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- PDB-1t5t: Structure of the (SR)Ca2+-ATPase Ca2-E1-ADP:AlF4- form -

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Basic information

Entry
Database: PDB / ID: 1t5t
TitleStructure of the (SR)Ca2+-ATPase Ca2-E1-ADP:AlF4- form
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1 isoform SERCA1A
KeywordsHYDROLASE / Calcium pump / membrane protein / transition state / catalytic mechanism / phosphorylation / occlusion
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 / TETRAFLUOROALUMINATE ION / : / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSorensen, T.L.-M. / Moller, J.V. / Nissen, P.
CitationJournal: Science / Year: 2004
Title: Phosphoryl transfer and calcium ion occlusion in the calcium pump.
Authors: Sorensen, T.L. / Moller, J.V. / Nissen, P.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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_atom_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE RESIDUE 994 IS G BECAUSE AS STATED IN SWS: DPEDERRK -> G in isoform SERCA1A.

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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 isoform SERCA1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,3018
Polymers109,6031
Non-polymers6987
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.477, 75.617, 151.651
Angle α, β, γ (deg.)90.00, 108.82, 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 isoform SERCA1A / Calcium pump 1 / SERCA1 / SR Ca(2+)-ATPase 1 / Calcium-transporting ATPase sarcoplasmic reticulum ...Calcium pump 1 / SERCA1 / SR Ca(2+)-ATPase 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.: 1 / 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, 50 molecules

#2: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 6000, tert-butanol, sodium acetate, potassium chloride, magnesium chloride, glycerol, MOPS, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.110.952
SYNCHROTRONBESSY 14.120.952
SYNCHROTRONEMBL/DESY, HAMBURG X1130.8116
Detector
TypeIDDetectorDate
MARRESEARCH1CCDFeb 24, 2004
MARRESEARCH2CCDFeb 24, 2004
MARRESEARCH3IMAGE PLATEMar 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9521
20.81161
ReflectionResolution: 2.9→50 Å / Num. all: 38895 / Num. obs: 38895 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 23.9
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2554 / Rsym value: 0.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.872 / SU B: 33.012 / SU ML: 0.292 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.774 / ESU R Free: 0.39 / Stereochemistry target values: Engh & Huber
Details: Hydrogens have been added in the riding positions. Identification of a potassium ion binding site was verified by difference Fourier maps using a data set collected on a crystal prepared ...Details: Hydrogens have been added in the riding positions. Identification of a potassium ion binding site was verified by difference Fourier maps using a data set collected on a crystal prepared under conditions with rubidium substituting for potassium. This additional data set is also included in the accompanying structure factor file.
RfactorNum. reflection% reflectionSelection details
Rfree0.29348 1153 3 %RANDOM
Rwork0.24602 ---
all0.24746 38895 --
obs0.24746 37727 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 74.729 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å2-3.83 Å2
2--6.38 Å20 Å2
3----7.51 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 37 43 7751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227845
X-RAY DIFFRACTIONr_bond_other_d0.0010.027322
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.96310645
X-RAY DIFFRACTIONr_angle_other_deg0.878317030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6625993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53724.357319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.904151382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0611548
X-RAY DIFFRACTIONr_chiral_restr0.0850.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021508
X-RAY DIFFRACTIONr_nbd_refined0.2510.22187
X-RAY DIFFRACTIONr_nbd_other0.2030.28027
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.24689
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1560.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6071.54947
X-RAY DIFFRACTIONr_mcbond_other0.0741.52013
X-RAY DIFFRACTIONr_mcangle_it1.13928012
X-RAY DIFFRACTIONr_scbond_it1.35332921
X-RAY DIFFRACTIONr_scangle_it2.3344.52633
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.405 73
Rwork0.335 2763
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)
10.8551-0.08130.24870.6936-0.4811.53390.1417-0.0274-0.4248-0.02070.1403-0.02030.40360.2088-0.282-0.19830.0123-0.00760.2055-0.0326-0.3813-6.5328-9.296564.1621
20.54470.06180.60970.6412-0.15453.1441-0.1114-0.21640.07990.08710.0297-0.0906-0.43520.33020.0817-0.1419-0.1151-0.01910.2883-0.1271-0.5324-5.51089.74271.2839
31.43420.17850.25090.3905-0.15671.6580.2395-0.0932-0.1092-0.0722-0.23070.0559-0.0545-0.1317-0.0088-0.09620.024-0.0121-0.163-0.02590.0216-21.8451-4.503511.6936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA45 - 12245 - 122
2X-RAY DIFFRACTION1AA238 - 329238 - 329
3X-RAY DIFFRACTION2AA742 - 994742 - 994
4X-RAY DIFFRACTION2AC - D1003 - 10041
5X-RAY DIFFRACTION3AA1 - 441 - 44
6X-RAY DIFFRACTION3AA123 - 237123 - 237
7X-RAY DIFFRACTION3AA330 - 741330 - 741
8X-RAY DIFFRACTION3AH - B1001 - 10021
9X-RAY DIFFRACTION3AE - G1005 - 10071

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