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- PDB-6hef: Room temperature structure of the (SR)Ca2+-ATPase Ca2-E1-CaAMPPCP form -

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Basic information

Entry
Database: PDB / ID: 6hef
TitleRoom temperature structure of the (SR)Ca2+-ATPase Ca2-E1-CaAMPPCP form
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1a
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
P-type ATPase, subfamily IIA, SERCA-type / 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, subfamily IIA, SERCA-type / 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 superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.538 Å
AuthorsHjorth-Jensen, S. / Sorensen, T.L.M. / Oksanen, E. / Andersen, J.L. / Olesen, C. / Moller, J.V. / Nissen, P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
European Commission722687 Denmark
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Membrane-protein crystals for neutron diffraction.
Authors: Sorensen, T.L.M. / Hjorth-Jensen, S.J. / Oksanen, E. / Andersen, J.L. / Olesen, C. / Moller, J.V. / Nissen, P.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)111,0547
Polymers109,6031
Non-polymers1,4526
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-25 kcal/mol
Surface area44180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.840, 77.770, 152.220
Angle α, β, γ (deg.)90.000, 109.280, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / Sarcoplasmic Reticulum Ca2+-ATPase 1a


Mass: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P04191
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: 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.: 1 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM

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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: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growTemperature: 293.15 K / Method: batch mode / pH: 6.8
Details: PEG 6000, ter-butanol, sodium acetate, potassium chloride, magnesium chloride, glycerol, C12E8, AMPPCP, BME, MOPS pH 6.8, BATCH, temperature 293.15K

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54187 Å
DetectorType: RIGAKU / Detector: CCD / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 3.538→45.039 Å / Num. obs: 22565 / % possible obs: 94.91 % / Redundancy: 5 % / Biso Wilson estimate: 84.71 Å2 / Rmerge(I) obs: 0.3055 / Rpim(I) all: 0.1529 / Rrim(I) all: 0.3433 / Net I/σ(I): 4.63
Reflection shellResolution: 3.538→3.665 Å / Rmerge(I) obs: 1.111 / Rpim(I) all: 0.5416 / Rrim(I) all: 1.241

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2614refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3n8g

3n8g


Resolution: 3.538→45.039 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.23
RfactorNum. reflection% reflection
Rfree0.2566 1080 5.03 %
Rwork0.2227 --
obs0.2243 21491 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 276.62 Å2 / Biso mean: 92.6567 Å2 / Biso min: 30.08 Å2
Refinement stepCycle: final / Resolution: 3.538→45.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 89 0 7760
Biso mean--92.88 --
Num. residues----994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067911
X-RAY DIFFRACTIONf_angle_d0.71610707
X-RAY DIFFRACTIONf_chiral_restr0.0461240
X-RAY DIFFRACTIONf_plane_restr0.0051363
X-RAY DIFFRACTIONf_dihedral_angle_d7.7134817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5384-3.69940.34431040.32131877198171
3.6994-3.89440.28621390.27472446258593
3.8944-4.13820.27711340.25252644277899
4.1382-4.45740.26281450.216726552800100
4.4574-4.90550.22741550.200926532808100
4.9055-5.61420.27841280.223826832811100
5.6142-7.06890.26741380.236327112849100
7.0689-45.04240.21291370.18072742287999
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)
12.0012-0.09781.13220.85780.33741.03860.5273-0.6668-0.60640.40640.16750.24570.8062-0.2673-0.69871.2004-0.1439-0.16110.98450.16020.9912-22.5364-22.656942.1475
21.09130.24281.83610.13441.42882.61350.4779-0.6437-0.5340.26870.0333-0.12480.9337-1.0911-0.52580.782-0.1913-0.10180.64650.18190.7965-25.7533-13.233138.1396
30.6550.33490.82370.03331.38341.09180.5708-0.6881-0.43380.50660.05270.05761.17110.2274-0.70381.2066-0.1202-0.36930.91120.10391.0819-11.1413-18.645232.7075
40.4498-0.58170.27861.7207-0.04042.3182-0.0279-0.81510.02630.31780.2461-0.14230.73820.0488-0.28920.8055-0.06710.02671.2814-0.05270.5091-7.7897-2.396654.8169
53.5812-0.2748-0.38222.5021-1.07854.09090.20790.1102-0.0729-0.26180.06910.4250.1378-0.3053-0.25010.43080.0552-0.06330.3366-0.07690.5617-30.35131.1289-1.1623
62.214-0.33991.25120.4563-0.70384.44010.1262-0.23980.20030.1291-0.1498-0.0764-0.2140.18450.03630.3639-0.07830.10360.346-0.0490.4996-10.89856.142121.2425
71.21390.4028-0.2022.4266-0.16691.57180.2641-1.0530.0910.8588-0.1802-0.3336-1.00750.78340.00261.0652-0.2979-0.06061.6978-0.18350.7387-2.9110.0474.3722
82.66641.32210.58526.3378-1.99913.938-0.3276-1.1021-0.10850.4546-0.0987-0.5224-0.85030.51740.42010.8988-0.00730.02181.2703-0.15730.6456-11.404711.893873.9396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 83 )A1 - 83
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 165 )A84 - 165
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 276 )A166 - 276
4X-RAY DIFFRACTION4chain 'A' and (resid 277 through 361 )A277 - 361
5X-RAY DIFFRACTION5chain 'A' and (resid 362 through 538 )A362 - 538
6X-RAY DIFFRACTION6chain 'A' and (resid 539 through 780 )A539 - 780
7X-RAY DIFFRACTION7chain 'A' and (resid 781 through 930 )A781 - 930
8X-RAY DIFFRACTION8chain 'A' and (resid 931 through 994 )A931 - 994

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