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- PDB-2zbd: Crystal Structure of the SR Calcium Pump with Bound Aluminium Flu... -

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Basic information

Entry
Database: PDB / ID: 2zbd
TitleCrystal Structure of the SR Calcium Pump with Bound Aluminium Fluoride, ADP and Calcium
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / MEMBRANE PROTEIN / P-TYPE ATPASE / HAD FOLD / 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 / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / regulation of striated muscle contraction / calcium ion import into sarcoplasmic reticulum / negative 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 / regulation of striated muscle contraction / calcium ion import into sarcoplasmic reticulum / negative 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 / 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 / haloacid dehalogenase-like hydrolase / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / 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 / haloacid dehalogenase-like hydrolase / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / 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 / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / HAD superfamily/HAD-like / 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 / Distorted Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsToyoshima, C. / Nomura, H. / Tsuda, T. / Ogawa, H. / Norimatsu, Y.
Citation
Journal: Nature / Year: 2004
Title: Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues
Authors: Toyoshima, C. / Nomura, H. / Tsuda, T.
#1: Journal: Nature / Year: 2000
Title: Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution
Authors: Toyoshima, C. / Nakasako, M. / Nomura, H. / Ogawa, H.
#2: Journal: Nature / Year: 2002
Title: Structural changes in the calcium pump accompanying the dissociation of calcium
Authors: Toyoshima, C. / Nomura, H.
#3: Journal: Nature / Year: 2004
Title: Crystal structure of the calcium pump with a bound ATP analogue
Authors: Toyoshima, C. / Mizutani, T.
#4: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+)
Authors: Obara, K. / Miyashita, N. / Xu, C. / Toyoshima, I. / Sugita, Y. / Inesi, G. / Toyoshima, C.
#5: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Interdomain communication in calcium pump as revealed in the crystal structures with transmembrane inhibitors
Authors: Takahashi, M. / Kondou, Y. / Toyoshima, C.
History
DepositionOct 20, 2007Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 20, 2007ID: 2Z9R
Revision 1.0Nov 20, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The C-terminal residues in UNP entry P04191 are from 994 to 1001, DPEDERRK. In isoform ...SEQUENCE The C-terminal residues in UNP entry P04191 are from 994 to 1001, DPEDERRK. In isoform SERCA1A, there is only one c-terminal residue 994 GLY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8689
Polymers109,6291
Non-polymers2,2398
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.900, 75.100, 152.100
Angle α, β, γ (deg.)90.00, 109.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 109628.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8

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Non-polymers , 6 types, 106 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.01 Å3/Da / Density % sol: 69.29 %
Crystal growTemperature: 283 K / pH: 6.1 / Details: PEG 400, pH 6.10, MICRODIALYSIS, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2005
RadiationMonochromator: ROTATED-INCLINED DOUBLE- CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 61807 / % possible obs: 90.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 27.7
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 58.5

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Processing

Software
NameVersionClassification
CNSrefinement
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WPE

1wpe
PDB Unreleased entry


Resolution: 2.4→12 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.929 / SU B: 22.182 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27136 3093 5 %RANDOM
Rwork0.24633 ---
obs0.24759 58265 100 %-
all-58529 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 92.569 Å2
Baniso -1Baniso -2Baniso -3
1--4.73 Å20 Å2-5.97 Å2
2--12.1 Å20 Å2
3----11.31 Å2
Refinement stepCycle: LAST / Resolution: 2.4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 147 98 7916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227954
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.011.9910770
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7225993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69624.357319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.348151382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9241548
X-RAY DIFFRACTIONr_chiral_restr0.0650.21245
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025816
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1820.23774
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.25525
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4071.55112
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.60728013
X-RAY DIFFRACTIONr_scbond_it0.60233216
X-RAY DIFFRACTIONr_scangle_it0.9694.52757
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 156 -
Rwork0.376 2663 -
obs--100 %
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)
17.28211.528.83051.24921.534916.49360.59750.613-0.76480.01240.3864-0.10341.8220.5476-0.98390.02410.11120.00080.4233-0.0055-0.247271.021216.10367.2371
24.70460.35135.31661.05691.292311.21570.38190.5868-0.41310.13820.21420.05841.1708-0.5869-0.5961-0.1306-0.06360.01930.72290.1502-0.359957.867921.85036.9987
31.21950.08030.96151.56291.08229.1425-0.19940.5720.0627-0.17410.11940.1065-1.1526-0.7670.0801-0.06670.16550.0230.69390.2485-0.541361.450738.7967-0.5729
45.6627-0.07540.13951.5749-0.2842.75310.47930.6641-0.8461-0.2493-0.3380.34040.59430.2922-0.14130.09020.2261-0.2175-0.2485-0.20910.335883.39753.943552.0783
52.22870.22190.78290.0414-0.21574.73310.23150.48220.07370.151-0.16770.0268-0.3579-0.0254-0.06390.03160.1360.0663-0.28310.02780.028567.624434.545248.1159
63.0833-0.36840.11760.50970.33272.50190.257-0.3002-0.18440.0241-0.2313-0.0568-0.11030.2369-0.0257-0.0221-0.1764-0.0168-0.24490.08650.042183.099427.992373.0619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA45 - 12245 - 122
2X-RAY DIFFRACTION2AA238 - 329238 - 329
3X-RAY DIFFRACTION3AA751 - 994751 - 994
4X-RAY DIFFRACTION3AB - C995 - 996
5X-RAY DIFFRACTION4AA1 - 441 - 44
6X-RAY DIFFRACTION4AA123 - 237123 - 237
7X-RAY DIFFRACTION5AA330 - 364330 - 364
8X-RAY DIFFRACTION5AA601 - 750601 - 750
9X-RAY DIFFRACTION5AE998
10X-RAY DIFFRACTION6AA365 - 600365 - 600
11X-RAY DIFFRACTION6AD997
12X-RAY DIFFRACTION6AF - G1001 - 1002

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