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- PDB-5a3s: Crystal structure of the (SR) Calcium ATPase E2-vanadate complex ... -

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Basic information

Entry
Database: PDB / ID: 5a3s
TitleCrystal structure of the (SR) Calcium ATPase E2-vanadate complex bound to thapsigargin and TNP-ATP
ComponentsSARCOPLASMIC RETICULUM CALCIUM ATPASE 1 MOLECULE SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
KeywordsHYDROLASE / SARCO(ENDO)PLASMIC RETICULUM CALCIUM ATPASE / BERYLLIUM FLUORIDE / P-TYPE ATPASE / SERCA / TRINITROPHENYL-NUCLEOTIDE ANALOGES / TNP-ATP / CALCIUM TRANSPORT / INHIBITION / TRANSITION STATE
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
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 / HAD superfamily/HAD-like / 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
Chem-128 / : / Chem-TG1 / oxido(dioxo)vanadium / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsClausen, J.D. / Bublitz, M. / Arnou, B. / Olesen, C. / Andersen, J.P. / Moller, J.V. / Nissen, P.
CitationJournal: Structure / Year: 2016
Title: Crystal Structure of the Vanadate-Inhibited Ca(2+)-ATPase.
Authors: Clausen, J.D. / Bublitz, M. / Arnou, B. / Olesen, C. / Andersen, J.P. / Moller, J.V. / Nissen, P.
History
DepositionJun 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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 RETICULUM CALCIUM ATPASE 1 MOLECULE SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
B: SARCOPLASMIC RETICULUM CALCIUM ATPASE 1 MOLECULE SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,43916
Polymers219,2572
Non-polymers3,18214
Water1448
1
A: SARCOPLASMIC RETICULUM CALCIUM ATPASE 1 MOLECULE SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2208
Polymers109,6291
Non-polymers1,5917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SARCOPLASMIC RETICULUM CALCIUM ATPASE 1 MOLECULE SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2208
Polymers109,6291
Non-polymers1,5917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.556, 93.778, 135.692
Angle α, β, γ (deg.)90.00, 107.26, 90.00
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 RETICULUM CALCIUM ATPASE 1 MOLECULE 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 ENDOPLASMIC RETICULUM CLASS 1/2 CA(2+) ATPASE / SARCOPLASMIC RETICULUM


Mass: 109628.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Organ: HIND LEG / Tissue: SKELETAL MUSCLE / References: UniProt: P04191, EC: 3.6.3.8

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Non-polymers , 7 types, 22 molecules

#2: Chemical ChemComp-TG1 / OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER / THAPSIGARGIN


Mass: 650.754 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H50O12 / Comment: inhibitor*YM
#3: Chemical ChemComp-VN4 / oxido(dioxo)vanadium


Mass: 98.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO3
#4: Chemical ChemComp-128 / SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE


Type: RNA linking / Mass: 718.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17N8O19P3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


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

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Details

Sequence detailsTHE SEQUENCE OF THIS ISOFORM DIFFERS FROM THE CANONICAL SEQUENCE BY THE RESIDUES 994-1001 IN WHICH ...THE SEQUENCE OF THIS ISOFORM DIFFERS FROM THE CANONICAL SEQUENCE BY THE RESIDUES 994-1001 IN WHICH DPEDERRK IS REPLACED BY G

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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: 3.78 Å3/Da / Density % sol: 67.4 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 19% (W/V) PEG2000-MME, 11% (V/V) GLYCEROL, 100 MM MGCL2, 3% (V/V) T-BUTANOL. THE CRYSTALLIZATION DROP WAS EQUILIBRATED AT 19 DEG C, AND THE CRYSTAL WAS FLASH FROZEN 9 DAYS AFTER SET-UP., pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.90501
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90501 Å / Relative weight: 1
ReflectionResolution: 3.3→93.8 Å / Num. obs: 47392 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 97.15 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A3Q

5a3q


Resolution: 3.3→78.906 Å / SU ML: 0.41 / σ(F): 1.35 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 783 1.6 %
Rwork0.2105 --
obs0.211 47351 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→78.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15346 0 200 8 15554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615865
X-RAY DIFFRACTIONf_angle_d0.62421506
X-RAY DIFFRACTIONf_dihedral_angle_d11.6549536
X-RAY DIFFRACTIONf_chiral_restr0.0422476
X-RAY DIFFRACTIONf_plane_restr0.0042742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.50680.32451290.27147711X-RAY DIFFRACTION100
3.5068-3.77750.2991170.24257706X-RAY DIFFRACTION100
3.7775-4.15770.25441280.21137719X-RAY DIFFRACTION100
4.1577-4.75920.20441430.1887749X-RAY DIFFRACTION100
4.7592-5.99580.28191240.2167792X-RAY DIFFRACTION100
5.9958-78.92830.21761420.19747891X-RAY DIFFRACTION99
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)
16.1426-0.818-3.87032.57871.67687.45630.5871-0.7951-0.3870.4335-0.13940.09240.4548-0.5606-1.06210.7611-0.0632-0.2331.1058-0.0341.1381.1602-6.7101-1.0286
29.6719-4.19241.46845.37250.1822.9591-0.3136-0.3680.95680.18660.11730.5031-0.1069-1.42090.06190.95110.1426-0.32031.5090.04831.08674.61724.7486-8.3488
36.9179-2.67742.82523.0067-0.65563.3176-0.10731.65710.9683-0.7624-0.3660.7199-0.6374-0.4220.45361.29370.2095-0.42681.60060.18481.32099.52070.7646-23.4688
45.8184-0.3761-0.19224.832-0.50255.2421-0.2677-0.72160.02540.9140.2543-0.08440.3819-0.27420.04190.64590.0890.06370.6497-0.03540.417242.7541-18.940835.0359
52.56644.11112.75126.79444.32482.9813-0.55820.2011-0.8027-2.01280.37581.6788-0.541-2.1934-0.14481.1733-0.0798-0.15081.28010.08290.758126.5785-18.051218.5904
60.9344-1.90922.41884.0875-5.03286.29520.2576-0.36151.8701-0.26131.3906-0.1591-2.2314-0.801-1.29581.33280.48630.2541.1434-0.00511.199228.1183-4.619711.5029
77.2696-0.02571.95514.99691.11246.5387-0.07020.14450.5705-0.5053-0.13310.1182-0.4306-0.09370.1830.5099-0.00360.09140.30140.0630.453844.915-7.39945.9105
87.15410.06922.11034.07370.58525.07290.0027-0.094-0.04010.10280.0633-0.51870.35760.4836-0.00990.65380.10850.13580.41590.02920.671468.6355-32.609613.4836
91.10080.6372-0.04166.03340.54648.9477-0.1002-0.5636-0.5727-0.4047-0.1720.0687-0.2522-0.26850.38690.79860.0142-0.22120.92480.03291.322-6.872220.816920.0363
104.43550.05461.36872.41261.37425.37020.33240.23-1.2246-0.4652-0.3680.43870.0214-0.9745-0.13210.7707-0.1424-0.01441.37040.18991.4768-8.12367.297522.0232
110.91520.54511.16730.15490.6581.26810.5709-1.0479-1.4977-0.2817-0.2170.22870.243-0.7829-0.29541.0506-0.4061-0.15031.89250.60211.9782-13.59183.565936.6605
123.60131.6223-0.33043.1267-1.98964.8912-0.0640.3537-0.1599-0.56460.11690.010.07860.0812-0.0940.67860.0640.11090.3821-0.02570.4748.449734.370823.832
132.08590.5973-1.79496.8182-1.89837.42240.9730.60280.0268-1.79260.39792.89590.0949-1.8354-1.27941.44880.1686-0.33270.98350.26091.435525.776631.722925.8727
147.06746.5598-3.00326.0834-2.7851.287-1.00381.119-0.1657-1.6027-0.19250.60280.5030.31811.18161.9092-0.4074-0.27231.26920.02981.092322.632217.532625.927
156.6797-1.33061.53492.82530.03573.92740.3932-0.3902-1.2916-0.00490.0940.44010.7679-0.5884-0.40970.9716-0.1199-0.13550.58540.1490.938832.311313.142740.1482
167.0513-0.0279-0.03254.7855-0.90315.50880.118-0.68870.49760.079-0.0297-0.0182-0.75160.5462-0.02310.7411-0.0490.09670.7107-0.00510.41655.642631.827359.3248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 48:111)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 248:329 OR RESID 997)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 741:994 OR RESID 1000)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 1:41 OR RESID 123:237)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 42:47 OR RESID 112:122)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 238:247)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 330:358 OR RESID 604:740 OR RESID 995:996)
8X-RAY DIFFRACTION8CHAIN A AND (RESID 359:603)
9X-RAY DIFFRACTION9CHAIN B AND (RESID 48:111)
10X-RAY DIFFRACTION10CHAIN B AND (RESID 248:329 OR RESID 997)
11X-RAY DIFFRACTION11CHAIN B AND (RESID 741:994 OR RESID 1000)
12X-RAY DIFFRACTION12CHAIN B AND (RESID 1:41 OR RESID 123:237)
13X-RAY DIFFRACTION13CHAIN B AND (RESID 42:47 OR RESID 112:122)
14X-RAY DIFFRACTION14CHAIN B AND (RESID 238:247)
15X-RAY DIFFRACTION15CHAIN B AND (RESID 330:358 OR RESID 604:740 OR RESID 995:996)
16X-RAY DIFFRACTION16CHAIN B AND (RESID 359:603)

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