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- PDB-4y3u: The structure of phospholamban bound to the calcium pump SERCA1a -

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Basic information

Entry
Database: PDB / ID: 4y3u
TitleThe structure of phospholamban bound to the calcium pump SERCA1a
Components
  • (Cardiac phospholamban) x 2
  • Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsMEMBRANE PROTEIN / Ca-ATPase / SERCA1a
Function / homology
Function and homology information


Ion transport by P-type ATPases / Ion homeostasis / circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of calcium ion transmembrane transporter activity / phospholamban complex / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of the force of heart contraction by cardiac conduction ...Ion transport by P-type ATPases / Ion homeostasis / circadian sleep/wake cycle, sleep / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of calcium ion transmembrane transporter activity / phospholamban complex / negative regulation of calcium ion import into sarcoplasmic reticulum / regulation of relaxation of muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / acrosome assembly / 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 / regulation of calcium ion import / P-type calcium transporter activity / negative regulation of ATP-dependent activity / ATPase inhibitor activity / regulation of cardiac muscle cell contraction / I band / cardiac muscle tissue development / negative regulation of heart rate / muscle cell cellular homeostasis / endoplasmic reticulum-Golgi intermediate compartment / locomotor rhythm / regulation of calcium ion transport / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Notch signaling pathway / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / visual learning / mitochondrial membrane / intracellular calcium ion homeostasis / calcium ion transport / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Phospholamban / Phospholamban / 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 ...Phospholamban / Phospholamban / 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
: / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / Phospholamban
Similarity search - Component
Biological speciesCanis familiaris (dog)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.51 Å
AuthorsHurley, T.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R37-HL049428 United States
CitationJournal: J. Biol. Chem. / Year: 2013
Title: The structural basis for phospholamban inhibition of the calcium pump in sarcoplasmic reticulum.
Authors: Akin, B.L. / Hurley, T.D. / Chen, Z. / Jones, L.R.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / entity_src_nat ...entity_src_gen / entity_src_nat / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag ..._entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn_type.id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
B: Cardiac phospholamban
C: Cardiac phospholamban
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4764
Polymers117,4373
Non-polymers391
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-38 kcal/mol
Surface area46570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.745, 91.825, 316.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / SR Ca(2+)-ATPase 1 / Calcium pump 1 / Calcium-transporting ATPase sarcoplasmic reticulum type / ...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


Mass: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: Muscle / Tissue: skeletal muscle / References: UniProt: P04191, EC: 3.6.3.8
#2: Protein/peptide Cardiac phospholamban / PLB


Mass: 5859.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis familiaris (dog) / Gene: PLN / Plasmid: PVL1393 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61012
#3: Protein/peptide Cardiac phospholamban


Mass: 1975.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This is a second copy of phospholamban bound in this structure, but the side chain electron density is insufficient to assign the correct sequence register
Source: (gene. exp.) Canis familiaris (dog) / Gene: PLN / Production host: Spodoptera frugiperda (fall armyworm)
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.73 Å3/Da / Density % sol: 67.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1 UL OF SERCA1A AT 15 MG/ML IN 2% N- NONYL-BETA-D-MALTOPYRANOSIDE (NONYL MALTOSIDE) (ANATRACE), 20% GLYCEROL, 100 MM MOPS (PH 7.0), 0.12 M SUCROSE, 80 MM KCL, 3 MM MGCL2, AND 2.8 MM EGTA WAS ...Details: 1 UL OF SERCA1A AT 15 MG/ML IN 2% N- NONYL-BETA-D-MALTOPYRANOSIDE (NONYL MALTOSIDE) (ANATRACE), 20% GLYCEROL, 100 MM MOPS (PH 7.0), 0.12 M SUCROSE, 80 MM KCL, 3 MM MGCL2, AND 2.8 MM EGTA WAS MIXED WITH 1 UL OF PHOSPHOLAMBAN AT 2.1 MG/ML IN 20 MM MOPS (PH 7.2), 20% GLYCEROL, AND 0.1 % DECYLMALTOSIDE OR 0.01% DODECYL MALTOSIDE. THIS PROTEIN MIXTURE WAS THEN ADDED TO AN EQUAL VOLUME OF CRYSTALLIZATION LIQUOR; 15 % GLYCEROL, 17% (W/V) PEG-2000, 200MM NAOAC, AND 5 MM BETA-MERCOPTOETHANOL)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 23282 / % possible obs: 99 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 0.2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.46
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.47 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 4KYT

4kyt


Resolution: 3.51→48.79 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.852 / SU B: 56.647 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.592 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27735 1195 5.1 %RANDOM
Rwork0.23478 20836 --
obs0.23697 22031 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 135.931 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å2-0 Å20 Å2
2--1.61 Å2-0 Å2
3----3.15 Å2
Refinement stepCycle: 1 / Resolution: 3.51→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7811 0 1 0 7812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197955
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0211.97310783
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27751009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73424.393321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.114151399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5581548
X-RAY DIFFRACTIONr_chiral_restr0.0680.21272
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215847
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5097.4224060
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.29111.1155061
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6437.7693895
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.47963.03212083
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.51→3.598 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 100 -
Rwork0.285 1581 -
obs--98.65 %
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)
10.3569-0.38440.56310.7871-0.5620.98470.20420.0289-0.1562-0.41260.0299-0.19720.07890.1027-0.23420.77140.0323-0.00470.79840.06020.4719-44.5734-31.6363-123.6795
20.37290.04680.58820.29680.40961.38420.043-0.00540.114-0.0003-0.02260.01050.03420.003-0.02040.5685-0.0466-0.09120.61050.03840.6781-55.5198-18.3549-89.6622
30.8074-0.09380.12360.05-0.23155.12-0.3260.11560.1132-0.0121-0.1124-0.0968-1.1613-0.33780.43841.50850.0642-0.18370.52570.31120.274-59.1911.3371-144.6857
40.5598-1.46110.38073.883-0.99910.2687-0.04460.24360.81260.2597-0.523-2.11490.0270.07370.56760.8026-0.41550.04781.03670.23851.2021-38.9497-7.0594-132.6139
54.3105-3.934-3.26793.59533.269449.16560.3476-0.1747-0.7322-0.2870.17580.6899-0.66920.4392-0.52340.6911-0.20950.2080.65250.06110.4725-35.0001-8.5086-155.272
60.0775-0.0919-0.03550.19480.09630.05050.13110.2261-0.11060.0516-0.33530.37140.0721-0.15380.20420.8312-0.16060.33091.7272-0.36460.8536-27.576-7.1484-147.5218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 330
2X-RAY DIFFRACTION2A331 - 803
3X-RAY DIFFRACTION3A804 - 992
4X-RAY DIFFRACTION4B21 - 41
5X-RAY DIFFRACTION5B42 - 50
6X-RAY DIFFRACTION6C101 - 116

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