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- PDB-3b9r: SERCA Ca2+-ATPase E2 aluminium fluoride complex without thapsigargin -

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Basic information

Entry
Database: PDB / ID: 3b9r
TitleSERCA Ca2+-ATPase E2 aluminium fluoride complex without thapsigargin
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / Calcium pump / membrane protein / transition state / aluminium fluoride / dephosphorylation / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / TETRAFLUOROALUMINATE ION / : / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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
B: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,54810
Polymers219,2052
Non-polymers1,3438
Water1448
1
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2745
Polymers109,6031
Non-polymers6724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2745
Polymers109,6031
Non-polymers6724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules

B: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,54810
Polymers219,2052
Non-polymers1,3438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area4410 Å2
ΔGint-27 kcal/mol
Surface area87970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.980, 94.430, 136.180
Angle α, β, γ (deg.)90.000, 107.790, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2 / 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

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Non-polymers , 5 types, 16 molecules

#2: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.69 Å3/Da / Density % sol: 66.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 12% PEG2000, 200mM MgSO4, 6% MPD, 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: ID29 / Wavelength: 1.066 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.066 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 64221 / Num. obs: 63839 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 77.2 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 12.93
Reflection shellResolution: 3→3.1 Å / Redundancy: 4.09 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.94 / Num. unique all: 5951 / Rsym value: 0.749 / % possible all: 99.9

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Processing

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

1xp5


Resolution: 3→19.986 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / Isotropic thermal model: isotropic and TLS / σ(F): 1.35 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1037 1.63 %random
Rwork0.185 62659 --
obs0.186 63696 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.858 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso max: 427.1 Å2 / Biso mean: 116.457 Å2 / Biso min: 15.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.348 Å20 Å2-10.888 Å2
2---2.123 Å20 Å2
3----0.819 Å2
Refinement stepCycle: LAST / Resolution: 3→19.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15342 0 76 8 15426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01215702
X-RAY DIFFRACTIONf_angle_d1.59721304
X-RAY DIFFRACTIONf_chiral_restr0.0942470
X-RAY DIFFRACTIONf_plane_restr0.0072720
X-RAY DIFFRACTIONf_dihedral_angle_d20.2375822
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.1580.321470.2548924907199.96
3.158-3.3550.3351320.2498903903599.89
3.355-3.6120.3061490.2218917906699.29
3.612-3.9730.2741380.1958835897398.8
3.973-4.5420.1851620.1518968913099.99
4.542-5.7010.2071530.1658998915199.89
5.701-19.9860.211560.1699114927099.68
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)
10.53380.45230.30210.6305-0.76261.6847-0.077-0.14770.14490.283-0.0186-0.09380.1325-0.023700.4253-0.03560.0930.4555-0.10560.234742.8058-16.382434.8477
21.5467-0.11350.17151.6519-0.74660.33340.0705-0.0638-0.1959-0.40220.05510.14760.05250.104700.65210.04960.05770.40280.01020.387548.732737.395823.8623
30.29140.77350.3973-1.1628-0.35210.7997-0.2707-0.2090.04650.0946-0.0340.03680.0769-0.2685-0.00160.51220.0875-0.44510.5835-0.27420.83077.74710.3252-2.0634
40.231-0.5755-0.2188-0.26230.72020.3535-0.0789-0.14080.1262-0.1785-0.15940.16570.0694-0.0243-0.00010.433-0.1445-0.36150.4780.35310.9218-2.28118.994222.6513
51.2357-0.04471.03151.9760.14731.26750.0031-0.07510.2075-0.3443-0.10160.1461-0.14320.050800.2378-0.03680.06820.1156-0.01080.200545.1638-5.2255.3674
60.8619-0.12170.24590.4850.22680.6060.1344-0.1518-0.5147-0.26850.20370.04050.3046-0.2434-0.00010.582-0.0767-0.16640.36470.29950.798531.909916.764541.0645
72.1983-0.1148-0.28931.6105-0.25081.76180.0798-0.0376-0.01620.0849-0.0664-0.23540.06180.2455-00.25940.0124-0.00210.21720.01020.254868.7672-29.982113.4916
81.93640.40730.21711.0364-0.75273.11370.0478-0.34750.0811-0.02820.02820.2324-0.29520.3557-00.3490.02650.12490.56520.06460.312855.449935.170559.3529
90.2974-1.0542-0.3062-0.0278-0.65590.5961-0.07780.32370.0315-0.1385-0.13820.0075-0.2549-0.0322-0.00240.44250.2594-0.4750.5534-0.13510.74689.23463.6163-24.6443
10-0.0291-0.7462-0.13330.34610.8707-0.15940.2205-0.4227-0.67460.1315-0.28740.22150.1935-0.1436-00.5985-0.3767-0.28261.13670.61791.5485-14.82097.652338.1817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 1-43 or resid 123-235)A1 - 43
2X-RAY DIFFRACTION1chain A and (resid 1-43 or resid 123-235)A123 - 235
3X-RAY DIFFRACTION2chain B and (resid 1-43 or resid 123-235)B1 - 43
4X-RAY DIFFRACTION2chain B and (resid 1-43 or resid 123-235)B123 - 235
5X-RAY DIFFRACTION3chain A and (resid 44-122 or resid 236-329)A44 - 122
6X-RAY DIFFRACTION3chain A and (resid 44-122 or resid 236-329)A236 - 329
7X-RAY DIFFRACTION4chain B and (resid 44-122 or resid 236-329)B44 - 122
8X-RAY DIFFRACTION4chain B and (resid 44-122 or resid 236-329)B236 - 329
9X-RAY DIFFRACTION5chain A and (resid 330-359 or resid 605-745) or (chain A and resid 995-997) or (chain A and resid 999-1002)A330 - 359
10X-RAY DIFFRACTION5chain A and (resid 330-359 or resid 605-745) or (chain A and resid 995-997) or (chain A and resid 999-1002)A605 - 745
11X-RAY DIFFRACTION6chain B and (resid 330-359 or resid 605-745) or (chain B and resid 995-997) or (chain B and resid 999-1002)B330 - 359
12X-RAY DIFFRACTION6chain B and (resid 330-359 or resid 605-745) or (chain B and resid 995-997) or (chain B and resid 999-1002)B605 - 745
13X-RAY DIFFRACTION7chain A and (resid 360-604) or (chain A and resid 998)A0
14X-RAY DIFFRACTION8chain B and (resid 360-604) or (chain B and resid 998)B0
15X-RAY DIFFRACTION9chain A and resid 746-994A746 - 994
16X-RAY DIFFRACTION10chain B and resid 746-994B746 - 994

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