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- PDB-6agh: Crystal structure of EFHA1 in Apo-State -

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Basic information

Entry
Database: PDB / ID: 6agh
TitleCrystal structure of EFHA1 in Apo-State
ComponentsCalcium uptake protein 2, mitochondrial
KeywordsMETAL BINDING PROTEIN / mitochondrial / calcium / Calcium Binding Protein
Function / homology
Function and homology information


negative regulation of mitochondrial calcium ion concentration / 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 channel complex / mitochondrial intermembrane space ...negative regulation of mitochondrial calcium ion concentration / 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 channel complex / mitochondrial intermembrane space / mitochondrial inner membrane / protein heterodimerization activity / calcium ion binding / mitochondrion
Similarity search - Function
Calcium uptake protein 1/2/3 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calcium uptake protein 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.742 Å
AuthorsYangfei, X. / Xue, Y. / Yuequan, S.
Funding support China, 1items
OrganizationGrant numberCountry
China
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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium uptake protein 2, mitochondrial
B: Calcium uptake protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)79,4852
Polymers79,4852
Non-polymers00
Water25214
1
A: Calcium uptake protein 2, mitochondrial

B: Calcium uptake protein 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)79,4852
Polymers79,4852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area1530 Å2
ΔGint-22 kcal/mol
Surface area29300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.712, 63.199, 66.115
Angle α, β, γ (deg.)92.36, 101.75, 96.74
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Calcium uptake protein 2, mitochondrial / EF-hand domain-containing family member A1


Mass: 39742.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICU2, EFHA1 / Production host: Escherichia coli (E. coli) / Strain (production host): Codon Plus / References: UniProt: Q8IYU8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mM Tris-HCl pH 8.5, 200 mM NaCl, 1 mM EGTA, 2 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 17757 / % possible obs: 98.4 % / Redundancy: 3.5 % / Rsym value: 0.09 / Net I/σ(I): 14.48
Reflection shellResolution: 2.74→2.8 Å / Num. unique obs: 885 / Rsym value: 0.519

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Processing

Software
NameVersionClassification
PHENIX(dev_2666: ???)refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AGJ

6agj


Resolution: 2.742→38.04 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 31.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 1762 9.94 %
Rwork0.2134 --
obs0.219 17726 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.742→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 0 14 4544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054632
X-RAY DIFFRACTIONf_angle_d0.8576190
X-RAY DIFFRACTIONf_dihedral_angle_d8.1292759
X-RAY DIFFRACTIONf_chiral_restr0.047670
X-RAY DIFFRACTIONf_plane_restr0.005777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7424-2.81650.3571010.2983935X-RAY DIFFRACTION72
2.8165-2.89940.33871310.27481242X-RAY DIFFRACTION98
2.8994-2.99290.37031430.27781278X-RAY DIFFRACTION98
2.9929-3.09980.32871240.30151230X-RAY DIFFRACTION98
3.0998-3.22390.3371500.27531271X-RAY DIFFRACTION98
3.2239-3.37050.32081380.24181239X-RAY DIFFRACTION99
3.3705-3.54810.26891340.2281248X-RAY DIFFRACTION99
3.5481-3.77020.31571490.2141269X-RAY DIFFRACTION99
3.7702-4.0610.25131340.19681267X-RAY DIFFRACTION98
4.061-4.46910.25451390.18121251X-RAY DIFFRACTION98
4.4691-5.11450.25031410.17921239X-RAY DIFFRACTION98
5.1145-6.43860.25321440.22581259X-RAY DIFFRACTION98
6.4386-38.04320.22651340.18531236X-RAY DIFFRACTION97
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)
16.71-2.08712.88995.5338-1.11695.60620.4897-0.2084-0.7441-0.2433-0.18460.32170.8209-0.5775-0.25530.6489-0.1067-0.09470.47150.04470.417685.7454-103.4814-94.6776
25.47316.33156.03488.59015.28668.21220.5617-0.08460.65490.2709-0.66480.3320.4273-0.62140.16110.51390.0096-0.10430.46680.03680.362387.8851-88.8183-95.1943
33.895-0.7542-1.84463.85280.685.1928-0.20790.43190.3435-0.14580.0818-0.1213-0.2572-0.24390.16250.6579-0.0753-0.16630.51380.08050.4894101.9271-76.3255-103.042
47.00582.98140.06355.4351-0.21848.31590.1391.15160.19710.2940.43430.02-1.1185-0.2799-0.1850.86640.1769-0.10390.80520.120.6544102.4329-74.3183-106.8222
58.9068-5.22372.7296.186-1.4282.17240.06930.73850.24180.3582-0.0542-1.145-0.13571.02390.16730.6727-0.0399-0.07520.6685-0.04820.675121.9488-73.7829-81.5754
66.6802-0.4269-1.08474.6025-2.01997.6351-0.19340.40870.3145-0.54270.220.1149-0.3697-0.6510.04110.6138-0.0136-0.13740.46530.01180.5169109.7035-73.08-81.4081
73.40620.9822-0.67242.46644.20228.8501-0.1143-0.8455-0.09850.96080.0311-0.36731.18720.3925-0.13060.78790.0098-0.21570.61110.10060.6373117.0864-77.1971-63.1036
83.31122.04583.37344.1249-1.17347.468-0.1218-0.57090.70410.49590.2387-0.04330.04780.21090.04990.91560.0757-0.22060.7781-0.19180.6165114.688-65.8309-63.5169
94.75224.38594.32364.47943.65364.2572-0.4948-0.6524-0.011-0.15760.10560.9791-0.0516-0.4740.13140.59050.006-0.1620.71970.10870.5039105.5781-82.2683-68.0259
105.959-5.27935.42924.8381-5.45877.42440.31290.84550.259-0.3523-0.5441-0.573-0.40050.78530.14790.7875-0.026-0.120.6860.10330.6971105.0502-99.5607-77.2091
113.6025-1.67413.23485.8919-1.37869.209-0.1794-0.0464-0.08580.4170.3203-0.28530.38210.1594-0.08670.6759-0.0481-0.11640.5775-0.02610.5315105.4903-103.7159-64.0841
128.1637-1.1812.18337.76142.30933.0465-0.99070.43610.36790.30740.9110.08290.20420.0390.13050.7484-0.0642-0.11130.87260.19140.548107.3231-105.0225-65.5674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 84 through 248 )
2X-RAY DIFFRACTION2chain 'A' and (resid 249 through 272 )
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 358 )
4X-RAY DIFFRACTION4chain 'A' and (resid 359 through 394 )
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 105 )
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 159 )
7X-RAY DIFFRACTION7chain 'B' and (resid 160 through 184 )
8X-RAY DIFFRACTION8chain 'B' and (resid 185 through 248 )
9X-RAY DIFFRACTION9chain 'B' and (resid 249 through 271 )
10X-RAY DIFFRACTION10chain 'B' and (resid 272 through 295 )
11X-RAY DIFFRACTION11chain 'B' and (resid 296 through 358 )
12X-RAY DIFFRACTION12chain 'B' and (resid 359 through 394 )

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