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- PDB-4ehq: Crystal Structure of Calmodulin Binding Domain of Orai1 in Comple... -

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Basic information

Entry
Database: PDB / ID: 4ehq
TitleCrystal Structure of Calmodulin Binding Domain of Orai1 in Complex with Ca2+/Calmodulin Displays a Unique Binding Mode
Components
  • Calcium release-activated calcium channel protein 1
  • Calmodulin
KeywordsPROTEIN BINDING / calmodulin / Orai1 / calcium dependent inactivation / EF hand / Calcium binding / calcium-dependent inactivation / Calmodulin binding domain of Orai1 / none / cytosol
Function / homology
Function and homology information


store-operated calcium entry / regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / ion channel modulating, G protein-coupled receptor signaling pathway / store-operated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Elevation of cytosolic Ca2+ levels ...store-operated calcium entry / regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / ion channel modulating, G protein-coupled receptor signaling pathway / store-operated calcium channel activity / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / Elevation of cytosolic Ca2+ levels / positive regulation of adenylate cyclase activity / : / mammary gland epithelium development / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / positive regulation of calcium ion transport / calcium ion import / establishment of protein localization to membrane / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / protein phosphatase activator activity / plasma membrane raft / ligand-gated ion channel signaling pathway / calcium channel regulator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of calcium ion transport / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / regulation of cardiac muscle contraction / calcium channel inhibitor activity / positive regulation of DNA binding / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / potassium ion transmembrane transport / sperm midpiece / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / adenylate cyclase activator activity / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / regulation of cytokinesis / positive regulation of nitric-oxide synthase activity / calcium-mediated signaling / spindle microtubule / calcium ion transmembrane transport / positive regulation of receptor signaling pathway via JAK-STAT / calcium channel activity / positive regulation of insulin secretion / spindle pole / cellular response to type II interferon / response to calcium ion / calcium-dependent protein binding / disordered domain specific binding / G2/M transition of mitotic cell cycle / myelin sheath / phospholipase C-activating G protein-coupled receptor signaling pathway / growth cone / basolateral plasma membrane / vesicle / transmembrane transporter binding / adaptive immune response / protein autophosphorylation / calmodulin binding / neuron projection / positive regulation of apoptotic process / membrane raft / protein domain specific binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Calcium release-activated calcium channel protein / Orai superfamily / Mediator of CRAC channel activity / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
GAMMA-BUTYROLACTONE / Calmodulin-1 / Calmodulin-1 / Calcium release-activated calcium channel protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9005 Å
AuthorsLiu, Y. / Zheng, X. / Mueller, G.A. / Sobhany, M. / DeRose, E.F. / Zhang, Y. / London, R.E. / Birnbaumer, L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of calmodulin binding domain of orai1 in complex with ca2+*calmodulin displays a unique binding mode.
Authors: Liu, Y. / Zheng, X. / Mueller, G.A. / Sobhany, M. / Derose, E.F. / Zhang, Y. / London, R.E. / Birnbaumer, L.
History
DepositionApr 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references
Revision 1.3Sep 13, 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 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Calmodulin
G: Calcium release-activated calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,62010
Polymers19,1152
Non-polymers5058
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-75 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.074, 24.709, 60.903
Angle α, β, γ (deg.)90.00, 100.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calmodulin / / CaM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Gene: Calm1, Calm, Cam, Cam1, Calm2, Cam2, Camb, Calm3, Cam3, Camc
Production host: Escherichia coli (E. coli) / References: UniProt: P62161, UniProt: P0DP29*PLUS
#2: Protein/peptide Calcium release-activated calcium channel protein 1 / Protein orai-1 / Transmembrane protein 142A


Mass: 2393.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96D31
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GBL / GAMMA-BUTYROLACTONE / DIHYDROFURAN-2(3H)-ONE / Gamma-Butyrolactone


Mass: 86.089 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.94 Å3/Da / Density % sol: 36.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris pH 6.0, 40% PPG P400, 14% butyrolactone, 1% n-octyl-beta-D-glucopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 23, 2010
RadiationMonochromator: copper anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 11939 / Num. obs: 11497 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.084 / Net I/σ(I): 12.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3.9 / Num. unique all: 853 / % possible all: 73.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IWQ

1iwq


Resolution: 1.9005→19.987 Å / SU ML: 0.21 / σ(F): 0 / σ(I): 0 / Phase error: 19.33 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.216 524 4.71 %RANDOM
Rwork0.1789 ---
all0.1806 11497 --
obs0.1806 11118 93.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.125 Å2 / ksol: 0.415 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9482 Å2-0 Å20.6951 Å2
2---0.6742 Å20 Å2
3----0.274 Å2
Refinement stepCycle: LAST / Resolution: 1.9005→19.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 28 88 1426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141443
X-RAY DIFFRACTIONf_angle_d0.8791991
X-RAY DIFFRACTIONf_dihedral_angle_d13.077581
X-RAY DIFFRACTIONf_chiral_restr0.064210
X-RAY DIFFRACTIONf_plane_restr0.003251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9005-2.09160.21691230.16472213X-RAY DIFFRACTION80
2.0916-2.39380.19361440.15732728X-RAY DIFFRACTION98
2.3938-3.01430.23911250.18242766X-RAY DIFFRACTION97
3.0143-19.98770.21481320.18832887X-RAY DIFFRACTION98

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