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- PDB-3trq: Crystal structure of native rabbit skeletal calsequestrin -

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Basic information

Entry
Database: PDB / ID: 3trq
TitleCrystal structure of native rabbit skeletal calsequestrin
ComponentsCalsequestrin-1
KeywordsCalcium-binding protein
Function / homology
Function and homology information


positive regulation of store-operated calcium channel activity / regulation of store-operated calcium entry / sarcoplasmic reticulum lumen / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / sarcomere organization / potassium ion binding / protein polymerization / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum ...positive regulation of store-operated calcium channel activity / regulation of store-operated calcium entry / sarcoplasmic reticulum lumen / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / sarcomere organization / potassium ion binding / protein polymerization / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / Z disc / mitochondrial matrix / calcium ion binding / magnesium ion binding / protein homodimerization activity / metal ion binding
Similarity search - Function
Calsequestrin / Calsequestrin, conserved site / Calsequestrin, middle TRX-fold domain / Calsequestrin, N-terminal TRX-fold domain / Calsequestrin, C-terminal TRX-fold domain / Calsequestrin / Calsequestrin signature 1. / Calsequestrin signature 2. / Glutaredoxin / Glutaredoxin ...Calsequestrin / Calsequestrin, conserved site / Calsequestrin, middle TRX-fold domain / Calsequestrin, N-terminal TRX-fold domain / Calsequestrin, C-terminal TRX-fold domain / Calsequestrin / Calsequestrin signature 1. / Calsequestrin signature 2. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.76 Å
AuthorsSanchez, E.J. / Lewis, K.M. / Munske, G.R. / Nissen, M.S. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Glycosylation of Skeletal Calsequestrin: IMPLICATIONS FOR ITS FUNCTION.
Authors: Sanchez, E.J. / Lewis, K.M. / Munske, G.R. / Nissen, M.S. / Kang, C.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references
Revision 1.2Feb 15, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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 / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,36015
Polymers40,8291
Non-polymers1,53114
Water10,016556
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Calsequestrin-1
hetero molecules

A: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,71930
Polymers81,6582
Non-polymers3,06228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area11120 Å2
ΔGint-254 kcal/mol
Surface area35050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.271, 144.565, 111.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Calsequestrin-1 / Aspartactin / Calsequestrin / skeletal muscle isoform / Laminin-binding protein


Mass: 40828.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / References: UniProt: P07221
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 569 molecules

#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.92 Å3/Da / Density % sol: 57.88 %

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONALS 8.2.11
SYNCHROTRONALS 8.2.22
Detector
TypeIDDetector
ADSC QUANTUM 315r1CCD
ADSC QUANTUM 3152CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.76→31.1 Å / Num. obs: 46768

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.1_357) / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1A8Y

1a8y


Resolution: 1.76→30.704 Å / SU ML: 0.21 / σ(F): 0.12 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 1974 4.22 %
Rwork0.1783 --
obs0.1798 46768 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.185 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9804 Å20 Å20 Å2
2--1.7852 Å20 Å2
3---0.1952 Å2
Refinement stepCycle: LAST / Resolution: 1.76→30.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 91 556 3512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123053
X-RAY DIFFRACTIONf_angle_d0.8074151
X-RAY DIFFRACTIONf_dihedral_angle_d17.6971148
X-RAY DIFFRACTIONf_chiral_restr0.06457
X-RAY DIFFRACTIONf_plane_restr0.003536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.8040.24241290.20292997X-RAY DIFFRACTION93
1.804-1.85280.24891380.19833100X-RAY DIFFRACTION96
1.8528-1.90730.22851360.1953067X-RAY DIFFRACTION95
1.9073-1.96890.24321400.18943160X-RAY DIFFRACTION98
1.9689-2.03920.24141410.18683192X-RAY DIFFRACTION99
2.0392-2.12090.23271430.18273212X-RAY DIFFRACTION99
2.1209-2.21740.21331410.17973218X-RAY DIFFRACTION99
2.2174-2.33420.22441420.18193209X-RAY DIFFRACTION99
2.3342-2.48040.23591420.18363243X-RAY DIFFRACTION99
2.4804-2.67180.19961420.18253236X-RAY DIFFRACTION99
2.6718-2.94050.22451440.18973258X-RAY DIFFRACTION100
2.9405-3.36550.21611450.17463281X-RAY DIFFRACTION100
3.3655-4.23850.1891460.15193323X-RAY DIFFRACTION100
4.2385-30.70880.18551450.17063298X-RAY DIFFRACTION96

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