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- PDB-4nsc: Crystal Structure of CBARA1 in the Apo-form -

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Basic information

Entry
Database: PDB / ID: 4nsc
TitleCrystal Structure of CBARA1 in the Apo-form
ComponentsCalcium uptake protein 1, mitochondrial
KeywordsCalcium Binding protein / EF-hand
Function / homology
Function and homology information


mitochondrial crista junction / positive regulation of cristae formation / regulation of cellular hyperosmotic salinity response / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion sensor activity ...mitochondrial crista junction / positive regulation of cristae formation / regulation of cellular hyperosmotic salinity response / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion sensor activity / calcium import into the mitochondrion / cellular response to calcium ion starvation / calcium ion import / calcium channel inhibitor activity / calcium channel complex / cellular response to calcium ion / mitochondrial membrane / protein homooligomerization / mitochondrial intermembrane space / defense response / mitochondrial inner membrane / protein heterodimerization activity / calcium ion binding / mitochondrion / identical protein binding
Similarity search - Function
Calcium uptake protein 1/2/3 / EF hand / 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
Calcium uptake protein 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsWang, L. / Yang, X. / Li, S. / Shen, Y.
CitationJournal: Embo J. / Year: 2014
Title: Structural and mechanistic insights into MICU1 regulation of mitochondrial calcium uptake.
Authors: Wang, L. / Yang, X. / Li, S. / Wang, Z. / Liu, Y. / Feng, J. / Zhu, Y. / Shen, Y.
History
DepositionNov 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium uptake protein 1, mitochondrial
B: Calcium uptake protein 1, mitochondrial
C: Calcium uptake protein 1, mitochondrial
D: Calcium uptake protein 1, mitochondrial
E: Calcium uptake protein 1, mitochondrial
F: Calcium uptake protein 1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)278,0586
Polymers278,0586
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13630 Å2
ΔGint-117 kcal/mol
Surface area90170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.879, 146.819, 115.872
Angle α, β, γ (deg.)90.00, 111.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Calcium uptake protein 1, mitochondrial / Atopy-related autoantigen CALC / ara CALC / Calcium-binding atopy-related autoantigen 1


Mass: 46342.980 Da / Num. of mol.: 6 / Fragment: UNP residues 97-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICU1, CALC, CBARA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BPX6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8% PEG 3350 and 0.075 M ammonium citrate tribasic pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 25, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 46641 / Num. obs: 44146 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.2 %
Reflection shellResolution: 3.2→3.4 Å / % possible all: 69

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX1.7model building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7phasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→36.72 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1854 4.3 %RANDOM
Rwork0.254 ---
all0.259 46641 --
obs0.254 43232 92.3 %-
Displacement parametersBiso mean: 69.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.14 Å20 Å2-18.32 Å2
2---4.56 Å20 Å2
3---11.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 3.2→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15336 0 0 13 15349
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.5
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d21.6
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d0.86
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.421.5
X-RAY DIFFRACTIONo_mcangle_it2.512
X-RAY DIFFRACTIONo_scbond_it1.752
X-RAY DIFFRACTIONo_scangle_it2.842.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 266 4.3 %
Rwork0.348 5917 -
obs-3207 79.4 %

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