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- PDB-7pv0: Crystal structure of a Mic60-Mic19 fusion protein -

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Basic information

Entry
Database: PDB / ID: 7pv0
TitleCrystal structure of a Mic60-Mic19 fusion protein
ComponentsMICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19
KeywordsSTRUCTURAL PROTEIN / MICOS / mitofilin / CHCH / mitochondria
Function / homologyProtein of unknown function DUF1690 / Protein of Unknown function (DUF1690) / MICOS complex / Mitochondrial inner membrane protein Mitofilin / Mitochondrial inner membrane protein / cristae formation / Chem-JEF / MICOS complex subunit mic19 / MICOS complex subunit MIC60
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFunck, K. / Bock-Bierbaum, T. / Daumke, O.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2013-CoG-616024 Germany
German Research Foundation (DFG)FOR2848/P06 Germany
CitationJournal: Sci Adv / Year: 2022
Title: Structural insights into crista junction formation by the Mic60-Mic19 complex.
Authors: Bock-Bierbaum, T. / Funck, K. / Wollweber, F. / Lisicki, E. / von der Malsburg, K. / von der Malsburg, A. / Laborenz, J. / Noel, J.K. / Hessenberger, M. / Jungbluth, S. / Bernert, C. / Kunz, ...Authors: Bock-Bierbaum, T. / Funck, K. / Wollweber, F. / Lisicki, E. / von der Malsburg, K. / von der Malsburg, A. / Laborenz, J. / Noel, J.K. / Hessenberger, M. / Jungbluth, S. / Bernert, C. / Kunz, S. / Riedel, D. / Lilie, H. / Jakobs, S. / van der Laan, M. / Daumke, O.
History
DepositionOct 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19
B: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19
C: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19
D: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19
E: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19
F: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8237
Polymers62,2256
Non-polymers5981
Water34219
1
A: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9692
Polymers10,3711
Non-polymers5981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19


Theoretical massNumber of molelcules
Total (without water)10,3711
Polymers10,3711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19


Theoretical massNumber of molelcules
Total (without water)10,3711
Polymers10,3711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19


Theoretical massNumber of molelcules
Total (without water)10,3711
Polymers10,3711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19


Theoretical massNumber of molelcules
Total (without water)10,3711
Polymers10,3711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19


Theoretical massNumber of molelcules
Total (without water)10,3711
Polymers10,3711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.815, 48.517, 70.739
Angle α, β, γ (deg.)82.700, 79.140, 72.410
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 10 or resid 12...
21(chain B and (resid 6 through 10 or resid 12...
31(chain C and (resid 6 through 10 or resid 12...
41(chain D and (resid 6 through 10 or resid 12...
51(chain E and (resid 6 through 10 or resid 12...
61(chain F and (resid 6 through 10 or resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 6 through 10 or resid 12...A6 - 10
121(chain A and (resid 6 through 10 or resid 12...A12 - 15
131(chain A and (resid 6 through 10 or resid 12...A17 - 19
141(chain A and (resid 6 through 10 or resid 12...A21 - 23
151(chain A and (resid 6 through 10 or resid 12...A25 - 27
161(chain A and (resid 6 through 10 or resid 12...A29
171(chain A and (resid 6 through 10 or resid 12...A32
181(chain A and (resid 6 through 10 or resid 12...A35
191(chain A and (resid 6 through 10 or resid 12...A5 - 82
1101(chain A and (resid 6 through 10 or resid 12...A5 - 82
1111(chain A and (resid 6 through 10 or resid 12...A5 - 82
1121(chain A and (resid 6 through 10 or resid 12...A5 - 82
211(chain B and (resid 6 through 10 or resid 12...B6 - 10
221(chain B and (resid 6 through 10 or resid 12...B12 - 15
231(chain B and (resid 6 through 10 or resid 12...B17 - 19
241(chain B and (resid 6 through 10 or resid 12...B29
251(chain B and (resid 6 through 10 or resid 12...B32
261(chain B and (resid 6 through 10 or resid 12...B5 - 84
271(chain B and (resid 6 through 10 or resid 12...B5 - 84
281(chain B and (resid 6 through 10 or resid 12...B5 - 84
291(chain B and (resid 6 through 10 or resid 12...B5 - 84
311(chain C and (resid 6 through 10 or resid 12...C6 - 10
321(chain C and (resid 6 through 10 or resid 12...C12 - 15
331(chain C and (resid 6 through 10 or resid 12...C17 - 19
341(chain C and (resid 6 through 10 or resid 12...C21 - 23
351(chain C and (resid 6 through 10 or resid 12...C29
361(chain C and (resid 6 through 10 or resid 12...C4 - 83
371(chain C and (resid 6 through 10 or resid 12...C4 - 83
381(chain C and (resid 6 through 10 or resid 12...C4 - 83
391(chain C and (resid 6 through 10 or resid 12...C4 - 83
3101(chain C and (resid 6 through 10 or resid 12...C4 - 83
411(chain D and (resid 6 through 10 or resid 12...D6 - 10
421(chain D and (resid 6 through 10 or resid 12...D12 - 15
431(chain D and (resid 6 through 10 or resid 12...D5 - 85
441(chain D and (resid 6 through 10 or resid 12...D0
451(chain D and (resid 6 through 10 or resid 12...D25 - 27
461(chain D and (resid 6 through 10 or resid 12...D29
471(chain D and (resid 6 through 10 or resid 12...D32
481(chain D and (resid 6 through 10 or resid 12...D5 - 85
491(chain D and (resid 6 through 10 or resid 12...D5 - 85
4101(chain D and (resid 6 through 10 or resid 12...D5 - 85
4111(chain D and (resid 6 through 10 or resid 12...D5 - 85
511(chain E and (resid 6 through 10 or resid 12...E6 - 10
521(chain E and (resid 6 through 10 or resid 12...E12 - 15
531(chain E and (resid 6 through 10 or resid 12...E17 - 19
541(chain E and (resid 6 through 10 or resid 12...E29
551(chain E and (resid 6 through 10 or resid 12...E32
561(chain E and (resid 6 through 10 or resid 12...E5 - 82
571(chain E and (resid 6 through 10 or resid 12...E5 - 82
581(chain E and (resid 6 through 10 or resid 12...E5 - 82
591(chain E and (resid 6 through 10 or resid 12...E5 - 82
611(chain F and (resid 6 through 10 or resid 12...F6 - 10
621(chain F and (resid 6 through 10 or resid 12...F12 - 15
631(chain F and (resid 6 through 10 or resid 12...F4 - 82
641(chain F and (resid 6 through 10 or resid 12...F0
651(chain F and (resid 6 through 10 or resid 12...F25 - 27
661(chain F and (resid 6 through 10 or resid 12...F29
671(chain F and (resid 6 through 10 or resid 12...F32
681(chain F and (resid 6 through 10 or resid 12...F4 - 82
691(chain F and (resid 6 through 10 or resid 12...F4 - 82
6101(chain F and (resid 6 through 10 or resid 12...F4 - 82
6111(chain F and (resid 6 through 10 or resid 12...F4 - 82

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Components

#1: Protein
MICOS complex subunit MIC60,MICOS complex subunit MIC60-MIC19,Mic60-Mic19 / Mitofilin


Mass: 10370.867 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: derived from limited proteolysis validated by mass spectrometry,derived from limited proteolysis validated by mass spectrometry,derived from limited proteolysis validated by mass ...Details: derived from limited proteolysis validated by mass spectrometry,derived from limited proteolysis validated by mass spectrometry,derived from limited proteolysis validated by mass spectrometry,derived from limited proteolysis validated by mass spectrometry,derived from limited proteolysis validated by mass spectrometry,derived from limited proteolysis validated by mass spectrometry,derived from limited proteolysis validated by mass spectrometry,derived from limited proteolysis validated by mass spectrometry
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0073820, CTHT_0012250 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SHY5, UniProt: G0S140
#2: Chemical ChemComp-JEF / O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) / JEFFAMINE


Mass: 597.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H63NO10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 33% (v/v) Jeffamine M-600, 0.1 M HEPES/NaOH pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.15→46.12 Å / Num. obs: 27300 / % possible obs: 91.8 % / Redundancy: 2.501 % / Biso Wilson estimate: 49.892 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.09 / Χ2: 1.097 / Net I/σ(I): 8.28 / Num. measured all: 68282
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.282.4960.8810.9211094481744450.5291.11592.3
2.28-2.432.5310.4851.710489454041450.8140.61491.3
2.43-2.632.450.3222.448914416136390.8880.40987.5
2.63-2.882.5550.24.259463389337040.9480.25595.1
2.88-3.222.5330.1127.348375349033070.9850.14394.8
3.22-3.712.4560.06312.956774307327580.9940.0889.7
3.71-4.542.4840.03621.365948260323950.9980.04592
4.54-6.392.4770.03324.054659202218810.9980.04193
6.39-46.122.5010.02333.092566112810260.9990.02991

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alpha-helices

Resolution: 2.15→46.12 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 35.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 1362 5 %
Rwork0.2497 25900 -
obs0.2512 27262 91.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.1 Å2 / Biso mean: 66.2464 Å2 / Biso min: 23.55 Å2
Refinement stepCycle: final / Resolution: 2.15→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3610 0 88 19 3717
Biso mean--102.96 44.25 -
Num. residues----445
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1163X-RAY DIFFRACTION6.177TORSIONAL
12B1163X-RAY DIFFRACTION6.177TORSIONAL
13C1163X-RAY DIFFRACTION6.177TORSIONAL
14D1163X-RAY DIFFRACTION6.177TORSIONAL
15E1163X-RAY DIFFRACTION6.177TORSIONAL
16F1163X-RAY DIFFRACTION6.177TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.220.41681350.38292593272891
2.22-2.310.32541390.34352629276893
2.31-2.420.35211350.29952564269991
2.42-2.550.31271320.28052508264088
2.55-2.710.27971330.2882537267090
2.71-2.910.33031410.27372683282495
2.91-3.210.29391410.26792668280994
3.21-3.670.2961340.23932548268291
3.67-4.630.24081350.20652569270491
4.63-46.120.2311370.2252601273892
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)
12.30850.59040.12378.63626.17567.9644-0.3651-0.13610.15430.4880.14070.26020.98230.81650.11540.3304-0.03270.06930.18050.08920.374670.968658.384290.2332
21.99951.9989-7.26959.71136.70244.6252-0.4226-2.05210.9253.32291.4312-0.48681.00471.7238-0.63791.49270.08550.03480.99-0.06470.711573.105961.7701111.8124
37.6207-0.9961-2.7727.10611.42683.3319-0.6646-0.4196-0.50380.49890.5434-1.44751.25271.3886-0.07970.68630.0379-0.07610.6088-0.10810.604379.339455.798395.3425
44.6757-1.7543-3.12344.83293.69878.6132-0.1927-0.243-0.0876-0.17020.27920.1947-0.02110.74990.09510.4546-0.15960.12620.22560.020.36573.058636.387871.5967
59.0132-4.7816-2.66555.05714.78945.3444-1.201-1.0334-1.66471.11380.6078-0.16581.71061.16710.68390.74040.02430.05050.52850.00010.844582.689830.406577.5238
66.6691-3.6813-6.58992.1843.91536.91820.29840.11760.424-0.79570.4009-0.8221-2.00631.7645-0.71480.5971-0.32070.10090.6543-0.06440.519582.906438.329270.8101
72.4451.4476-0.13674.56982.70813.17150.638-0.35680.03640.8077-0.05560.15630.43910.28970.17220.6942-0.20090.26670.3611-0.03570.422172.038371.504593.6597
86.8808-0.05926.00052.565-0.86969.6905-0.1131-0.42650.65260.7322-0.20510.1058-1.15040.26660.27630.8519-0.1910.18650.4492-0.02980.54575.742382.187194.9728
96.9855-4.9914-4.98198.07064.86218.2895-0.22230.3277-0.1034-0.68310.0995-0.44710.54880.39260.02630.6605-0.08890.21040.3275-0.01470.478869.45324.269768.041
106.4257-2.7376-1.26835.1922.13486.3608-0.0245-0.0486-0.9343-0.9283-0.0477-0.09931.4533-0.15320.07710.839-0.16690.22920.3185-0.05380.576866.582313.721767.4595
113.33421.3152.08385.41244.93149.90890.1545-0.19370.29680.3252-0.330.5413-0.4258-0.22310.12070.5993-0.1570.1920.3064-0.00930.603663.159469.7191100.7135
128.84374.0772.38231.98650.36238.3047-0.33481.13181.6471-0.7587-0.321.2465-1.0926-1.35990.31190.55190.04180.07940.69420.22440.858153.252872.098490.8661
137.2793.44562.05056.68592.73777.72710.1967-0.69320.94030.1896-0.5351.6025-0.0911-1.13880.18460.6739-0.08790.30380.538-0.0510.684554.725269.605199.6367
144.7738-3.0612-2.86956.92243.72646.1941-0.35640.3353-0.2157-1.0045-0.01460.0170.0516-0.45870.07910.6724-0.14450.13020.2679-0.02660.457569.884429.431957.677
155.994-3.1918-0.66133.20673.74139.0297-0.11360.7373-0.0941-1.67730.45320.3183-0.7929-0.7099-0.00820.8444-0.0810.07610.6820.02930.48661.708532.045453.6231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 34 )A5 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 43 )A35 - 43
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 83 )A44 - 83
4X-RAY DIFFRACTION4chain 'D' and (resid 5 through 35 )D5 - 35
5X-RAY DIFFRACTION5chain 'D' and (resid 36 through 63 )D36 - 63
6X-RAY DIFFRACTION6chain 'D' and (resid 64 through 85 )D64 - 85
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 34 )B5 - 34
8X-RAY DIFFRACTION8chain 'B' and (resid 35 through 84 )B35 - 84
9X-RAY DIFFRACTION9chain 'E' and (resid 5 through 34 )E5 - 34
10X-RAY DIFFRACTION10chain 'E' and (resid 35 through 84 )E35 - 84
11X-RAY DIFFRACTION11chain 'C' and (resid 4 through 35 )C4 - 35
12X-RAY DIFFRACTION12chain 'C' and (resid 36 through 59 )C36 - 59
13X-RAY DIFFRACTION13chain 'C' and (resid 60 through 83 )C60 - 83
14X-RAY DIFFRACTION14chain 'F' and (resid 4 through 43 )F4 - 43
15X-RAY DIFFRACTION15chain 'F' and (resid 44 through 83 )F44 - 83

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