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- PDB-2yfy: SERCA in the HnE2 State Complexed With Debutanoyl Thapsigargin -

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Basic information

Entry
Database: PDB / ID: 2yfy
TitleSERCA in the HnE2 State Complexed With Debutanoyl Thapsigargin
ComponentsSARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
KeywordsMEMBRANE PROTEIN / SERCA / P-TYPE ATPASE / PROSTATE CANCER / HYDROLASE / 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
DEBUTANOYL THAPSIGARGIN / : / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSonntag, Y. / Musgaard, M. / Olesen, C. / Schiott, B. / Moller, J.V. / Nissen, P. / Thogersen, L.
CitationJournal: Nat.Commun. / Year: 2011
Title: Mutual Adaptation of a Membrane Protein and its Lipid Bilayer During Conformational Changes.
Authors: Sonntag, Y. / Musgaard, M. / Olesen, C. / Schiott, B. / Moller, J.V. / Nissen, P. / Thogersen, L.
History
DepositionApr 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)110,2474
Polymers109,6031
Non-polymers6443
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.360, 71.360, 587.910
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 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: 109602.578 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-994 / 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
#2: Chemical ChemComp-9TN / DEBUTANOYL THAPSIGARGIN


Mass: 580.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H44O11
#3: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.4 Å3/Da / Density % sol: 63.9 % / Description: NONE
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM 12% GLYCEROL, 17% PEG 6000, 0.2 M NACL, 6% MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0718414
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718414 Å / Relative weight: 1
ReflectionResolution: 3.1→60 Å / Num. obs: 29230 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Biso Wilson estimate: 92.82 Å2 / Rmerge(I) obs: 0.1
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 2.1 / % 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 / Resolution: 3.1→57.684 Å / SU ML: 0.43 / σ(F): 1.99 / Phase error: 29.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 848 2.9 %
Rwork0.2393 --
obs0.2405 29224 99.96 %
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.804 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso mean: 90.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.3632 Å20 Å20 Å2
2--8.3632 Å20 Å2
3----16.7265 Å2
Refinement stepCycle: LAST / Resolution: 3.1→57.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 43 0 7714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047856
X-RAY DIFFRACTIONf_angle_d0.73710660
X-RAY DIFFRACTIONf_dihedral_angle_d17.9232992
X-RAY DIFFRACTIONf_chiral_restr0.0491243
X-RAY DIFFRACTIONf_plane_restr0.0031359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.29420.40271250.37064556X-RAY DIFFRACTION100
3.2942-3.54850.33131380.32444627X-RAY DIFFRACTION100
3.5485-3.90560.3171270.27514663X-RAY DIFFRACTION100
3.9056-4.47050.2691380.2274694X-RAY DIFFRACTION100
4.4705-5.63170.27811590.21034743X-RAY DIFFRACTION100
5.6317-57.69390.24391610.20915093X-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)
11.3656-0.25010.35661.5053-0.20511.6495-0.04250.08670.24080.20630.1373-0.13670.00370.1453-0.0620.5791-0.0365-0.09870.6287-0.06990.767729.088134.0768129.7675
2-0.3852-0.54980.5897-0.1854-0.05630.81060.0653-0.11410.0303-0.0251-0.2782-0.05590.02350.02040.18380.8493-0.01380.01520.9178-0.03650.61510.043820.795683.3278
30.7554-0.07330.46680.47760.36071.7049-0.12590.3589-0.13890.07470.02060.08710.1255-0.4290.07650.5737-0.034-0.0240.7683-0.13780.6693-3.031924.8722118.4764
42.1182-0.13250.29811.24790.44313.0527-0.0537-0.46240.3713-0.0269-0.0965-0.1055-0.2819-0.170.13990.50190.0395-0.10240.7204-0.13120.6709-2.803445.2632146.3744
5-0.20850.08480.08880.60780.39392.17210.0910.00970.0225-0.2804-0.2166-0.04070.2597-0.49820.11490.81150.0474-0.07811.1549-0.10720.576-10.824921.201373.3385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:43 OR RESID 123:228) OR (CHAIN E AND RESID 1)
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 (CHAIN B AND RESID 1) OR (CHAIN D AND RESID 1)
4X-RAY DIFFRACTION4CHAIN A AND RESID 360:604
5X-RAY DIFFRACTION5CHAIN A AND RESID 746:994

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