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- PDB-4nsd: Crystal Structure of CBARA1 in the Ca2+ Binding Form -

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Basic information

Entry
Database: PDB / ID: 4nsd
TitleCrystal Structure of CBARA1 in the Ca2+ Binding Form
ComponentsCalcium uptake protein 1, mitochondrial
KeywordsCalcium Binding protein / EF-hand
Function / homology
Function and homology information


regulation of cellular hyperosmotic salinity response / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / calcium import into the mitochondrion / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion import / calcium channel complex ...regulation of cellular hyperosmotic salinity response / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / calcium import into the mitochondrion / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion import / calcium channel complex / mitochondrial membrane / protein homooligomerization / defense response / mitochondrial intermembrane space / 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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 / _struct_ref_seq_dif.details / _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: Calcium uptake protein 1, mitochondrial
B: Calcium uptake protein 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,54611
Polymers80,9602
Non-polymers5869
Water54030
1
A: Calcium uptake protein 1, mitochondrial
hetero molecules

A: Calcium uptake protein 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1928
Polymers80,9602
Non-polymers2316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y,-z1
Buried area2140 Å2
ΔGint-97 kcal/mol
Surface area30760 Å2
MethodPISA
2
B: Calcium uptake protein 1, mitochondrial
hetero molecules

B: Calcium uptake protein 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,90114
Polymers80,9602
Non-polymers94012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area4190 Å2
ΔGint-149 kcal/mol
Surface area29640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.283, 105.804, 156.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-503-

CL

21B-602-

HOH

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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: 40480.199 Da / Num. of mol.: 2 / 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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 43% reservoir solution composed of (w/v) 2-methyl-2,4-pentanediol, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: Feb 17, 2012
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: 2.7→50 Å / Num. all: 22761 / Num. obs: 22533 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.4 %
Reflection shellResolution: 2.7→2.8 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→32.38 Å / SU ML: 0.36 / σ(F): 2 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 1138 5.14 %
Rwork0.212 --
obs0.216 22144 96.2 %
all-22761 -
Solvent computationShrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.47 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7278 Å20 Å20 Å2
2--0.9471 Å2-0 Å2
3---1.7808 Å2
Refinement stepCycle: LAST / Resolution: 2.7→32.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4531 0 30 30 4591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074651
X-RAY DIFFRACTIONf_angle_d1.0856268
X-RAY DIFFRACTIONf_dihedral_angle_d17.9061678
X-RAY DIFFRACTIONf_chiral_restr0.072702
X-RAY DIFFRACTIONf_plane_restr0.004805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.8250.41241160.3012402X-RAY DIFFRACTION89
2.825-2.97380.3721330.25492507X-RAY DIFFRACTION93
2.9738-3.160.31831420.22212545X-RAY DIFFRACTION95
3.16-3.40370.31911500.2242620X-RAY DIFFRACTION97
3.4037-3.74580.281390.20472669X-RAY DIFFRACTION98
3.7458-4.28680.24781490.18442718X-RAY DIFFRACTION99
4.2868-5.39680.23971510.17932717X-RAY DIFFRACTION99
5.3968-32.38370.27981580.22922828X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.8581 Å / Origin y: -10.9619 Å / Origin z: -19.7357 Å
111213212223313233
T0.11 Å20.0546 Å20.0046 Å2-0.0805 Å20.0023 Å2--0.0443 Å2
L0.5562 °2-0.354 °2-0.1782 °2-0.4862 °20.1443 °2--0.3158 °2
S-0.0087 Å °-0.0604 Å °-0.0253 Å °0.0799 Å °-0.0436 Å °-0.0282 Å °0.0347 Å °-0.0609 Å °0.0538 Å °
Refinement TLS groupSelection details: all

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