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- PDB-5a3q: Crystal structure of the (SR) Calcium ATPase E2-vanadate complex ... -

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Basic information

Entry
Database: PDB / ID: 5a3q
TitleCrystal structure of the (SR) Calcium ATPase E2-vanadate complex bound to thapsigargin and TNP-AMPPCP
ComponentsSARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
KeywordsHYDROLASE / SARCO(ENDO)PLASMIC RETICULUM CALCIUM ATPASE / VANADATE / P-TYPE ATPASE / SERCA / TRINITROPHENYL-NUCLEOTIDE ANALOGES / 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-DL5 / : / 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: 3.05 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. / Clausen, J.D. / Bublitz, M. / Arnou, B. / Olesen, C. / Andersen, J.P. / Moller, J.V. / Nissen, P.
History
DepositionJun 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 15, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 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 1.5Jan 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.pdbx_dist_value / _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_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

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Assembly

Deposited unit
A: SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2188
Polymers109,6291
Non-polymers1,5897
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.427, 118.781, 141.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 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 SKELETAL MUSCLE ISOFORM / ENDOPLASMIC RETICULUM CLASS 1/2 CA(2+) ATPASE / SARCOPLASMIC RETICULUM CALCIUM ATPASE 1


Mass: 109628.617 Da / Num. of mol.: 1 / 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, 15 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.: 1 / Source method: obtained synthetically / Formula: C34H50O12 / Comment: inhibitor*YM
#3: Chemical ChemComp-VN4 / oxido(dioxo)vanadium


Mass: 98.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO3
#4: Chemical ChemComp-DL5 / Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate / TNP-AMPPCP


Mass: 716.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N8O18P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / 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: 3.3 Å3/Da / Density % sol: 62.8 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 19.5% (W/V) PEG2000-MME, 11% (V/V) GLYCEROL, 100 MM MGCL2, 3% (V/V) T-BUTANOL. THE CRYSTALLIZATION DROP WAS EQUILIBRATED AT 19 DEGREES C, AND THE CRYSTAL WAS FLASH FROZEN 13 DAYS AFTER SET-UP., pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.05→141.8 Å / Num. obs: 28547 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 82.73 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13
Reflection shellResolution: 3.05→3.24 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XP5

1xp5


Resolution: 3.05→73.803 Å / SU ML: 0.38 / σ(F): 1.36 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 1448 5.1 %
Rwork0.1998 --
obs0.2027 28497 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→73.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7667 0 100 8 7775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117934
X-RAY DIFFRACTIONf_angle_d0.79710755
X-RAY DIFFRACTIONf_dihedral_angle_d12.9914771
X-RAY DIFFRACTIONf_chiral_restr0.0471238
X-RAY DIFFRACTIONf_plane_restr0.0051371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0501-3.15910.31221490.26882636X-RAY DIFFRACTION100
3.1591-3.28560.37251460.26732675X-RAY DIFFRACTION100
3.2856-3.43510.3141540.23472635X-RAY DIFFRACTION100
3.4351-3.61620.28891450.21352698X-RAY DIFFRACTION100
3.6162-3.84280.26151550.18582652X-RAY DIFFRACTION100
3.8428-4.13950.2321450.18012682X-RAY DIFFRACTION100
4.1395-4.5560.2051330.15612716X-RAY DIFFRACTION100
4.556-5.21510.21851470.16062703X-RAY DIFFRACTION100
5.2151-6.56990.26981490.22022746X-RAY DIFFRACTION100
6.5699-73.8250.26151250.21342906X-RAY DIFFRACTION100
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)
18.78251.47534.4354.12670.93652.9231-0.2282-0.9738-0.409-0.4712-0.19510.50570.33060.9890.37511.98150.49620.55351.45020.33691.165420.153718.6877-69.6251
22.18090.33620.72751.63472.69474.16770.24870.4501-0.2335-1.0631-0.13530.1311-0.4149-0.5489-0.02911.95520.0245-0.03091.22630.30690.90317.68525.4369-69.7228
31.1590.0831.94660.4112-0.91994.77650.03640.80050.2435-1.3133-0.1097-0.0524-1.3616-0.25910.13212.56940.42620.17841.38920.32770.980710.05341.5484-67.985
43.2244-1.062-0.13936.41010.44664.29890.00680.0548-0.09470.03840.1306-0.26170.4459-0.0614-0.11290.32690.02250.00970.40520.00940.558123.1079-7.1323-19.6682
53.72641.34280.23898.4111-3.30511.58760.3642.64520.5954-2.5650.0151-1.1116-0.54321.62030.01461.12830.1460.28991.05380.10330.820826.6276.0448-38.2842
67.8576-8.67873.63899.6241-4.05671.7060.7010.94680.0039-1.1082-1.38650.27710.1064-0.28780.72161.08430.0065-0.03940.91910.14820.946313.539912.3199-41.6719
73.32390.8277-0.48576.4114-0.65077.271-0.07770.29260.431-0.51380.14840.0241-0.5124-0.3602-0.07960.33560.07220.030.3990.07230.498111.744521.3079-26.2971
82.8858-0.0595-0.67323.3049-1.37676.628-0.0092-0.24040.26420.5529-0.0687-0.2917-0.33030.54960.04160.46160.0326-0.14790.488-0.08390.695529.690419.3484.4954
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)

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