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- PDB-4j2t: Inhibitor-bound Ca2+ ATPase -

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Basic information

Entry
Database: PDB / ID: 4j2t
TitleInhibitor-bound Ca2+ ATPase
ComponentsSERCA1a
KeywordsHYDROLASE/HYDROLASE INHIBITOR / P-type ATPase / calcium transport / Thapsigargin analog / Sarco(endo)plasmic reticulum / HYDROLASE-HYDROLASE INHIBITOR complex
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
Chem-1HT / : / PHOSPHATIDYLETHANOLAMINE / Calcium-transporting ATPase / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPaulsen, E.S. / Villadsen, J. / Tenori, E. / Liu, H. / Lie, M.A. / Bonde, D.F. / Bublitz, M. / Olesen, C. / Autzen, H.E. / Dach, I. ...Paulsen, E.S. / Villadsen, J. / Tenori, E. / Liu, H. / Lie, M.A. / Bonde, D.F. / Bublitz, M. / Olesen, C. / Autzen, H.E. / Dach, I. / Sehgal, P. / Moller, J.V. / Schiott, B. / Nissen, P. / Christensen, S.B.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Water-mediated interactions influence the binding of thapsigargin to sarco/endoplasmic reticulum calcium adenosinetriphosphatase.
Authors: Paulsen, E.S. / Villadsen, J. / Tenori, E. / Liu, H. / Bonde, D.F. / Lie, M.A. / Bublitz, M. / Olesen, C. / Autzen, H.E. / Dach, I. / Sehgal, P. / Nissen, P. / Moller, J.V. / Schiott, B. / Christensen, S.B.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Data collection / Structure summary / Category: audit_author / diffrn_source
Item: _audit_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 20, 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.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

Downloads & links

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Assembly

Deposited unit
A: SERCA1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0974
Polymers109,6031
Non-polymers1,4943
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.900, 70.900, 587.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein SERCA1a


Mass: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: fast twitch skeletal muscle
References: UniProt: B6CAM1, UniProt: P04191*PLUS, EC: 3.6.3.8
#2: Chemical ChemComp-1HT / (3S,3aR,4S,6S,6aR,7S,8S,9bS)-6-(acetyloxy)-3a,4-bis(butanoyloxy)-3-hydroxy-3,6,9-trimethyl-8-{[(2E)-2-methylbut-2-enoyl]oxy}-2-oxo-2,3,3a,4,5,6,6a,7,8,9b-decahydroazuleno[4,5-b]furan-7-yl octanoate


Mass: 720.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H56O13
#3: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM magnesium chloride, 23% w/v PEG6000, 3% tert-butanol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 16, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 31414 / Num. obs: 31414 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.81 % / Rmerge(I) obs: 0.106 / Rsym value: 0.11 / Net I/σ(I): 15.78
Reflection shellResolution: 3→3.5 Å / Redundancy: 7.11 % / Rmerge(I) obs: 0.037 / Rsym value: 0.502 / % possible all: 97.6

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Processing

Software
NameVersionClassification
MAXLABPROGRAMdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NAN

3nan


Resolution: 3.2→28.715 Å / SU ML: 0.43 / σ(F): 1.99 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2859 1668 6.36 %
Rwork0.26 --
obs0.2617 26207 99.67 %
all-26208 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→28.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 76 1 7748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117889
X-RAY DIFFRACTIONf_angle_d1.54310700
X-RAY DIFFRACTIONf_dihedral_angle_d15.4462924
X-RAY DIFFRACTIONf_chiral_restr0.1251254
X-RAY DIFFRACTIONf_plane_restr0.0071358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.2940.34511340.34811971X-RAY DIFFRACTION100
3.294-3.40020.3391360.31862007X-RAY DIFFRACTION100
3.4002-3.52150.31361350.32041976X-RAY DIFFRACTION99
3.5215-3.66230.36411360.31971988X-RAY DIFFRACTION100
3.6623-3.82860.32891350.30091987X-RAY DIFFRACTION100
3.8286-4.02990.31981370.29342033X-RAY DIFFRACTION100
4.0299-4.28160.3081380.2662016X-RAY DIFFRACTION100
4.2816-4.6110.25011390.24082037X-RAY DIFFRACTION100
4.611-5.07270.2411410.23542082X-RAY DIFFRACTION100
5.0727-5.80150.31471400.24382053X-RAY DIFFRACTION100
5.8015-7.28940.2891440.25122128X-RAY DIFFRACTION100
7.2894-28.7160.22021530.2052261X-RAY DIFFRACTION99
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)
10.2892-0.1218-0.040.24140.09740.28090.3444-0.6191-0.3487-0.0016-0.081-0.1429-0.48980.32240.14280.15310.17390.31370.3171-0.40350.7263-33.277929.4307-17.1736
20.0579-0.0641-0.10830.12980.02470.40510.31660.02660.0094-0.2005-0.31750.0850.39830.2479-00.75220.01590.13920.4126-0.0980.5458-23.4172-2.7959-25.5649
30.337-0.54350.09530.321-0.11870.4027-0.38090.04070.19240.2802-0.03970.00480.1122-0.1288-0.31440.9132-0.11140.21790.3301-0.17360.7047-44.3213-2.2628-0.356
40.03810.0793-0.00650.0726-0.04510.0113-0.4815-0.2909-0.2080.18030.418-0.3963-0.078-0.17-01.1852-0.0696-0.12880.828-0.10320.4002-22.381113.8328-72.187
5-0.05250.11370.0924-0.0827-0.01190.0790.08730.1841-0.057-0.1414-0.2030.3978-0.38760.057-0.00921.13050.03850.01780.74750.11680.4758-15.57673.5777-73.2038
60.0289-0.1978-0.28380.25370.23690.2917-0.44540.3174-0.1004-0.00190.10940.20440.76790.1875-0.13611.2376-0.00260.14990.7303-0.16030.4549-19.4767-10.8272-73.4697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:39 or chain A and resid 123:229A1 - 39
2X-RAY DIFFRACTION1chain A and resid 1:39 or chain A and resid 123:229A123 - 229
3X-RAY DIFFRACTION2chain A and resid 346:356 or chain A and resid 603:741A346 - 356
4X-RAY DIFFRACTION2chain A and resid 346:356 or chain A and resid 603:741A603 - 741
5X-RAY DIFFRACTION3chain A and resid 361:601A361 - 601
6X-RAY DIFFRACTION4chain A and resid 50:107A50 - 107
7X-RAY DIFFRACTION5chain A and resid 274:329A274 - 329
8X-RAY DIFFRACTION6chain A and resid 745:994A745 - 994

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