1027-0.0274-0.1413-0.3640.04310.1120.09640.04360.21340.00410.33541.98324.099264.0257
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 RESID 1000:1001)A45 - 122
2X-RAY DIFFRACTION1CHAIN A AND (RESID 45:122 OR RESID 238:359 OR RESID 1000:1001)A238 - 359
3X-RAY DIFFRACTION1CHAIN A AND (RESID 45:122 OR RESID 238:359 OR RESID 1000:1001)A1000 - 1001
4X-RAY DIFFRACTION2CHAIN A AND (RESID 742:994 OR RESID 995:997)A742 - 994
5X-RAY DIFFRACTION2CHAIN A AND (RESID 742:994 OR RESID 995:997)A995 - 997
6X-RAY DIFFRACTION3CHAIN A AND (RESID 1:44 OR RESID 123:237)A1 - 44
7X-RAY DIFFRACTION3CHAIN A AND (RESID 1:44 OR RESID 123:237)A123 - 237
8X-RAY DIFFRACTION4CHAIN A AND (RESID 360:741 OR RESID 1002)A360 - 741
9X-RAY DIFFRACTION4CHAIN A AND (RESID 360:741 OR RESID 1002)A1002

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