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Basic information

Entry
Database: PDB / ID: 4kyt
TitleThe structure of superinhibitory phospholamban bound to the calcium pump SERCA1a
Components
  • Cardiac phospholamban
  • SERCA1a
KeywordsMEMBRANE PROTEIN / transmembrane helices / Calcium pump / P-type ATPase / membrane
Function / homology
Function and homology information


Ion transport by P-type ATPases / Ion homeostasis / negative regulation of calcium ion import into sarcoplasmic reticulum / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of relaxation of muscle / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / negative regulation of calcium ion transmembrane transporter activity / acrosome assembly ...Ion transport by P-type ATPases / Ion homeostasis / negative regulation of calcium ion import into sarcoplasmic reticulum / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of relaxation of muscle / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / negative regulation of calcium ion transmembrane transporter activity / acrosome assembly / 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 / regulation of calcium ion import / P-type Ca2+ transporter / P-type calcium transporter activity / ATPase inhibitor activity / negative regulation of ATP-dependent activity / cardiac muscle tissue development / regulation of cardiac muscle cell contraction / I band / negative regulation of heart rate / muscle cell cellular homeostasis / regulation of calcium ion transport / endoplasmic reticulum-Golgi intermediate compartment / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Notch signaling pathway / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / 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 / metal ion binding
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 / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / haloacid dehalogenase-like hydrolase ...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 / 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
alpha-maltose / : / Calcium-transporting ATPase / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / Cardiac phospholamban
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.833 Å
AuthorsHurley, T.D. / Akin, B.L. / Jones, L.R.
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
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 13, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERCA1a
B: Cardiac phospholamban
C: Cardiac phospholamban
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2216
Polymers121,4973
Non-polymers7243
Water00
1
A: SERCA1a
B: Cardiac phospholamban
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2745
Polymers115,5502
Non-polymers7243
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-32 kcal/mol
Surface area47110 Å2
MethodPISA
2
C: Cardiac phospholamban


Theoretical massNumber of molelcules
Total (without water)5,9471
Polymers5,9471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-46 kcal/mol
Surface area47910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.591, 93.094, 316.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is one monomer of SERCA1a bound to one monomer of phospholamban. The second monomer of phospholamban present in this complex appears to be a crystallization artifact.

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Components

#1: Protein SERCA1a


Mass: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: skeletal muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B6CAM1, UniProt: P04191*PLUS
#2: Protein Cardiac phospholamban / PLB


Mass: 5947.329 Da / Num. of mol.: 2 / Mutation: N27A, N30C, L37A, V49G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: PLN / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61012
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-K / POTASSIUM ION


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

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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: 3.73 Å3/Da / Density % sol: 67.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
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 % decyl maltoside 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), VAPOR DIFFUSION, HANGING DROP, temperature 277K
PH range: 7.0 - 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.833→50 Å / Num. all: 44230 / Num. obs: 42992 / % possible obs: 97.2 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 0.2 / Redundancy: 5.5 % / Biso Wilson estimate: 88.5 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.4
Reflection shellResolution: 2.833→2.89 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2106 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c8l

2c8l


Resolution: 2.833→50 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.875 / SU B: 27.224 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0.2 / ESU R: 0.649 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28388 2167 5 %RANDOM
Rwork0.23908 ---
all0.242 42925 --
obs0.24139 40758 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.343 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2--2.36 Å20 Å2
3----3.79 Å2
Refinement stepCycle: LAST / Resolution: 2.833→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7861 0 47 0 7908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228047
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.98110911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67851012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32424.303323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.303151415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0061549
X-RAY DIFFRACTIONr_chiral_restr0.0810.21298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215874
X-RAY DIFFRACTIONr_mcbond_it0.4091.55070
X-RAY DIFFRACTIONr_mcangle_it0.828204
X-RAY DIFFRACTIONr_scbond_it1.17232977
X-RAY DIFFRACTIONr_scangle_it2.0134.52707
LS refinement shellResolution: 2.833→2.907 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 147 -
Rwork0.29 2733 -
obs--89 %
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)
11.577-0.60941.10241.63060.02311.42050.14670.61850.178-0.8869-0.1569-0.3497-0.16980.20730.01020.55280.01790.08440.6310.11340.313-32.3836-39.8949-116.3156
20.4088-0.39760.4991.5074-0.98552.52760.07440.2392-0.0303-0.51410.06710.053-0.0843-0.2684-0.14150.3131-0.0002-0.04690.48260.02950.304-41.8557-34.8663-117.282
31.0532-0.17170.83770.7898-0.94081.95750.13690.3121-0.0628-0.74770.13280.08990.4176-0.0731-0.26971.30980.0318-0.12470.8790.15440.3458-59.0515-21.1597-143.2518
41.49840.10120.9450.88530.85052.276-0.0059-0.1538-0.02790.00440.0095-0.00040.0967-0.0632-0.00370.1674-0.0253-0.01360.230.04640.3666-54.8629-19.4685-83.7172
51.59-0.1244-0.44421.1825-1.42525.31010.02360.60560.4658-0.6108-0.08320.0977-0.5444-0.29690.05971.1780.0368-0.15610.59180.36320.3335-59.098-0.3639-145.229
651.8179-3.952252.72890.3185-4.010453.6705-1.13330.99521.08070.2260.0516-0.137-1.17571.16121.08172.0285-0.05130.01731.8893-0.07790.8979-39.0992-5.211-122.2769
70.7916-0.6767-1.38081.85264.740813.4034-0.1046-0.31240.3082-0.57080.2243-0.3206-1.44371.4179-0.11981.4464-0.090.20131.19840.29110.6391-37.3992-8.0593-144.3912
80.05020.1477-0.058525.8915-12.56836.10530.13410.23590.15840.00240.54071.7678-0.0125-0.1428-0.67470.6379-0.05770.36461.18660.4431.6589-27.995-10.073-142.794
916.1002-6.2523-14.37322.43195.585412.8388-0.7813-1.6951-0.20770.21740.61560.08740.58721.58040.16571.0573-0.119-0.1381.06940.22611.0947-26.567-6.459-150.765
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 61
2X-RAY DIFFRACTION2A62 - 232
3X-RAY DIFFRACTION3A233 - 324
4X-RAY DIFFRACTION4A325 - 758
5X-RAY DIFFRACTION5A759 - 992
6X-RAY DIFFRACTION6B21 - 28
7X-RAY DIFFRACTION7B29 - 49
8X-RAY DIFFRACTION8C30 - 36
9X-RAY DIFFRACTION9C37 - 40

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