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- PDB-3n8g: Structure of the (SR)Ca2+-ATPase Ca2-E1-CaAMPPCP form -

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Basic information

Entry
Database: PDB / ID: 3n8g
TitleStructure of the (SR)Ca2+-ATPase Ca2-E1-CaAMPPCP form
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1 isoform SERCA 1a
KeywordsHYDROLASE / Adenosine Diphosphate / Adenosine Triphosphate / Aluminum Compounds / Calcium-Transporting ATPases / Crystallization / Cytosol / Fluorides / Muscle Fibers / Fast-Twitch / Phosphorylation / Protein Conformation / Sarcoplasmic Reticulum Calcium-Transporting ATPases
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / Calcium-transporting ATPase / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Re-refinement / Resolution: 2.585 Å
AuthorsBublitz, M. / Olesen, C. / Poulsen, H. / Morth, J.P. / Moller, J.V. / Nissen, P.
Citation
Journal: 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.
#1: Journal: Science / Year: 2004
Title: Phosphoryl transfer and calcium ion occlusion in the calcium pump.
Authors: Sorensen, T.L. / Moller, J.V. / Nissen, P.
#2: Journal: J.Mol.Biol. / Year: 2007
Title: Ca2+ versus Mg2+ coordination at the nucleotide-binding site of the sarcoplasmic reticulum Ca2+-ATPase.
Authors: Picard, M. / Jensen, A.M. / Sorensen, T.L. / Champeil, P. / Moller, J.V. / Nissen, P.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Other
Revision 1.3Feb 27, 2013Group: Database references
Revision 1.4Mar 19, 2014Group: Other
Revision 1.5Sep 6, 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_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_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 isoform SERCA 1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2676
Polymers109,6031
Non-polymers6655
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.000, 76.000, 151.000
Angle α, β, γ (deg.)90.00, 108.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 isoform SERCA 1a


Mass: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: B6CAM1, UniProt: P04191*PLUS, EC: 3.6.3.8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 6000, ter-butanol, sodium acetate, potassium chloride, magnesium chloride, glycerol, MOPS, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 929Kk, temperature 292K

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Data collection

Diffraction
IDCrystal-ID
11
21
31
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONBESSY 14.11
SYNCHROTRONESRF ID292
SYNCHROTRONESRF ID293
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJan 13, 2004
ADSC QUANTUM 42CCDFeb 4, 2004
ADSC QUANTUM 43CCDFeb 4, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDRelative weight
11
21
31
ReflectionResolution: 2.6→40 Å / Num. all: 53349 / Num. obs: 53349 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 77 Å2 / Rmerge(I) obs: 0.092
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3518 / Rsym value: 0.75 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.1_357) / Classification: refinement
RefinementMethod to determine structure: Re-refinement
Starting model: PDB ENTRY 1T5S

1t5s


Resolution: 2.585→30.132 Å / SU ML: 0.36 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 1529 2.83 %Random
Rwork0.2022 ---
obs0.2035 54059 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 63.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.4474 Å20 Å22.3325 Å2
2---5.4049 Å20 Å2
3---3.9575 Å2
Refinement stepCycle: LAST / Resolution: 2.585→30.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 35 92 7798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077845
X-RAY DIFFRACTIONf_angle_d1.09310646
X-RAY DIFFRACTIONf_dihedral_angle_d16.0862933
X-RAY DIFFRACTIONf_chiral_restr0.0761235
X-RAY DIFFRACTIONf_plane_restr0.0051359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5846-2.6680.35921370.31124022X-RAY DIFFRACTION84
2.668-2.76330.27711340.26044829X-RAY DIFFRACTION100
2.7633-2.87380.3209870.2364896X-RAY DIFFRACTION100
2.8738-3.00450.29721170.23084842X-RAY DIFFRACTION100
3.0045-3.16270.24181360.22724855X-RAY DIFFRACTION100
3.1627-3.36070.29081570.23354778X-RAY DIFFRACTION100
3.3607-3.61970.28241440.20474876X-RAY DIFFRACTION100
3.6197-3.98330.21511550.18354824X-RAY DIFFRACTION100
3.9833-4.5580.19141550.1644854X-RAY DIFFRACTION100
4.558-5.73610.24141570.17634870X-RAY DIFFRACTION100
5.7361-30.13430.22361500.19024884X-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)
10.2703-0.2486-0.00060.62090.08440.0476-0.0145-0.0772-0.0799-0.19840.27560.04790.550.3655-0.21010.59370.021-0.02351.7096-0.02250.2822-5.7089-9.436964.0738
2-0.04730.01490.00720.1650.12430.196-0.2255-0.48210.06690.0320.1051-0.1591-0.72510.6170.10650.7425-0.2183-0.022.01-0.21850.3474-4.25459.883371.6019
32.7830.10320.46370.5117-0.18562.4810.38-0.2566-0.3095-0.0473-0.27130.1006-0.01-0.156-0.12060.17330.0032-0.04080.1465-0.04570.2311-21.5533-4.477911.6651
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 OR RESID 1003:1004 ) )A742 - 994
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 742:994 OR RESID 1003:1004 ) )A1003 - 1004
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 1:44 OR RESID 123:237 OR RESID 330:741 OR RESID 1001:1001 OR RESID 1006:1006 ) )A1 - 44
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 1:44 OR RESID 123:237 OR RESID 330:741 OR RESID 1001:1001 OR RESID 1006:1006 ) )A123 - 237
7X-RAY DIFFRACTION3( CHAIN A AND ( RESID 1:44 OR RESID 123:237 OR RESID 330:741 OR RESID 1001:1001 OR RESID 1006:1006 ) )A330 - 741
8X-RAY DIFFRACTION3( CHAIN A AND ( RESID 1:44 OR RESID 123:237 OR RESID 330:741 OR RESID 1001:1001 OR RESID 1006:1006 ) )A1001
9X-RAY DIFFRACTION3( CHAIN A AND ( RESID 1:44 OR RESID 123:237 OR RESID 330:741 OR RESID 1001:1001 OR RESID 1006:1006 ) )A1006

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