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- PDB-6agj: Crystal Structure of EFHA2 in Apo State -

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Basic information

Entry
Database: PDB / ID: 6agj
TitleCrystal Structure of EFHA2 in Apo State
ComponentsCalcium uptake protein 3, mitochondrial
KeywordsMETAL BINDING PROTEIN / mitochondrial / calcium
Function / homology
Function and homology information


Processing of SMDT1 / uniplex complex / Mitochondrial calcium ion transport / calcium import into the mitochondrion / mitochondrial calcium ion homeostasis / mitochondrial inner membrane / calcium ion binding
Similarity search - Function
Calcium uptake protein 1/2/3 / 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 3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.999 Å
AuthorsYangfei, X. / Xue, Y. / Yuequan, S.
CitationJournal: Cell Rep / Year: 2019
Title: Dimerization of MICU Proteins Controls Ca2+Influx through the Mitochondrial Ca2+Uniporter.
Authors: Xing, Y. / Wang, M. / Wang, J. / Nie, Z. / Wu, G. / Yang, X. / Shen, Y.
History
DepositionAug 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium uptake protein 3, mitochondrial
B: Calcium uptake protein 3, mitochondrial


Theoretical massNumber of molelcules
Total (without water)89,4732
Polymers89,4732
Non-polymers00
Water724
1
A: Calcium uptake protein 3, mitochondrial

B: Calcium uptake protein 3, mitochondrial


Theoretical massNumber of molelcules
Total (without water)89,4732
Polymers89,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1750 Å2
ΔGint-19 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.363, 72.363, 339.751
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Calcium uptake protein 3, mitochondrial / EF-hand domain-containing family member A2


Mass: 44736.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICU3, EFHA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86XE3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M imidazole pH 9.5, 15% ethanol, 0.2 M MgCl2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 19171 / % possible obs: 99.7 % / Redundancy: 8.4 % / Rsym value: 0.092 / Net I/σ(I): 22.3
Reflection shellResolution: 2.99→3.11 Å / Num. unique obs: 885 / Rsym value: 0.781

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Processing

Software
NameVersionClassification
PHENIX(dev_2999: 000)refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.999→46.63 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 25.07
RfactorNum. reflection% reflection
Rfree0.2862 1909 10 %
Rwork0.2176 --
obs0.2244 19086 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.999→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5058 0 0 4 5062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115175
X-RAY DIFFRACTIONf_angle_d1.5196965
X-RAY DIFFRACTIONf_dihedral_angle_d7.8143094
X-RAY DIFFRACTIONf_chiral_restr0.072765
X-RAY DIFFRACTIONf_plane_restr0.009892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9992-3.07420.3511260.28211134X-RAY DIFFRACTION96
3.0742-3.15730.31091340.25721206X-RAY DIFFRACTION100
3.1573-3.25020.31441330.23431191X-RAY DIFFRACTION100
3.2502-3.3550.29841330.23561201X-RAY DIFFRACTION100
3.355-3.47490.29691340.2321214X-RAY DIFFRACTION100
3.4749-3.6140.27381360.21991213X-RAY DIFFRACTION100
3.614-3.77840.31621330.21081200X-RAY DIFFRACTION100
3.7784-3.97750.26551340.21291212X-RAY DIFFRACTION100
3.9775-4.22660.27051370.20751229X-RAY DIFFRACTION100
4.2266-4.55260.30791360.18921229X-RAY DIFFRACTION100
4.5526-5.01030.23191370.17191228X-RAY DIFFRACTION100
5.0103-5.73420.26661400.19851262X-RAY DIFFRACTION100
5.7342-7.22010.26981430.24541283X-RAY DIFFRACTION100
7.2201-46.63540.28621530.21291375X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2669-0.0110.04290.12820.00650.3144-0.0286-0.23390.00280.06380.1282-0.10150.05240.09350.10790.09560.04710.03370.56640.1454-0.083843.47610.4334149.0443
20.0929-0.0586-0.08620.12190.07070.0777-0.07710.0469-0.01570.06180.11220.02620.08780.09590.0675-0.1582-0.020.11170.29370.00130.080346.565113.2801145.3637
31.06270.17660.3040.4647-0.03230.6267-0.0116-0.3140.14780.1604-0.0629-0.4344-0.05340.21190.0187-0.2877-0.041-0.0340.5659-0.05890.369546.980640.6955143.0482
40.85930.02580.40470.1783-0.01480.2249-0.1027-0.38340.48110.11120.1021-0.231-0.08450.20820.0826-0.15540.0112-0.18520.5902-0.21160.214819.911245.657142.3685
51.90990.1911-0.13160.4683-0.06420.73070.0232-0.01430.01750.0102-0.00160.06410.0072-0.0563-0.0220.0041-0.05830.09030.44550.13270.3443-2.796141.0334133.8636
60.0244-0.04480.3290.089-0.53724.4232-0.0328-0.1815-0.10590.29930.1194-0.07740.0013-0.26-0.05410.36060.0881-0.07280.5910.04460.14233.197246.161155.0182
70.355-0.08210.09730.0934-0.0060.034-0.06280.1150.112-0.0282-0.05550.0568-0.0698-0.0713-0.1744-0.2502-0.0068-0.03580.28620.07940.003412.284239.0993135.0008
80.91990.0587-0.28210.16860.14230.32960.0171-0.2765-0.10090.1981-0.01040.34980.0821-0.3384-0.004-0.112-0.09190.22390.75350.34350.520111.191515.3459148.4224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 138 through 266 )
2X-RAY DIFFRACTION2chain 'A' and (resid 267 through 380 )
3X-RAY DIFFRACTION3chain 'A' and (resid 381 through 507 )
4X-RAY DIFFRACTION4chain 'B' and (resid 139 through 231 )
5X-RAY DIFFRACTION5chain 'B' and (resid 232 through 253 )
6X-RAY DIFFRACTION6chain 'B' and (resid 254 through 287 )
7X-RAY DIFFRACTION7chain 'B' and (resid 288 through 380 )
8X-RAY DIFFRACTION8chain 'B' and (resid 381 through 504 )

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