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- PDB-3n5k: Structure Of The (Sr)Ca2+-ATPase E2-AlF4- Form -

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Basic information

Entry
Database: PDB / ID: 3n5k
TitleStructure Of The (Sr)Ca2+-ATPase E2-AlF4- Form
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / SERCA / Adenosine Triphosphate / Calcium-Transporting ATPases / Thapsigargin
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
ACETATE ION / TETRAFLUOROALUMINATE ION / : / Chem-TG1 / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBublitz, M. / Olesen, C. / Poulsen, H. / Morth, J.P. / Moller, J.V. / Nissen, P.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Ion pathways in the sarcoplasmic reticulum Ca2+-ATPase.
Authors: Bublitz, M. / Musgaard, M. / Poulsen, H. / Thogersen, L. / Olesen, C. / Schiott, B. / Morth, J.P. / Moller, J.V. / Nissen, P.
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3Mar 19, 2014Group: Refinement description
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)221,07614
Polymers219,2052
Non-polymers1,87012
Water14,772820
1
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5387
Polymers109,6031
Non-polymers9356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5387
Polymers109,6031
Non-polymers9356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.930, 109.420, 276.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 109602.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P04191, EC: 3.6.3.8

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Non-polymers , 6 types, 832 molecules

#2: Chemical ChemComp-TG1 / OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER / THAPSIGARGIN / Thapsigargin


Mass: 650.754 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H50O12 / Comment: inhibitor*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 820 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES DPEDERRK (994-1001) HAVE BEEN REPLACED BY G IN ISOFORM P04191-2

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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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 13% PEG 6000, 6% 2-methyl-2,4-pentane diol, 70mM sodium acetate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0007 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2009
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 2.2→82 Å / Num. obs: 156560 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
remdaq.pilatusdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FGO

3fgo


Resolution: 2.2→72 Å / SU ML: 0.3 / Isotropic thermal model: anisotropic / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 7823 5 %
Rwork0.184 --
obs0.186 156449 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.33 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 37.54 Å2
Baniso -1Baniso -2Baniso -3
1--3.6891 Å20 Å2-0 Å2
2--8.5793 Å2-0 Å2
3----4.8901 Å2
Refinement stepCycle: LAST / Resolution: 2.2→72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15342 0 122 820 16284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115742
X-RAY DIFFRACTIONf_angle_d1.17921356
X-RAY DIFFRACTIONf_dihedral_angle_d13.4555998
X-RAY DIFFRACTIONf_chiral_restr0.0792474
X-RAY DIFFRACTIONf_plane_restr0.0052720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.26962540.23794889X-RAY DIFFRACTION100
2.225-2.25120.31222650.27324851X-RAY DIFFRACTION99
2.2512-2.27860.23712530.2344903X-RAY DIFFRACTION99
2.2786-2.30750.24282600.21484892X-RAY DIFFRACTION99
2.3075-2.33790.25072600.2144944X-RAY DIFFRACTION100
2.3379-2.36990.24692560.21044912X-RAY DIFFRACTION100
2.3699-2.40370.27262510.20454808X-RAY DIFFRACTION99
2.4037-2.43960.21042590.19814940X-RAY DIFFRACTION100
2.4396-2.47770.23562620.19314912X-RAY DIFFRACTION100
2.4777-2.51840.25992540.19274905X-RAY DIFFRACTION100
2.5184-2.56180.23672580.1824931X-RAY DIFFRACTION100
2.5618-2.60840.22962630.17764939X-RAY DIFFRACTION100
2.6084-2.65860.23792600.17354910X-RAY DIFFRACTION100
2.6586-2.71280.20432620.1794927X-RAY DIFFRACTION100
2.7128-2.77180.19712590.16834951X-RAY DIFFRACTION100
2.7718-2.83630.20382540.16954922X-RAY DIFFRACTION100
2.8363-2.90720.21682640.17844937X-RAY DIFFRACTION100
2.9072-2.98580.21462580.17594925X-RAY DIFFRACTION100
2.9858-3.07370.22872610.17814925X-RAY DIFFRACTION100
3.0737-3.17290.2032600.17835001X-RAY DIFFRACTION100
3.1729-3.28630.22542630.17924948X-RAY DIFFRACTION100
3.2863-3.41790.20692630.18464997X-RAY DIFFRACTION100
3.4179-3.57340.20782590.17744961X-RAY DIFFRACTION100
3.5734-3.76180.20582670.17294996X-RAY DIFFRACTION100
3.7618-3.99750.17842610.16414954X-RAY DIFFRACTION100
3.9975-4.30610.18532630.15665020X-RAY DIFFRACTION100
4.3061-4.73940.20872660.1545036X-RAY DIFFRACTION100
4.7394-5.4250.18972650.16545054X-RAY DIFFRACTION100
5.425-6.8340.20562680.18835103X-RAY DIFFRACTION99
6.834-72.04050.19282750.1795233X-RAY DIFFRACTION98
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)
10.3817-0.4941-0.14420.51120.17940.09520.24290.4516-0.0452-0.6666-0.23070.16480.1973-0.3546-0.00530.89860.0427-0.15020.80.07060.256536.189156.97399.1808
21.33610.0684-0.03061.15550.14390.04240.04970.78890.0996-0.87430.0493-0.0359-0.5544-0.1524-0.0891.10150.11010.03490.72710.2380.180946.599374.54261.1783
30.83940.04080.18670.37250.2190.4045-0.0131-0.007-0.00540.00780.01260.00830.0199-0.01850.00440.2002-0.01250.02190.08140.01640.211154.638349.099260.6381
40.0304-0.0361-0.11410.04560.1880.58880.01680.31810.0118-0.2915-0.04140.0427-0.326-0.29980.04190.74640.03570.05010.64480.00690.242210.889217.4664.7501
50.5602-0.1003-0.27930.67210.25540.2046-0.02540.04580.0125-0.3333-0.0364-0.1280.09830.70290.06230.6067-0.00490.14380.76380.01950.22529.72636.91951.5198
60.983-0.0517-0.33490.6361-0.30960.6773-0.0291-0.0303-0.0749-0.0395-0.02150.08360.00730.05670.04640.12140.0164-0.02020.1072-0.02270.1637-5.43317.123456.2834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 45:122 OR RESID 238:329 ) )A45 - 122
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 45:122 OR RESID 238:329 ) )A238 - 329
3X-RAY DIFFRACTION2( CHAIN A AND RESID 742:994 )A742 - 994
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 1:44 OR RESID 123:237 ) )A1 - 44
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 1:44 OR RESID 123:237 ) )A123 - 237
6X-RAY DIFFRACTION4( CHAIN B AND ( RESID 45:122 OR RESID 238:329 ) )B45 - 122
7X-RAY DIFFRACTION4( CHAIN B AND ( RESID 45:122 OR RESID 238:329 ) )B238 - 329
8X-RAY DIFFRACTION5( CHAIN B AND RESID 742:994 )B742 - 994
9X-RAY DIFFRACTION6( CHAIN B AND ( RESID 1:44 OR RESID 123:237 ) )B1 - 44
10X-RAY DIFFRACTION6( CHAIN B AND ( RESID 1:44 OR RESID 123:237 ) )B123 - 237

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