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- PDB-4bew: SERCA bound to phosphate analogue -

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Basic information

Entry
Database: PDB / ID: 4bew
TitleSERCA bound to phosphate analogue
ComponentsSARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
KeywordsHYDROLASE / P-TYPE ATPASE / CALCIUM TRANSPORT / ION TRANSPORT
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 / ACETATE ION / Chem-CZA / : / TRIFLUOROMAGNESATE / : / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDrachmann, N.D. / Mattle, D. / Laursen, M. / Bublitz, M. / Olesen, C. / Moeller, J.V. / Nissen, P. / Morth, J.P.
CitationJournal: To be Published
Title: Serca Bound to Phosphate Analogue
Authors: Mattle, D. / Drachmann, N.D. / Liu, X.Y. / Gourdon, P. / Pedersen, B.P. / Morth, P. / Wang, J. / Nissen, P.
History
DepositionMar 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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

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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
B: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,69519
Polymers219,3212
Non-polymers2,37417
Water8,413467
1
A: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,87510
Polymers109,6611
Non-polymers1,2149
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)110,8209
Polymers109,6611
Non-polymers1,1598
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.430, 108.870, 274.310
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 / SERCA1 / SR CA(2+)-ATPASE 1 / CALCIUM PUMP 1 / CALCIUM-TRANSPORTING ATPASE SARCOPLASMIC RETICULUM ...SERCA1 / SR CA(2+)-ATPASE 1 / CALCIUM PUMP 1 / CALCIUM-TRANSPORTING ATPASE SARCOPLASMIC RETICULUM TYPE / FAST TWITCH SKELETAL MUSCLE ISOFORM / ENDOPLASMIC RETICULUM CLASS 1/2 CA(2+) ATPASE


Mass: 109660.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: FAST TWITCH SKELETAL MUSCLE / References: UniProt: P04191, EC: 3.6.3.8

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Non-polymers , 8 types, 484 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: 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.: 2 / Source method: obtained synthetically / Formula: C20H20N2O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: F3Mg
#8: Chemical
ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 467 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.38 % / Description: NONE
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 14% PEG 6000, 6% 2-METHYL-2,4- PENTANE DIOL, 70MM SODIUM ACETATE, 10MM MANGANESE CHLORIDE, 3MM ZWITTERGENT 3-12 , PH 6.8, 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
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 103185 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 52.03 Å2 / Rmerge(I) obs: 0.58 / Net I/σ(I): 13.89
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.71 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O9J

2o9j


Resolution: 2.5→45.972 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 3075 3 %
Rwork0.1687 --
obs0.1698 103173 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→45.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15340 0 143 467 15950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815768
X-RAY DIFFRACTIONf_angle_d1.16221408
X-RAY DIFFRACTIONf_dihedral_angle_d15.6495908
X-RAY DIFFRACTIONf_chiral_restr0.0772470
X-RAY DIFFRACTIONf_plane_restr0.0052728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5390.30351430.26434556X-RAY DIFFRACTION99
2.539-2.58070.28851110.24194570X-RAY DIFFRACTION99
2.5807-2.62510.28031540.23084494X-RAY DIFFRACTION98
2.6251-2.67290.26621310.21144596X-RAY DIFFRACTION99
2.6729-2.72430.24551420.20114537X-RAY DIFFRACTION99
2.7243-2.77990.20441390.18184604X-RAY DIFFRACTION100
2.7799-2.84030.24181450.17774557X-RAY DIFFRACTION99
2.8403-2.90640.23651360.17664533X-RAY DIFFRACTION98
2.9064-2.97910.1991440.16944595X-RAY DIFFRACTION99
2.9791-3.05960.22491430.17774543X-RAY DIFFRACTION99
3.0596-3.14960.21731400.17274575X-RAY DIFFRACTION99
3.1496-3.25120.21881450.17214608X-RAY DIFFRACTION99
3.2512-3.36740.24571380.17474570X-RAY DIFFRACTION99
3.3674-3.50220.21811390.1724609X-RAY DIFFRACTION98
3.5022-3.66150.21541410.17244525X-RAY DIFFRACTION98
3.6615-3.85450.20211400.16354516X-RAY DIFFRACTION97
3.8545-4.09580.17951380.15194557X-RAY DIFFRACTION97
4.0958-4.41180.17071410.13914552X-RAY DIFFRACTION97
4.4118-4.85540.17671360.13814543X-RAY DIFFRACTION96
4.8554-5.55690.17371440.1614497X-RAY DIFFRACTION95
5.5569-6.99710.22711410.19294492X-RAY DIFFRACTION94
6.9971-45.97950.19721440.15884469X-RAY DIFFRACTION90
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)
12.15460.12230.07443.3986-0.55471.66680.0419-0.0421-0.2936-0.0655-0.13180.29840.1304-0.08140.07770.2648-0.02440.00450.25380.01260.409538.499334.429958.8682
2-0.2625-0.4314-0.60630.1455-0.06531.28050.33640.6473-0.0402-0.9982-0.2684-0.01660.1161-0.6385-0.02441.53570.2051-0.09951.36370.10880.598236.516155.925111.2734
32.12150.45940.38742.89090.06832.95070.0810.22270.4589-0.3187-0.07010.1455-0.3715-0.14290.07860.36390.0203-0.02720.28550.06520.388947.756762.41246.0814
42.3049-0.28940.22991.48220.00192.6171-0.0045-0.2253-0.04070.15220.0957-0.14650.08060.0403-0.06490.23840.0043-0.01610.20720.00150.338569.066548.91170.8974
50.9370.16070.19270.48250.5160.04980.07140.71270.1734-1.3075-0.1136-0.1715-0.8775-0.39770.23852.41260.29730.04581.34080.27090.756446.330174.20060.5963
62.8634-0.9647-0.42962.77390.04171.72230.03990.2529-0.0273-0.20740.09330.4878-0.1297-0.2594-0.09770.2670.0326-0.08440.33790.02740.4555-19.926222.089249.4644
70.1981-0.2854-1.387-0.6281.1192.05540.20480.4890.358-0.39460.21220.0582-0.6486-0.4152-0.24771.1601-0.0380.07351.06410.04020.53739.550517.57456.746
82.5351-0.5453-0.27272.0186-0.38252.5484-0.04210.22360.0795-0.2067-0.0656-0.25140.03310.30070.10440.30080.0205-0.02140.38750.00370.30979.659312.128143.0045
92.90450.0469-0.6511.63-0.43132.2989-0.0849-0.2981-0.3737-0.00240.04310.13310.21510.28820.08770.27120.0499-0.01960.40830.05530.4376-6.5562-5.627168.8925
100.03270.0202-0.8212-0.2042-0.6132.0972-0.18380.05790.0036-0.314-0.0752-0.12150.49720.76650.29791.22280.06220.16931.33040.01950.583729.72426.92120.8996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:43 OR RESID 123:228)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 44:122 OR RESID 229:329)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 330:359 OR RESID 605:745)
4X-RAY DIFFRACTION4CHAIN A AND RESID 360:604
5X-RAY DIFFRACTION5CHAIN A AND RESID 746:994
6X-RAY DIFFRACTION6CHAIN B AND (RESID 1:43 OR RESID 123:228)
7X-RAY DIFFRACTION7CHAIN B AND (RESID 44:122 OR RESID 229:329)
8X-RAY DIFFRACTION8CHAIN B AND (RESID 330:359 OR RESID 605:745)
9X-RAY DIFFRACTION9CHAIN B AND RESID 360:604
10X-RAY DIFFRACTION10CHAIN B AND RESID 746:994

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