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- PDB-7pv1: Crystal structure of the dimeric mitofilin domain of Mic60 in com... -

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Basic information

Entry
Database: PDB / ID: 7pv1
TitleCrystal structure of the dimeric mitofilin domain of Mic60 in complex with the CHCH domain of Mic19
ComponentsMICOS complex subunit MIC60 fused to MIC19
KeywordsSTRUCTURAL PROTEIN / MICOS / dimer / mitochondria / fusion protein
Function / homologyProtein of unknown function DUF1690 / Protein of Unknown function (DUF1690) / MICOS complex / Mitochondrial inner membrane protein Mitofilin / Mitochondrial inner membrane protein / cristae formation / MICOS complex subunit mic19 / MICOS complex subunit MIC60
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 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 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 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 fused to MIC19
B: MICOS complex subunit MIC60 fused to MIC19
C: MICOS complex subunit MIC60 fused to MIC19
D: MICOS complex subunit MIC60 fused to MIC19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9047
Polymers68,3214
Non-polymers5833
Water1448
1
A: MICOS complex subunit MIC60 fused to MIC19
B: MICOS complex subunit MIC60 fused to MIC19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5494
Polymers34,1612
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-31 kcal/mol
Surface area16040 Å2
MethodPISA
2
C: MICOS complex subunit MIC60 fused to MIC19
D: MICOS complex subunit MIC60 fused to MIC19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3553
Polymers34,1612
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-34 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.197, 85.371, 61.497
Angle α, β, γ (deg.)90.000, 101.720, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 through 5 and (name N...
21(chain B and (resid 4 through 5 or resid 7...
31(chain C and ((resid 4 through 5 and (name N...
41(chain D and ((resid 4 through 5 and (name N...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGALAALA(chain A and ((resid 4 through 5 and (name N...AA4 - 54 - 5
12THRTHRGLYGLY(chain A and ((resid 4 through 5 and (name N...AA3 - 1453 - 145
13THRTHRGLYGLY(chain A and ((resid 4 through 5 and (name N...AA3 - 1453 - 145
14THRTHRGLYGLY(chain A and ((resid 4 through 5 and (name N...AA3 - 1453 - 145
15THRTHRGLYGLY(chain A and ((resid 4 through 5 and (name N...AA3 - 1453 - 145
21ARGARGALAALA(chain B and (resid 4 through 5 or resid 7...BB4 - 54 - 5
22LEULEUPHEPHE(chain B and (resid 4 through 5 or resid 7...BB7 - 117 - 11
23ARGARGGLYGLY(chain B and (resid 4 through 5 or resid 7...BB13 - 2513 - 25
24GLYGLYGLYGLY(chain B and (resid 4 through 5 or resid 7...BB2727
25ASPASPASPASP(chain B and (resid 4 through 5 or resid 7...BB2929
26THRTHRGLYGLY(chain B and (resid 4 through 5 or resid 7...BB3 - 1453 - 145
27THRTHRGLYGLY(chain B and (resid 4 through 5 or resid 7...BB3 - 1453 - 145
28THRTHRGLYGLY(chain B and (resid 4 through 5 or resid 7...BB3 - 1453 - 145
29THRTHRGLYGLY(chain B and (resid 4 through 5 or resid 7...BB3 - 1453 - 145
31ARGARGALAALA(chain C and ((resid 4 through 5 and (name N...CC4 - 54 - 5
32GLYGLYGLYGLY(chain C and ((resid 4 through 5 and (name N...CC1 - 1451 - 145
33GLYGLYGLYGLY(chain C and ((resid 4 through 5 and (name N...CC1 - 1451 - 145
34GLYGLYGLYGLY(chain C and ((resid 4 through 5 and (name N...CC1 - 1451 - 145
35GLYGLYGLYGLY(chain C and ((resid 4 through 5 and (name N...CC1 - 1451 - 145
41ARGARGALAALA(chain D and ((resid 4 through 5 and (name N...DD4 - 54 - 5
42PROPROTRPTRP(chain D and ((resid 4 through 5 and (name N...DD2 - 1462 - 146
43PROPROTRPTRP(chain D and ((resid 4 through 5 and (name N...DD2 - 1462 - 146
44PROPROTRPTRP(chain D and ((resid 4 through 5 and (name N...DD2 - 1462 - 146
45PROPROTRPTRP(chain D and ((resid 4 through 5 and (name N...DD2 - 1462 - 146

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Components

#1: Protein
MICOS complex subunit MIC60 fused to MIC19 / Mitofilin


Mass: 17080.326 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) Jeffamine ED-2001, 0.1 M HEPES/NaOH pH 7.0.

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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 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→40.738 Å / Num. obs: 20339 / % possible obs: 98.8 % / Redundancy: 4.028 % / Biso Wilson estimate: 68.373 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rrim(I) all: 0.13 / Χ2: 0.81 / Net I/σ(I): 9.16 / Num. measured all: 81921
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
2.5-2.654.0091.6550.7512949330732300.3941.91197.7
2.65-2.833.8581.0491.2311809310130610.571.21998.7
2.83-3.064.180.6092.2612102290328950.8090.799.7
3.06-3.354.1330.3314.2310871265226300.930.3899.2
3.35-3.743.8730.1498.619183240723710.9840.17398.5
3.74-4.314.2230.08116.029062215221460.9940.09399.7
4.31-5.273.9930.05522.177167181617950.9960.06498.8
5.27-7.424.0580.04823.185710142314070.9980.05598.9
7.42-40.7383.8160.02443.7630688198040.9990.02898.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PV0

7pv0


Resolution: 2.497→40.738 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 1017 5 %
Rwork0.232 19305 -
obs0.2334 20322 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.76 Å2 / Biso mean: 80.0625 Å2 / Biso min: 32.38 Å2
Refinement stepCycle: final / Resolution: 2.497→40.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4385 0 93 8 4486
Biso mean--106.42 58.92 -
Num. residues----553
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2055X-RAY DIFFRACTION11.88TORSIONAL
12B2055X-RAY DIFFRACTION11.88TORSIONAL
13C2055X-RAY DIFFRACTION11.88TORSIONAL
14D2055X-RAY DIFFRACTION11.88TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4972-2.62880.45691430.4075271197
2.6288-2.79350.37731440.3481274999
2.7935-3.00910.33871450.31162746100
3.0091-3.31180.35371450.2911275299
3.3118-3.79070.22781450.2336275199
3.7907-4.77470.20551470.19692796100
4.7747-40.7380.22821480.1836280099
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)
17.0849-2.94612.34829.3223-2.92177.51580.08270.6655-0.794-1.1910.15950.1560.8563-0.0839-0.34350.715-0.1402-0.05790.6023-0.1650.626229.144659.316340.8642
28.88990.79766.00254.81170.08747.3652-0.0057-1.13440.24070.0725-0.31280.20040.9443-1.5941-0.18190.3219-0.02350.07210.29860.09860.580435.264657.26972.6129
36.47892.1327-5.19152.54-2.23544.31881.3598-0.88260.25950.7337-0.240.45880.5255-2.71211.43431.39540.1111-0.38591.4636-0.32211.092645.028961.796296.4423
44.05490.6042.78516.88411.23874.49590.0547-1.5661.14870.5836-0.1078-0.03140.053-1.5398-0.06580.57160.0070.06210.8592-0.05790.665335.253165.535883.8145
56.5805-2.97093.39913.8461-1.74935.10350.58480.91481.2787-0.044-0.6422-0.6907-0.23140.7327-0.12590.4353-0.0335-0.00530.47620.03470.694856.650183.772671.7506
61.9373.40710.95217.8957-1.57757.0061-0.25730.09861.14520.3437-0.0014-0.5536-0.47770.0554-0.0480.5494-0.0390.05690.5686-0.19370.492953.975486.544981.2758
79.75951.09184.01071.61790.78953.1503-0.0303-0.41920.166-0.0156-0.09890.0422-0.1596-0.26740.01240.28560.03520.03840.32660.00860.426634.363478.488571.0546
85.2044-2.0441-1.95525.692-0.97243.8184-0.2145-0.6767-0.8786-0.4002-0.05230.43250.6612-0.4572-0.8890.47020.04680.18190.52140.14861.105411.858368.861362.4907
93.9065-0.1023.61871.232.06367.1668-0.31850.1972-0.7742-0.133-0.00010.12570.4549-0.235-0.14530.45410.07770.02630.6233-0.03930.771919.196869.899355.7046
107.39921.02961.04548.2817-0.22054.6555-0.3712-1.0053-0.81180.9186-0.92180.65142.1708-2.16210.24380.591-0.12070.10520.63240.05550.712334.131847.992181.8566
114.7417-4.2436-4.71025.65815.88376.1491-0.43021.6616-0.6952-2.30171.4205-1.0292-1.890.34550.67690.9401-0.06690.11440.9558-0.24510.994838.347648.021465.5525
122.60820.93221.66292.2978-0.51452.02590.2294-0.0025-1.8668-0.68010.3143-0.97841.78181.12630.74070.93280.03960.10410.56520.16641.02343.848644.079678.7288
137.5437-0.30091.76022.74450.02463.1884-0.4053-0.0212-1.10090.7916-0.1157-1.615-0.34191.37890.91660.56480.0497-0.07430.54450.1190.859347.48352.480978.8491
145.8696-0.80060.57448.5489-2.89815.22740.0467-0.36390.2436-0.4809-0.0839-0.11820.6343-0.50240.02980.5069-0.01140.04730.3883-0.08440.524435.795363.801950.1107
152.7627-3.07353.23825.2647-0.814410.0029-0.203-0.80441.2022-1.0056-0.2253-0.5096-0.18250.17380.44070.7186-0.1071-0.02330.53230.0490.751639.996877.20841.9755
163.9638-0.90241.25878.1175-2.14268.5391-0.2318-0.35661.1853-0.01340.3240.7327-0.5804-0.95710.09370.38690.0356-0.00370.5019-0.08310.487930.945877.114547.0374
172.59642.8232-0.36323.39031.01386.711-0.2681-1.56510.8821-0.1344-0.40870.59370.1336-0.52590.28960.38080.1282-0.09210.4836-0.01710.907312.485885.592965.2654
184.40872.45550.22152.32151.01660.8338-0.4464-1.54121.88450.3364-0.6202-0.7528-0.95651.2328-0.54730.5518-0.0753-0.26930.7082-0.05271.419530.460388.705266.3121
195.1111.9872-0.64363.2606-4.10176.6682-0.8459-0.6042.0135-0.43990.05950.0834-1.0147-0.60060.17970.70250.1511-0.090.4848-0.14961.058718.155393.389159.3156
203.62142.35363.52783.789-0.76227.92370.0760.41870.1935-1.22750.177-0.101-0.39610.04560.25350.64170.10550.09410.62470.03790.713620.006686.070853.1542
216.7992-0.78772.27195.18460.35123.54520.3531-0.0922-0.0232-0.19090.0973-0.2780.19050.13520.07540.3268-0.03880.08260.3970.00430.60147.06978.126367.9454
220.03250.0058-0.06560.2908-0.17290.1886-0.23191.5152-1.65671.11241.1807-0.61820.28642.30510.55960.88690.4206-0.0331.4896-0.2051.838668.476861.919778.6236
235.7874-2.27773.61964.57871.59695.27560.69361.45940.4275-1.4005-1.291-1.71841.08051.9326-0.16950.66720.01020.07880.76170.08391.009658.006168.765361.5971
246.0779-0.45194.2346.5535-0.73867.4820.41170.3985-0.81030.1861-0.4035-0.00820.9130.1686-0.50760.4023-0.07780.03290.5296-0.01150.687652.892464.468971.135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 61 )A3 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 92 )A62 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 104 )A93 - 104
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 145 )A105 - 145
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 26 )C1 - 26
6X-RAY DIFFRACTION6chain 'C' and (resid 27 through 42 )C27 - 42
7X-RAY DIFFRACTION7chain 'C' and (resid 43 through 93 )C43 - 93
8X-RAY DIFFRACTION8chain 'C' and (resid 94 through 124 )C94 - 124
9X-RAY DIFFRACTION9chain 'C' and (resid 125 through 145 )C125 - 145
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 20 )B3 - 20
11X-RAY DIFFRACTION11chain 'B' and (resid 21 through 28 )B21 - 28
12X-RAY DIFFRACTION12chain 'B' and (resid 29 through 42 )B29 - 42
13X-RAY DIFFRACTION13chain 'B' and (resid 43 through 61 )B43 - 61
14X-RAY DIFFRACTION14chain 'B' and (resid 62 through 93 )B62 - 93
15X-RAY DIFFRACTION15chain 'B' and (resid 94 through 124 )B94 - 124
16X-RAY DIFFRACTION16chain 'B' and (resid 125 through 145 )B125 - 145
17X-RAY DIFFRACTION17chain 'D' and (resid 2 through 20 )D2 - 20
18X-RAY DIFFRACTION18chain 'D' and (resid 21 through 26 )D21 - 26
19X-RAY DIFFRACTION19chain 'D' and (resid 27 through 42 )D27 - 42
20X-RAY DIFFRACTION20chain 'D' and (resid 43 through 61 )D43 - 61
21X-RAY DIFFRACTION21chain 'D' and (resid 62 through 92 )D62 - 92
22X-RAY DIFFRACTION22chain 'D' and (resid 93 through 104 )D93 - 104
23X-RAY DIFFRACTION23chain 'D' and (resid 105 through 124 )D105 - 124
24X-RAY DIFFRACTION24chain 'D' and (resid 125 through 146 )D125 - 146

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