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- PDB-4uu0: CRYSTAL STRUCTURE OF (SR) CALCIUM-ATPASE E2(TG) IN THE PRESENCE O... -

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Basic information

Entry
Database: PDB / ID: 4uu0
TitleCRYSTAL STRUCTURE OF (SR) CALCIUM-ATPASE E2(TG) IN THE PRESENCE OF 14:1 PC
ComponentsSERCA1A
KeywordsHYDROLASE / CA2+-ATPASE / P-TYPE ATPASE / CATION PUMP / MEMBRANE PROTEIN / LIPID BINDING / LIPID BINDING SITES / DMPC
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 / metal ion binding
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
: / TERTIARY-BUTYL ALCOHOL / Chem-TG1 / Calcium-transporting ATPase / 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. / Olesen, C. / Moeller, J.V. / Guo, Z. / Nissen, P. / Bublitz, M.
CitationJournal: FEBS J. / Year: 2014
Title: Comparing Crystal Structures of Ca(2+) -ATPase in the Presence of Different Lipids.
Authors: Drachmann, N.D. / Olesen, C. / Moller, J.V. / Guo, Z. / Nissen, P. / Bublitz, M.
History
DepositionJul 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_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: SERCA1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6057
Polymers109,6291
Non-polymers9766
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.170, 71.170, 583.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SERCA1A / SARCOPLASMIC ENDOPLASMIC RETICULUM CALCIUM ATPASE


Mass: 109628.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Organ: HIND LEG MUSCLE / Tissue: FAST TWITCH SKELETAL MUSCLE
References: UniProt: B6CAM1, UniProt: P04191*PLUS, EC: 3.6.3.8

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Non-polymers , 7 types, 198 molecules

#2: Chemical ChemComp-TG1 / OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER / THAPSIGARGIN


Mass: 650.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H50O12 / Comment: inhibitor*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 64.42 % / Description: NONE
Crystal growpH: 6.8
Details: 21 % (W/V) PEG2000, 100 MM MGSO4, 3 % (V/V) TERT-BUOH, 10 % (V/V) GLYCEROL, pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.90501
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2011
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90501 Å / Relative weight: 1
ReflectionResolution: 2.5→72.9 Å / Num. obs: 54047 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.2 % / Biso Wilson estimate: 66.73 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.96
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.34 / Mean I/σ(I) obs: 2.02 / % possible all: 100

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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 2C8K

2c8k


Resolution: 2.5→72.904 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 2702 5 %
Rwork0.1935 --
obs0.1964 54035 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→72.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7674 0 64 192 7930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117888
X-RAY DIFFRACTIONf_angle_d1.14310693
X-RAY DIFFRACTIONf_dihedral_angle_d15.5283003
X-RAY DIFFRACTIONf_chiral_restr0.0441237
X-RAY DIFFRACTIONf_plane_restr0.0051358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54550.3661410.29412659X-RAY DIFFRACTION100
2.5455-2.59440.34641370.26952616X-RAY DIFFRACTION100
2.5944-2.64740.3341410.25882687X-RAY DIFFRACTION100
2.6474-2.7050.29031360.2322582X-RAY DIFFRACTION100
2.705-2.76790.29181380.22162629X-RAY DIFFRACTION100
2.7679-2.83710.28081400.21072673X-RAY DIFFRACTION100
2.8371-2.91380.27181380.21732612X-RAY DIFFRACTION100
2.9138-2.99960.28031410.21432682X-RAY DIFFRACTION100
2.9996-3.09640.29051410.21132685X-RAY DIFFRACTION100
3.0964-3.2070.32821380.21612635X-RAY DIFFRACTION100
3.207-3.33540.26751420.20542680X-RAY DIFFRACTION100
3.3354-3.48720.26731400.19952667X-RAY DIFFRACTION100
3.4872-3.67110.2651420.19492699X-RAY DIFFRACTION100
3.6711-3.90110.2341430.18662718X-RAY DIFFRACTION100
3.9011-4.20230.24121450.17432742X-RAY DIFFRACTION100
4.2023-4.62510.19511430.162706X-RAY DIFFRACTION100
4.6251-5.29420.25541460.17032774X-RAY DIFFRACTION100
5.2942-6.66940.30491480.2092827X-RAY DIFFRACTION100
6.6694-72.93470.20431620.18833060X-RAY DIFFRACTION100
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)
14.5738-0.45530.50823.96960.5067.04780.1909-0.2773-0.53380.0037-0.0426-0.36750.5729-0.0593-0.09180.36110.0061-0.08280.39170.11470.6084-1.4816.9001-17.3414
20.9408-0.16892.02240.3303-0.61056.1353-0.04280.4686-0.123-0.71350.06690.08610.15250.2879-0.10031.2664-0.1037-0.07040.7858-0.04140.5837-15.796125.909-63.4153
32.8373-0.12430.07123.30990.68864.8576-0.1733-0.24850.1529-0.3353-0.1020.3811-0.6937-0.29170.27840.71040.0317-0.1810.4470.05990.5338-10.466338.8943-27.0998
42.9173-0.1785-1.14934.9636-0.40685.469-0.07540.0751-0.1880.3387-0.0956-0.5949-0.28220.55180.14630.7375-0.1217-0.26240.4590.06730.66579.702238.817-0.6796
51.8018-0.2230.81950.2533-0.36141.8389-0.44670.88060.193-0.73080.12330.1305-1.09670.04620.24642.042-0.1416-0.21151.13430.19080.7293-15.315946.5495-73.3758
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 OR RESID 1301 OR RESID 1302 OR RESID 1995:1998)
4X-RAY DIFFRACTION4CHAIN A AND RESID 360:604
5X-RAY DIFFRACTION5CHAIN A AND RESID 746:994

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