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

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Basic information

Entry
Database: PDB / ID: 4xsj
TitleCrystal structure of the N-terminal domain of the human mitochondrial calcium uniporter fused with T4 lysozyme
ComponentsLysozyme,Calcium uniporter protein, mitochondrial
KeywordsTRANSPORT PROTEIN / Membrane protein / Calcium channel / Mitochondria
Function / homology
Function and homology information


mitochondrial calcium ion transmembrane transport / uniporter activity / Processing of SMDT1 / uniplex complex / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / cellular response to calcium ion starvation / positive regulation of neutrophil chemotaxis ...mitochondrial calcium ion transmembrane transport / uniporter activity / Processing of SMDT1 / uniplex complex / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / cellular response to calcium ion starvation / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / protein complex oligomerization / viral release from host cell by cytolysis / peptidoglycan catabolic process / calcium channel complex / calcium-mediated signaling / positive regulation of insulin secretion / calcium channel activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / glucose homeostasis / host cell cytoplasm / mitochondrial inner membrane / defense response to bacterium / mitochondrion / identical protein binding
Similarity search - Function
Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Endolysin / Calcium uniporter protein, mitochondrial
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 22, 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: Lysozyme,Calcium uniporter protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0764
Polymers29,7881
Non-polymers2883
Water7,764431
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.085, 98.085, 62.409
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 Lysozyme,Calcium uniporter protein, mitochondrial / Coiled-coil domain-containing protein 109A


Mass: 29788.135 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-161,UNP RESIDUES 75-165 / Mutation: D20N, C54T, C97A
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF LYSOZYME (1-161), LINKER GG, CALCIUM UNIPORTER PROTEIN (75-165), AND TAGS LEHHHHHH
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human)
Gene: e, T4Tp126, MCU, C10orf42, CCDC109A / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: Q8NE86, lysozyme
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 3350, 5% glycerol, 0.3 M ammonium sulphate and 0.1 M Bis-Tris-HCl (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 32604 / % possible obs: 97.9 % / Redundancy: 7.2 % / Net I/σ(I): 15.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
Cootmodel building
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LZM

2lzm


Resolution: 1.8→48.5 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.966 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1536 4.9 %RANDOM
Rwork0.127 ---
obs0.13 29581 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.253 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.3 Å20 Å2
2--0.59 Å20 Å2
3----1.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 15 431 2454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192081
X-RAY DIFFRACTIONr_bond_other_d0.0010.022093
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9722818
X-RAY DIFFRACTIONr_angle_other_deg0.89434732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.745257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39322.78497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76415376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6891524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02491
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_it2.5852.3311022
X-RAY DIFFRACTIONr_mcbond_other2.5842.3261021
X-RAY DIFFRACTIONr_mcangle_it3.1643.4931278
X-RAY DIFFRACTIONr_mcangle_other3.1633.4981279
X-RAY DIFFRACTIONr_scbond_it3.1572.9011059
X-RAY DIFFRACTIONr_scbond_other3.0512.8911048
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.594.1191522
X-RAY DIFFRACTIONr_long_range_B_refined6.75722.8612730
X-RAY DIFFRACTIONr_long_range_B_other4.91720.5212466
X-RAY DIFFRACTIONr_rigid_bond_restr1.45734174
X-RAY DIFFRACTIONr_sphericity_free48.5415144
X-RAY DIFFRACTIONr_sphericity_bonded21.78954429
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 93 -
Rwork0.169 1849 -
obs--82.89 %

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