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- PDB-4h1w: E1 structure of the (SR) Ca2+-ATPase in complex with Sarcolipin -

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Basic information

Entry
Database: PDB / ID: 4h1w
TitleE1 structure of the (SR) Ca2+-ATPase in complex with Sarcolipin
Components
  • SERCA1a
  • Sarcolipin
KeywordsHYDROLASE/HYDROLASE REGULATOR / P-type ATPase / Ca2+ transport / Sarcolipin / Phospholamban / Membrane protein / HYDROLASE-HYDROLASE REGULATOR complex
Function / homology
Function and homology information


positive regulation of protein depolymerization / regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of calcium ion transmembrane transporter activity / regulation of relaxation of muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion import / positive regulation of cardiac muscle cell contraction / negative regulation of protein-containing complex disassembly / positive regulation of calcium ion import into sarcoplasmic reticulum ...positive regulation of protein depolymerization / regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of calcium ion transmembrane transporter activity / regulation of relaxation of muscle / negative regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion import / positive regulation of cardiac muscle cell contraction / negative regulation of protein-containing complex disassembly / 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 / sarcoplasmic reticulum calcium ion transport / negative regulation of catalytic activity / regulation of striated muscle contraction / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / P-type Ca2+ transporter / P-type calcium transporter activity / I band / endoplasmic reticulum-Golgi intermediate compartment / regulation of calcium ion transport / enzyme inhibitor activity / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / calcium ion transport / ATPase binding / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / metal ion binding / membrane
Similarity search - Function
Sarcolipin / Sarcolipin / 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 ...Sarcolipin / Sarcolipin / 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 / Cation transport ATPase (P-type) / E1-E2 ATPase / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / Calcium-transporting ATPase / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / Sarcolipin
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBublitz, M. / Winther, A.-M.L. / Karlsen, J. / Moller, J.V. / Hansen, J.B. / Buch-Pedersen, M.J. / Nissen, P.
CitationJournal: Nature / Year: 2013
Title: The sarcolipin-bound calcium pump stabilizes calcium sites exposed to the cytoplasm.
Authors: Winther, A.M. / Bublitz, M. / Karlsen, J.L. / Moller, J.V. / Hansen, J.B. / Nissen, P. / Buch-Pedersen, M.J.
History
DepositionSep 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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: SERCA1a
B: Sarcolipin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9967
Polymers113,3792
Non-polymers6175
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-56 kcal/mol
Surface area46410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.870, 139.540, 141.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein SERCA1a


Mass: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: B6CAM1, UniProt: P04191*PLUS, Ca2+-transporting ATPase
#2: Protein/peptide Sarcolipin


Mass: 3776.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P42532

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Non-polymers , 4 types, 13 molecules

#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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#6: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.11 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG6000, glycerol, MgSO4, MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97935 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2012
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 31378 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 22.6 % / Biso Wilson estimate: 64.415 Å2 / Rmerge(I) obs: 0.267 / Net I/σ(I): 14.19
Reflection shell

Rmerge(I) obs: 0.019 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
3.1-3.22.21668742791279199.2
3.2-3.32.99586182463246398.9
3.3-3.43.62511712184218499.5
3.4-3.54.73446411944194499.2
3.5-3.65.72384011763176399.2
3.6-3.77.15351351552155299.4
3.7-3.88.18310711403140399.1
3.8-410.24566562412241299.4
4-618.17229476103081030899.5
6-1032.38757163513351399.7
10-2052.961829890490499
20-3064.331943989897
3049.15558434384.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RemDAqdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→43.007 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.802 / SU ML: 0.36 / σ(F): 2 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 1590 5.07 %Random
Rwork0.191 ---
obs0.1938 31374 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 284.93 Å2 / Biso mean: 105.4884 Å2 / Biso min: 41.72 Å2
Refinement stepCycle: LAST / Resolution: 3.1→43.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7869 0 13 8 7890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118038
X-RAY DIFFRACTIONf_angle_d1.26310911
X-RAY DIFFRACTIONf_chiral_restr0.0811272
X-RAY DIFFRACTIONf_plane_restr0.0061385
X-RAY DIFFRACTIONf_dihedral_angle_d14.7162976
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.20010.3181620.27362634279699
3.2001-3.31450.28551400.24072658279899
3.3145-3.44710.28291400.22012662280299
3.4471-3.60390.28871410.1972676281799
3.6039-3.79380.2691400.18772671281199
3.7938-4.03140.24851420.17442690283299
4.0314-4.34230.20881410.16522693283499
4.3423-4.77880.20621440.150127122856100
4.7788-5.46910.23291420.176527232865100
5.4691-6.8860.27221470.218527722919100
6.886-43.01120.22611510.1922893304499
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)
11.819-1.9441-2.03642.05952.18652.2656-0.4543-0.0997-0.2725-1.0094-0.20431.2612-0.4762-0.00520.56661.0162-0.00040.01810.9891-0.14440.812616.535512.1799149.3963
23.4127-1.8878-4.10813.28535.26669.3588-0.2419-0.1202-0.6157-0.1578-0.22090.44890.5105-0.12740.36390.85410.1864-0.00830.56190.16150.700331.334210.9614151.3448
30.5433-0.7672-0.24726.66463.18581.9341-0.2022-0.0931-0.3870.4327-0.08060.23240.81550.07610.32791.15630.02110.25160.73680.05470.905231.47533.0704165.835
44.02920.40280.02574.8247-0.84893.675-0.09170.3328-0.246-0.12470.1018-0.1009-0.01930.1263-0.00450.41290.03120.00221.0815-0.03380.42785.892159.8629162.1748
51.28931.0039-1.18013.84374.03669.70841.34480.6713-0.63920.4104-0.5478-0.33070.41950.8346-0.92181.16380.2697-0.05161.6070.00520.90977.508731.1599153.2242
69.5884-6.57053.84894.5034-2.64841.56490.39640.15870.01840.30070.6966-1.089-0.0332-0.3089-1.19371.75080.27010.31212.3878-0.65291.759121.525138.1809152.9138
72.21171.3457-0.19264.77821.83914.7773-0.1045-0.4291-0.16720.23040.1398-0.28990.12670.308-0.03670.43850.08240.01761.0120.06380.453834.616547.9438181.7917
82.42760.2854-0.48052.9054-0.26712.8323-0.10420.09170.116-0.05820.08240.12080.1508-0.1670.01510.41990.01950.00531.1980.030.412815.796869.2606197.7479
97.84135.00922.02664.5761-1.65188.04950.665-0.3972-1.5944-0.4804-0.2066-0.27720.90350.3489-0.52921.01780.1505-0.08321.0141-0.30471.85518.57094.9976160.0957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 50:122 )A50 - 122
2X-RAY DIFFRACTION2( CHAIN A AND RESID 248:329 )A248 - 329
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 741:994 OR RESID 1106:1107 ) )A741 - 994
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 741:994 OR RESID 1106:1107 ) )A1106 - 1107
5X-RAY DIFFRACTION4( CHAIN A AND ( RESID 1:41 OR RESID 123:237 ) )A1 - 41
6X-RAY DIFFRACTION4( CHAIN A AND ( RESID 1:41 OR RESID 123:237 ) )A123 - 237
7X-RAY DIFFRACTION5( CHAIN A AND RESID 42:49 )A42 - 49
8X-RAY DIFFRACTION6( CHAIN A AND RESID 238:247 )A238 - 247
9X-RAY DIFFRACTION7( CHAIN A AND ( RESID 330:358 OR RESID 604:740 OR RESID 1001:1002 OR RESID 1101:1104 ) )A330 - 358
10X-RAY DIFFRACTION7( CHAIN A AND ( RESID 330:358 OR RESID 604:740 OR RESID 1001:1002 OR RESID 1101:1104 ) )A604 - 740
11X-RAY DIFFRACTION7( CHAIN A AND ( RESID 330:358 OR RESID 604:740 OR RESID 1001:1002 OR RESID 1101:1104 ) )A1001 - 1002
12X-RAY DIFFRACTION7( CHAIN A AND ( RESID 330:358 OR RESID 604:740 OR RESID 1001:1002 OR RESID 1101:1104 ) )A1101 - 1104
13X-RAY DIFFRACTION8( CHAIN A AND RESID 359:603 )A359 - 603
14X-RAY DIFFRACTION9( CHAIN B AND RESID 1:31 )B1 - 31

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