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- PDB-5ncq: Structure of the (SR) Ca2+-ATPase bound to a Tetrahydrocarbazole ... -

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Basic information

Entry
Database: PDB / ID: 5ncq
TitleStructure of the (SR) Ca2+-ATPase bound to a Tetrahydrocarbazole and TNP-ATP
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / P-type ATPase / inhibitory complex / Calcium-transporting ATPase
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 / negative regulation of striated muscle contraction / 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 / negative regulation of striated muscle contraction / 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 / 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
Chem-128 / Chem-8T8 / : / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBublitz, M. / Kjellerup, L. / O'Hanlon Cohrt, K. / Gordon, S. / Mortensen, A.L. / Clausen, J.D. / Pallin, D. / Hansen, J.B. / Brown, W.D. / Fuglsang, A. / Winther, A.-M.L.
Funding support United Kingdom, Denmark, Germany, 5items
OrganizationGrant numberCountry
Wellcome Trust100480/Z/12 United Kingdom
Innovation Fund Denmark4019-00019B Denmark
Innovation Fund Denmark012-2011-5 Denmark
Novo Seeds Denmark
Boehringer Ingelheim Venture Fund Germany
CitationJournal: PLoS ONE / Year: 2018
Title: Tetrahydrocarbazoles are a novel class of potent P-type ATPase inhibitors with antifungal activity.
Authors: Bublitz, M. / Kjellerup, L. / Cohrt, K.O. / Gordon, S. / Mortensen, A.L. / Clausen, J.D. / Pallin, T.D. / Hansen, J.B. / Fuglsang, A.T. / Dalby-Brown, W. / Winther, A.L.
History
DepositionMar 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3736
Polymers109,6031
Non-polymers2,7715
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-11 kcal/mol
Surface area45490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.620, 224.630, 57.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / SR Ca(2+)-ATPase 1 / Calcium pump 1 / Calcium-transporting ATPase sarcoplasmic reticulum type / ...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: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: hind leg muscle / References: UniProt: P04191, EC: 3.6.3.8

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Non-polymers , 5 types, 7 molecules

#2: Chemical ChemComp-128 / SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE


Type: RNA linking / Mass: 718.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N8O19P3
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#5: Chemical ChemComp-8T8 / (1~{S})-~{N}-[(4-bromophenyl)methyl]-7-(trifluoromethyloxy)-2,3,4,9-tetrahydro-1~{H}-carbazol-1-amine


Mass: 439.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18BrF3N2O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.67 Å3/Da / Density % sol: 66.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: glycerol, PEG6000, Na acetate pH 7.2, MPD, beta-OG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→56.16 Å / Num. obs: 61971 / % possible obs: 99.4 % / Redundancy: 20 % / Biso Wilson estimate: 72.9 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.099 / Net I/σ(I): 15.1
Reflection shellResolution: 3→3.3 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 15091 / CC1/2: 0.78 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphenix.phaserphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AGV (individual domains)

2agv


Resolution: 3→56.158 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 30.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 3074 4.96 %Random selection
Rwork0.2129 ---
obs0.2156 61945 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→56.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7596 0 158 2 7756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037907
X-RAY DIFFRACTIONf_angle_d0.6310722
X-RAY DIFFRACTIONf_dihedral_angle_d14.9874823
X-RAY DIFFRACTIONf_chiral_restr0.0441235
X-RAY DIFFRACTIONf_plane_restr0.0041346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.04680.43691170.44672266X-RAY DIFFRACTION87
3.0468-3.09680.32391290.33452719X-RAY DIFFRACTION100
3.0968-3.15020.34631530.30342747X-RAY DIFFRACTION100
3.1502-3.20750.35071380.27192675X-RAY DIFFRACTION100
3.2075-3.26920.32691340.26692663X-RAY DIFFRACTION100
3.2692-3.33590.31551470.26872714X-RAY DIFFRACTION100
3.3359-3.40840.31981380.27332676X-RAY DIFFRACTION100
3.4084-3.48770.36291450.26882695X-RAY DIFFRACTION100
3.4877-3.57490.29711440.24392721X-RAY DIFFRACTION100
3.5749-3.67150.31921430.22372657X-RAY DIFFRACTION100
3.6715-3.77950.33121400.22362735X-RAY DIFFRACTION100
3.7795-3.90150.26541380.22132654X-RAY DIFFRACTION100
3.9015-4.04090.26421460.21842725X-RAY DIFFRACTION100
4.0409-4.20260.25051370.19832671X-RAY DIFFRACTION100
4.2026-4.39380.24441400.18592730X-RAY DIFFRACTION100
4.3938-4.62540.26081380.17342687X-RAY DIFFRACTION100
4.6254-4.9150.23061360.16772670X-RAY DIFFRACTION100
4.915-5.29430.27461430.17732710X-RAY DIFFRACTION100
5.2943-5.82650.24721500.1972685X-RAY DIFFRACTION100
5.8265-6.66850.29091400.20862680X-RAY DIFFRACTION100
6.6685-8.39710.26021400.18422718X-RAY DIFFRACTION100
8.3971-56.16730.16391380.17722673X-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)
15.20334.4609-1.86667.5567-3.05176.15130.08-0.06320.28960.4989-0.0705-1.0714-10.2323-0.03050.87480.0888-0.16940.6258-0.01160.780325.993418.069618.7746
21.3641-0.57420.30861.48840.67440.77870.0432-0.32650.01770.9303-0.1792-0.72720.01690.2939-0.04030.66150.08530.07220.44970.04441.14813.688112.844813.629
31.4872-0.0916-0.00225.846-0.41090.813-0.0177-0.1008-0.1072-0.15910.0049-0.14290.13370.1040.03940.46780.04790.0690.4452-0.01410.822714.84066.7805-0.8423
47.12450.58341.80375.96790.7025.0665-0.0914-1.53730.95770.42590.3162-0.74740.0528-0.1682-0.23530.5422-0.015-0.02920.8697-0.30040.882438.090565.133416.9301
56.10197.0515-2.83428.2202-3.25621.32060.52521.0963-0.8578-1.360.16951.24782.5145-2.0939-0.46611.9009-0.4328-0.18841.69620.12191.680229.966638.213622.214
60.74161.88440.48144.88221.22440.31160.5363-0.75291.19130.0496-0.2767-0.0578-0.21391.1341-0.58741.23850.00690.33911.0005-0.18831.428815.143140.612618.7486
74.0067-1.17880.45664.382-2.75412.5919-0.0395-0.1025-0.23250.14160.17160.48170.1173-0.3008-0.1510.5388-0.05140.11560.3709-0.12870.78185.482753.26580.1788
84.71010.9245-0.19234.6369-0.05123.71760.06920.09350.80540.2075-0.01660.2732-0.49720.0619-0.01210.6102-0.08460.10260.38480.00860.94216.39981.752-9.9323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 50:122)
2X-RAY DIFFRACTION2chain A and (resid 248:329)
3X-RAY DIFFRACTION3chain A and (resid 741:994)
4X-RAY DIFFRACTION4chain A and (resid 1:41 or resid 123:237)
5X-RAY DIFFRACTION5chain A and (resid 42:49)
6X-RAY DIFFRACTION6chain A and (resid 238:247)
7X-RAY DIFFRACTION7chain A and (resid 330:358 or resid 604:740)
8X-RAY DIFFRACTION8chain A and (resid 359:603)

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