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- PDB-3b9b: Structure of the E2 beryllium fluoride complex of the SERCA Ca2+-... -

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Basic information

Entry
Database: PDB / ID: 3b9b
TitleStructure of the E2 beryllium fluoride complex of the SERCA Ca2+-ATPase
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / P-type ATPase / Ca2+-ATPase / membrane protein / beryllium fluoride / Alternative splicing / ATP-binding / Calcium / Calcium transport / Endoplasmic reticulum / Ion transport / Magnesium / Metal-binding / Nucleotide-binding / Phosphorylation / 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 / 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
BERYLLIUM TRIFLUORIDE ION / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsOlesen, C. / Picard, M. / Winther, A.M.L. / Morth, J.P. / Moller, J.V. / Nissen, P.
CitationJournal: Nature / Year: 2007
Title: The structural basis of calcium transport by the calcium pump.
Authors: Olesen, C. / Picard, M. / Winther, A.M.L. / Gyrup, C. / Morth, J.P. / Oxvig, C. / Moller, J.V. / Nissen, P.
History
DepositionNov 4, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7405
Polymers109,6031
Non-polymers1384
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.600, 114.600, 229.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / Calcium pump 1 / SERCA1 / SR Ca2+ / -ATPase 1 / Calcium-transporting ATPase sarcoplasmic reticulum ...Calcium pump 1 / SERCA1 / SR Ca2+ / -ATPase 1 / Calcium-transporting ATPase sarcoplasmic reticulum type / fast twitch skeletal muscle isoform / Endoplasmic reticulum class 1/2 Ca2+ / ATPase


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: P04191, EC: 3.6.3.8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS 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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 18% PEG6000, 50mM MgSO4, 10% glycerol, 4% DMSO, pH 6.8, vapor diffusion, hanging drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2007 / Details: Pt coated Si mirror
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. all: 45166 / Num. obs: 44824 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 42.6 Å2 / Rmerge(I) obs: 0.274 / Rsym value: 0.274 / Net I/σ(I): 9.84
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 12 % / Rmerge(I) obs: 1.246 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2407 / Rsym value: 1.246 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xp5

1xp5


Resolution: 2.65→29.351 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Phase error: 28.24 / Stereochemistry target values: ML / Details: phenix.refine used for refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1345 3.01 %random
Rwork0.214 ---
obs0.216 44754 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 427.6 Å2 / Biso mean: 58.8 Å2 / Biso min: 1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 7 65 7743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077816
X-RAY DIFFRACTIONf_angle_d1.0910597
X-RAY DIFFRACTIONf_chiral_restr0.0741235
X-RAY DIFFRACTIONf_plane_restr0.0051358
X-RAY DIFFRACTIONf_dihedral_angle_d18.6652878
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.7450.361340.3194254438898.76
2.745-2.8550.3711320.2924279441199.77
2.855-2.9840.3081320.2624271440399.03
2.984-3.1410.3321330.2444264439799.19
3.141-3.3380.2961330.2254322445599.29
3.338-3.5950.2871320.2014307443999.11
3.595-3.9560.2451330.1824326445999.49
3.956-4.5270.2071360.1654366450299.49
4.527-5.6970.2331360.1834430456699.65
5.697-29.3530.2541440.2174590473499.02
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)
10.000500.00510.0015-0.0062-0.00910.1601-0.0522-0.1693-0.10930.12350.0502-0.010.010-0.4150.0785-0.1149-0.50710.03940.1565-41.3086-15.6276-116.9365
20.0124-0.00110.00420.0093-0.00620.0153-0.09750.0222-0.22520.08980.0534-0.1208-0.1364-0.02650-0.10050.0457-0.04720.06880.07390.092-17.6394-0.1319-102.2208
30.0684-0.04020.0090.05540.02040.0267-0.01020.0104-0.0082-0.03380.00720.0254-0.03840.012500.0585-0.0118-0.01110.0507-0.01590.0718-38.427518.0262-125.6197
4-0.053-0.0280.02130.00150.0122-0.00060.1056-0.0248-0.05250.1814-0.0310.15120.064-0.0863-00.1370.2012-0.2619-0.05490.4983-0.5364-20.7936-11.8123-68.458
50.0002-0.01320.00640.01830.01590.01130.02040.1383-0.07760.06340.1482-0.0989-0.0203-0.0009-00.67640.14-0.09970.44890.05460.1599-8.77893.3057-60.7618
60.0161-0.00580.0083-0.00360.00180.0074-0.0163-0.0224-0.0805-0.05-0.0211-0.0051-0.0688-0.0369-00.39250.315-0.3838-0.02370.3396-0.4396-9.8648.8344-50.0897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1-43 or resid 123-228A0
2X-RAY DIFFRACTION2chain A and resid 330-359 or resid 605-745A0
3X-RAY DIFFRACTION3chain A and resid 360-604A360 - 604
4X-RAY DIFFRACTION4chain A and resid 44-122 or resid 229-329A0
5X-RAY DIFFRACTION5chain A and resid 746-868A746 - 868
6X-RAY DIFFRACTION6chain A and resid 869-994A869 - 994

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