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- PDB-4xtb: Crystal structure of the N-terminal domain of the human mitochond... -

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Basic information

Entry
Database: PDB / ID: 4xtb
TitleCrystal structure of the N-terminal domain of the human mitochondrial calcium uniporter
ComponentsCalcium uniporter protein, mitochondrial
KeywordsTRANSPORT PROTEIN / Calcium channel / Membrane protein / Mitochondria
Function / homology
Function and homology information


uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / calcium import into the mitochondrion / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission ...uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / Mitochondrial calcium ion transport / calcium import into the mitochondrion / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / calcium channel complex / calcium-mediated signaling / calcium channel activity / positive regulation of insulin secretion / protein complex oligomerization / glucose homeostasis / mitochondrial inner membrane / mitochondrion / identical protein binding
Similarity search - Function
Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter
Similarity search - Domain/homology
Calcium uniporter protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.-S. ...Lee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.-S. / Lee, J.-G. / An, J.Y. / Park, K.R. / Lim, J.J. / Kim, J.H. / Kim, J.H. / Park, Z.Y. / Kim, Y.-S. / Wang, J. / Kim, D.H. / Eom, S.H.
CitationJournal: Embo Rep. / Year: 2015
Title: Structure and function of the N-terminal domain of the human mitochondrial calcium uniporter.
Authors: Lee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.S. / Lee, J.G. / An, J.Y. / Park, K.R. / Lim, J.J. / Kim, J.H. / Kim, J.H. / ...Authors: Lee, Y. / Min, C.K. / Kim, T.G. / Song, H.K. / Lim, Y. / Kim, D. / Shin, K. / Kang, M. / Kang, J.Y. / Youn, H.S. / Lee, J.G. / An, J.Y. / Park, K.R. / Lim, J.J. / Kim, J.H. / Kim, J.H. / Park, Z.Y. / Kim, Y.S. / Wang, J. / Kim, D.H. / Eom, S.H.
History
DepositionJan 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Other
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium uniporter protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2792
Polymers14,0851
Non-polymers1941
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.463, 55.463, 68.929
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Calcium uniporter protein, mitochondrial / Coiled-coil domain-containing protein 109A


Mass: 14085.148 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP RESIDUES 75-185)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCU, C10orf42, CCDC109A / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NE86
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.55 M lithium sulphate 0.1 M Bis-Tris propane (pH 8.0)
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.37→100 Å / Num. obs: 23888 / % possible obs: 99.4 % / Redundancy: 5 % / Net I/σ(I): 14.3
Reflection shellResolution: 1.37→1.39 Å / Mean I/σ(I) obs: 1.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data processing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XSJ

4xsj


Resolution: 1.5→48.03 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.308 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17626 947 5.1 %RANDOM
Rwork0.13959 ---
obs0.14152 17594 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.218 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms863 0 13 143 1019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019900
X-RAY DIFFRACTIONr_bond_other_d0.0030.02926
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9991218
X-RAY DIFFRACTIONr_angle_other_deg0.9493.0012098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.47222.68341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.79415159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7821511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021992
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02199
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6721.513440
X-RAY DIFFRACTIONr_mcbond_other1.661.507439
X-RAY DIFFRACTIONr_mcangle_it2.3152.268550
X-RAY DIFFRACTIONr_mcangle_other2.3182.273551
X-RAY DIFFRACTIONr_scbond_it2.4482.036460
X-RAY DIFFRACTIONr_scbond_other2.4672.038461
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other32.859669
X-RAY DIFFRACTIONr_long_range_B_refined4.77515.1861081
X-RAY DIFFRACTIONr_long_range_B_other4.29914.0871020
X-RAY DIFFRACTIONr_rigid_bond_restr1.32231826
X-RAY DIFFRACTIONr_sphericity_free43.252542
X-RAY DIFFRACTIONr_sphericity_bonded10.53251914
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 41 -
Rwork0.171 858 -
obs--65.33 %

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