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- PDB-3fgo: Crystal Structure of the E2 magnesium fluoride complex of the (SR... -

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Basic information

Entry
Database: PDB / ID: 3fgo
TitleCrystal Structure of the E2 magnesium fluoride complex of the (SR) Ca2+-ATPase with bound CPA and AMPPCP
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / Calcium pump / SERCA / nonhydrolyzable ATP analog / P-Type-ATPase / phosphorylation / cyclopiazonic acid / CPA / Alternative splicing / ATP-binding / Calcium / Calcium transport / Endoplasmic reticulum / Ion transport / Magnesium / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Sarcoplasmic reticulum / Transmembrane / Transport
Function / homology
Function and homology information


positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / 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 / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ACETATE ION / Chem-CZA / : / TETRAFLUOROMAGNESATE(2-) / : / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLaursen, M. / Bublitz, M. / Moncoq, K. / Olesen, C. / Moller, J.V. / Young, H.S. / Nissen, P. / Morth, J.P.
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. / Moeller, J.V. / Young, H.S. / Nissen, P. / Morth, J.P.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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
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_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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)221,61719
Polymers219,2052
Non-polymers2,41217
Water8,377465
1
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,83610
Polymers109,6031
Non-polymers1,2339
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)110,7819
Polymers109,6031
Non-polymers1,1788
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.427, 108.872, 274.308
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 / 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.: 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 , 8 types, 482 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.: 2 / Source method: obtained synthetically / Formula: F4Mg
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#7: 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
#8: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
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: 3.42 Å3/Da / Density % sol: 64.08 %
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 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2008 / Details: dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: 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: 97.5 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 51.97 Å2 / Rsym value: 0.061 / Net I/σ(I): 13.78
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.23 / Num. unique all: 5951 / Rsym value: 0.58 / % possible all: 98.6

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Processing

Software
NameVersionClassification
remdaq.pilatusdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2O9J

2o9j


Resolution: 2.5→24.934 Å / Occupancy max: 1 / Occupancy min: 0.75 / SU ML: 0.32 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 19.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3072 2.98 %RANDOM
Rwork0.174 100030 --
obs0.176 103102 97.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.157 Å2 / ksol: 0.293 e/Å3
Displacement parametersBiso max: 469.8 Å2 / Biso mean: 86.818 Å2 / Biso min: 13.99 Å2
Baniso -1Baniso -2Baniso -3
1--6.089 Å20 Å20 Å2
2--4.523 Å20 Å2
3---1.566 Å2
Refine analyzeLuzzati coordinate error obs: 0.3127 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15340 0 145 465 15950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115768
X-RAY DIFFRACTIONf_angle_d1.26821408
X-RAY DIFFRACTIONf_dihedral_angle_d17.3715864
X-RAY DIFFRACTIONf_chiral_restr0.0822470
X-RAY DIFFRACTIONf_plane_restr0.0062724
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.5390.31611430.2502455999
2.539-2.58060.26041110.2287456599
2.5806-2.62510.26991540.2209449398
2.6251-2.67270.26851310.2148458699
2.6727-2.72410.25931400.203453099
2.7241-2.77960.22091400.18674597100
2.7796-2.840.23241450.1837456699
2.84-2.9060.23511360.1803452898
2.906-2.97850.20161450.167458299
2.9785-3.05890.21511410.1689455199
3.0589-3.14870.21331420.1742456999
3.1487-3.25020.24291440.1774460099
3.2502-3.36610.23821390.1801457699
3.3661-3.50050.22641390.1731459298
3.5005-3.65930.21151410.1727451598
3.6593-3.85160.19611390.1623452297
3.8516-4.09190.18041370.1484455497
4.0919-4.40630.17511420.1401455597
4.4063-4.84680.18821340.136452096
4.8468-5.54140.18551470.161450495
5.5414-6.95640.23591400.18448594
6.9564-24.93540.19531420.1511448190
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)
1-0.1964-0.2842-0.24520.10430.13980.72580.27750.2923-0.0108-0.5783-0.2697-0.16140.1388-0.5051-0.01560.88280.1815-0.00850.74320.07940.126938.701557.074113.3112
21.08740.0575-0.0890.72170.5682-1.02240.07320.57840.2214-1.093-0.1488-0.1939-0.7416-0.26590.01861.91150.28520.06140.86790.25590.321946.481774.0731.0796
31.2238-0.2358-0.11741.8006-0.70330.98140.0369-0.0167-0.3067-0.0693-0.10720.22450.09140.01190.0640.2086-0.02920.00170.20840.00140.341738.369635.046557.9918
41.5011-0.34090.83520.6778-0.12551.3094-0.0434-0.07260.0737-0.00660.0578-0.0403-0.0577-0.0240.00050.1827-0.02010.02180.1151-0.00010.248661.133253.843362.7924
50.13880.0777-0.4318-0.54940.7921.10340.01020.35140.0579-0.22880.19230.0402-0.5596-0.4495-0.15950.8159-0.00920.03870.7195-0.01530.290910.343915.78249.2394
60.29510.2249-0.51660.2054-0.28350.3714-0.18330.071-0.023-0.3016-0.0978-0.16420.41890.58640.26120.87720.08870.17761.01680.03150.257829.50866.83741.3698
71.4003-0.7125-0.48021.51750.25420.98850.03050.134-0.0836-0.10980.07560.4409-0.044-0.1739-0.09620.19290.0331-0.09590.23110.02840.3499-19.186122.084848.6905
81.52050.1562-0.63281.0021-0.77051.3065-0.0331-0.2126-0.195-0.0456-0.06550.05340.07150.21760.0860.16170.0366-0.0520.2567-0.01460.2474-0.80411.166360.3436
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 1001:1002)A45 - 122
2X-RAY DIFFRACTION1chain A and (resid 45:122 or resid 238:359 or resid 1001:1002)A238 - 359
3X-RAY DIFFRACTION1chain A and (resid 45:122 or resid 238:359 or resid 1001:1002)A1001 - 1002
4X-RAY DIFFRACTION2chain A and (resid 742:994 or resid 1000)A742 - 994
5X-RAY DIFFRACTION2chain A and (resid 742:994 or resid 1000)A1000
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 1003)A360 - 741
9X-RAY DIFFRACTION4chain A and (resid 360:741 or resid 1003)A1003
10X-RAY DIFFRACTION5chain B and (resid 45:122 or resid 238:359 or resid 1001:1002)B45 - 122
11X-RAY DIFFRACTION5chain B and (resid 45:122 or resid 238:359 or resid 1001:1002)B238 - 359
12X-RAY DIFFRACTION5chain B and (resid 45:122 or resid 238:359 or resid 1001:1002)B1001 - 1002
13X-RAY DIFFRACTION6chain B and (resid 742:994 or resid 1000)B742 - 994
14X-RAY DIFFRACTION6chain B and (resid 742:994 or resid 1000)B1000
15X-RAY DIFFRACTION7chain B and (resid 1:44 or resid 123:237)B1 - 44
16X-RAY DIFFRACTION7chain B and (resid 1:44 or resid 123:237)B123 - 237
17X-RAY DIFFRACTION8chain B and (resid 360:741 or resid 1003)B360 - 741
18X-RAY DIFFRACTION8chain B and (resid 360:741 or resid 1003)B1003

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