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- PDB-5a3r: Crystal structure of the (SR) Calcium ATPase E2.BeF3- complex bou... -

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Basic information

Entry
Database: PDB / ID: 5a3r
TitleCrystal structure of the (SR) Calcium ATPase E2.BeF3- complex bound to TNP-AMPPCP
ComponentsSARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
KeywordsHYDROLASE / SARCO(ENDO)PLASMIC / SARCO(ENDO)PLASMIC RETICULUM CALCIUM ATPASE / BERYLLIUM FLUORIDE / P-TYPE ATPASE / SERCA / TRINITROPHENYL-NUCLEOTIDE ANALOGES / TNP-AMPPCP / CALCIUM TRANSPORT / INHIBITION / TRANSITION STATE
Function / homology
Function and homology information


positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / positive regulation of ATPase-coupled calcium transmembrane transporter activity / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / 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 fast-twitch skeletal muscle fiber contraction / H zone / positive regulation of ATPase-coupled calcium transmembrane transporter activity / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / P-type Ca2+ transporter / P-type calcium transporter activity / positive regulation of cardiac muscle cell contraction / 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 / P-type ATPase, cytoplasmic domain N / HAD superfamily/HAD-like / : / P-type ATPase actuator domain / 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 superfamily / Distorted Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Chem-DL5 / : / 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. / 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 1.2May 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 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Apr 15, 2026Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 3.0Sep 2, 2026Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_modification_feature.auth_comp_id / _pdbx_modification_feature.auth_seq_id / _pdbx_modification_feature.category / _pdbx_modification_feature.comp_id_linking_atom / _pdbx_modification_feature.label_asym_id / _pdbx_modification_feature.label_comp_id / _pdbx_modification_feature.label_seq_id / _pdbx_modification_feature.modified_residue_auth_asym_id / _pdbx_modification_feature.modified_residue_auth_comp_id / _pdbx_modification_feature.modified_residue_auth_seq_id / _pdbx_modification_feature.modified_residue_id / _pdbx_modification_feature.modified_residue_id_linking_atom / _pdbx_modification_feature.modified_residue_label_asym_id / _pdbx_modification_feature.modified_residue_label_comp_id / _pdbx_modification_feature.modified_residue_label_seq_id / _pdbx_modification_feature.modified_residue_symmetry / _pdbx_modification_feature.ref_comp_id / _pdbx_modification_feature.ref_pcm_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_site.pdbx_num_residues
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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)110,4967
Polymers109,6031
Non-polymers8936
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.530, 114.967, 227.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / SARCOP SARCOPLASMIC RETICULUM CALCIUM ATPASE 1


Mass: 109602.578 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 , 5 types, 13 molecules

#2: Chemical ChemComp-DL5 / Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate / TNP-AMPPCP


Mass: 715.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N8O18P3
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE OF THIS ISOFORM (2) DIFFERS FROM THE CANONICAL SEQUENCE BY THE RESIDUES 994-1001 IN ...THE SEQUENCE OF THIS ISOFORM (2) 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: 3.42 Å3/Da / Density % sol: 64.1 % / Description: NONE
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 37% (W/V) PEG400, 25 MM MGCL2, AND 50 MM GLYCINE. THE CRYSTALLIZATION DROP WAS EQUILIBRATED AT 12 DEGREES C, AND THE CRYSTAL WAS FLASH FROZEN 6 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: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→80.9 Å / Num. obs: 29733 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 81.26 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.4
Reflection shellResolution: 3.05→3.24 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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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 3B9B

3b9b


Resolution: 3.05→57.484 Å / SU ML: 0.5 / σ(F): 1.36 / Phase error: 29.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 1506 5.1 %
Rwork0.2141 --
obs0.2163 29584 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→57.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7675 0 50 7 7732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067880
X-RAY DIFFRACTIONf_angle_d0.60410683
X-RAY DIFFRACTIONf_dihedral_angle_d11.8044761
X-RAY DIFFRACTIONf_chiral_restr0.0311234
X-RAY DIFFRACTIONf_plane_restr0.0031361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0501-3.14850.39621400.31842474X-RAY DIFFRACTION99
3.1485-3.2610.33881370.29262478X-RAY DIFFRACTION99
3.261-3.39160.35131490.27932524X-RAY DIFFRACTION100
3.3916-3.54590.31751320.26092482X-RAY DIFFRACTION99
3.5459-3.73280.28861330.22922531X-RAY DIFFRACTION100
3.7328-3.96660.24921310.20912545X-RAY DIFFRACTION100
3.9666-4.27280.23481330.19222548X-RAY DIFFRACTION100
4.2728-4.70260.23981320.17692539X-RAY DIFFRACTION100
4.7026-5.38270.24041380.18462590X-RAY DIFFRACTION100
5.3827-6.77990.26161370.23412612X-RAY DIFFRACTION100
6.7799-57.49370.20551440.19512755X-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)
14.21164.20755.95584.38635.7938.7714-0.33140.03440.5216-0.41-0.2177-0.0181.310.33890.51291.33370.15620.03671.4804-0.0970.7255-2.6363-11.9631-51.0263
23.02493.6832.73752.83212.72277.8619-0.3784-0.03460.6223-0.9553-0.01570.51420.70640.17450.13491.44340.0418-0.20741.2837-0.02940.5188-17.141-11.7721-53.2023
30.79510.47012.17310.27721.2645.395-0.37510.1416-0.0149-0.26950.11250.0204-1.14340.52690.20341.3625-0.2406-0.14211.345-0.09510.6245-18.57636.5168-56.9758
46.7507-2.80821.98096.1310.63035.53450.39870.1899-1.44670.27140.16660.03110.46160.2286-0.43960.4239-0.0509-0.10930.7692-0.03850.848512.1367-15.4841.5659
50.9891-0.37861.80743.53661.87168.7810.6213-0.3689-0.65020.3429-0.2344-1.1340.8313-0.2065-0.48610.92870.2522-0.18591.3828-0.13310.717111.0786-6.4419-23.5938
66.7232-1.19975.67188.1893-2.41925.0140.83461.8688-1.3521-0.62841.28480.01141.12372.2117-2.03010.7774-0.0091-0.21051.1221-0.25840.974-6.9258-13.6697-22.7008
71.44230.83760.95344.75181.11035.8497-0.06450.128-0.2702-0.31510.01640.458-0.2916-0.33940.0230.4009-0.0229-0.06281.032-0.09550.4951-10.8694-0.1218-12.4207
84.007-0.3925-0.13583.14460.14834.4320.0003-0.3450.08840.3154-0.054-0.19930.04680.19850.05070.4327-0.02630.00420.82890.00730.357210.17117.831910.7955
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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