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- PDB-6ql4: Crystal structure of nucleotide-free Mgm1 -

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Basic information

Entry
Database: PDB / ID: 6ql4
TitleCrystal structure of nucleotide-free Mgm1
ComponentsPutative mitochondrial dynamin protein
KeywordsMOTOR PROTEIN / Mitochondrial genome maintenance 1 protein / Dynamin superfamily / Dynamin-like protein / mitochondrial inner membrane / membrane remodeling
Function / homology
Function and homology information


dynamin GTPase / mitochondrial fusion / microtubule binding / defense response to virus / microtubule / GTPase activity / GTP binding / membrane / nucleus / cytoplasm
Similarity search - Function
Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain ...Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynamin-like GTPase MGM1, mitochondrial
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6 Å
AuthorsFaelber, K. / Dietrich, L. / Noel, J.K. / Wollweber, F. / Pfitzner, A.-K. / Muehleip, A. / Sanchez, R. / Kudryashev, M. / Chiaruttin, N. / Lilie, H. ...Faelber, K. / Dietrich, L. / Noel, J.K. / Wollweber, F. / Pfitzner, A.-K. / Muehleip, A. / Sanchez, R. / Kudryashev, M. / Chiaruttin, N. / Lilie, H. / Schlegel, J. / Rosenbaum, E. / Hessenberger, M. / Matthaeus, C. / Noe, F. / Roux, A. / vanderLaan, M. / Kuehlbrandt, W. / Daumke, O.
Funding support Germany, Austria, 3items
OrganizationGrant numberCountry
European Research CouncilERC-2013-CoG-616024 Germany
German Research FoundationSFB958 Germany
Austrian Science Fund Austria
CitationJournal: Nature / Year: 2019
Title: Structure and assembly of the mitochondrial membrane remodelling GTPase Mgm1.
Authors: Katja Faelber / Lea Dietrich / Jeffrey K Noel / Florian Wollweber / Anna-Katharina Pfitzner / Alexander Mühleip / Ricardo Sánchez / Misha Kudryashev / Nicolas Chiaruttini / Hauke Lilie / ...Authors: Katja Faelber / Lea Dietrich / Jeffrey K Noel / Florian Wollweber / Anna-Katharina Pfitzner / Alexander Mühleip / Ricardo Sánchez / Misha Kudryashev / Nicolas Chiaruttini / Hauke Lilie / Jeanette Schlegel / Eva Rosenbaum / Manuel Hessenberger / Claudia Matthaeus / Séverine Kunz / Alexander von der Malsburg / Frank Noé / Aurélien Roux / Martin van der Laan / Werner Kühlbrandt / Oliver Daumke /
Abstract: Balanced fusion and fission are key for the proper function and physiology of mitochondria. Remodelling of the mitochondrial inner membrane is mediated by the dynamin-like protein mitochondrial ...Balanced fusion and fission are key for the proper function and physiology of mitochondria. Remodelling of the mitochondrial inner membrane is mediated by the dynamin-like protein mitochondrial genome maintenance 1 (Mgm1) in fungi or the related protein optic atrophy 1 (OPA1) in animals. Mgm1 is required for the preservation of mitochondrial DNA in yeast, whereas mutations in the OPA1 gene in humans are a common cause of autosomal dominant optic atrophy-a genetic disorder that affects the optic nerve. Mgm1 and OPA1 are present in mitochondria as a membrane-integral long form and a short form that is soluble in the intermembrane space. Yeast strains that express temperature-sensitive mutants of Mgm1 or mammalian cells that lack OPA1 display fragmented mitochondria, which suggests that Mgm1 and OPA1 have an important role in inner-membrane fusion. Consistently, only the mitochondrial outer membrane-not the inner membrane-fuses in the absence of functional Mgm1. Mgm1 and OPA1 have also been shown to maintain proper cristae architecture; for example, OPA1 prevents the release of pro-apoptotic factors by tightening crista junctions. Finally, the short form of OPA1 localizes to mitochondrial constriction sites, where it presumably promotes mitochondrial fission. How Mgm1 and OPA1 perform their diverse functions in membrane fusion, scission and cristae organization is at present unknown. Here we present crystal and electron cryo-tomography structures of Mgm1 from Chaetomium thermophilum. Mgm1 consists of a GTPase (G) domain, a bundle signalling element domain, a stalk, and a paddle domain that contains a membrane-binding site. Biochemical and cell-based experiments demonstrate that the Mgm1 stalk mediates the assembly of bent tetramers into helical filaments. Electron cryo-tomography studies of Mgm1-decorated lipid tubes and fluorescence microscopy experiments on reconstituted membrane tubes indicate how the tetramers assemble on positively or negatively curved membranes. Our findings convey how Mgm1 and OPA1 filaments dynamically remodel the mitochondrial inner membrane.
History
DepositionJan 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative mitochondrial dynamin protein
B: Putative mitochondrial dynamin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,3664
Polymers208,2422
Non-polymers1242
Water00
1
A: Putative mitochondrial dynamin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1832
Polymers104,1211
Non-polymers621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative mitochondrial dynamin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1832
Polymers104,1211
Non-polymers621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.400, 147.400, 344.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 225 through 253 or resid 501 through 546 or resid 880 through 908))
21(chain B and (resid 225 through 253 or resid 501 through 546 or resid 880 through 908))
12(chain A and (resid 547 through 595 or resid 622 through 713 or resid 818 through 879))
22(chain B and (resid 547 through 595 or resid 622 through 713 or resid 818 through 879))
13(chain A and resid 254 through 500)
23(chain B and resid 254 through 500)
14(chain A and resid 714 through 817)
24(chain B and resid 714 through 817)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 225 through 253 or resid 501 through 546 or resid 880 through 908))A225 - 253
121(chain A and (resid 225 through 253 or resid 501 through 546 or resid 880 through 908))A501 - 546
131(chain A and (resid 225 through 253 or resid 501 through 546 or resid 880 through 908))A880 - 908
211(chain B and (resid 225 through 253 or resid 501 through 546 or resid 880 through 908))B225 - 253
221(chain B and (resid 225 through 253 or resid 501 through 546 or resid 880 through 908))B501 - 546
231(chain B and (resid 225 through 253 or resid 501 through 546 or resid 880 through 908))B880 - 908
112(chain A and (resid 547 through 595 or resid 622 through 713 or resid 818 through 879))A547 - 595
122(chain A and (resid 547 through 595 or resid 622 through 713 or resid 818 through 879))A622 - 713
132(chain A and (resid 547 through 595 or resid 622 through 713 or resid 818 through 879))A818 - 879
212(chain B and (resid 547 through 595 or resid 622 through 713 or resid 818 through 879))B547 - 595
222(chain B and (resid 547 through 595 or resid 622 through 713 or resid 818 through 879))B622 - 713
232(chain B and (resid 547 through 595 or resid 622 through 713 or resid 818 through 879))B818 - 879
113(chain A and resid 254 through 500)A254 - 500
213(chain B and resid 254 through 500)B254 - 500
114(chain A and resid 714 through 817)A714 - 817
214(chain B and resid 714 through 817)B714 - 817

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Putative mitochondrial dynamin protein


Mass: 104120.758 Da / Num. of mol.: 2
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_0065850 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SGC7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2

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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: 4.53 Å3/Da / Density % sol: 72.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 8% PEG400, 3% isopropanol, 100 mM Na-citrate buffer (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.6→49.133 Å / Num. obs: 44814 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 113.61 Å2 / Net I/σ(I): 7.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.6-3.696.7611.8391.0761180.3521.99298.4
3.69-3.797.0331.4221.4160510.4951.53699.9
3.79-3.96.8841.1161.7958640.6051.20799.9
3.9-4.026.6760.8842.2657150.7050.95999.9
4.02-4.166.2890.6732.7855640.7740.73499.7
4.16-4.37.2370.5243.8853250.8870.565100
4.3-4.477.1980.4284.6552240.9180.461100
4.47-4.657.1530.3295.8449420.9550.35599.9
4.65-4.857.0970.2587.3447910.9660.279100
4.85-5.097.0180.232845760.9720.25199.9
5.09-5.376.5480.2357.6443360.9710.255100
5.37-5.696.8180.2517.3541140.9670.272100
5.69-6.097.3010.2467.8438500.9690.265100
6.09-6.577.1860.1889.9735940.9820.20399.9
6.57-7.27.0780.1381333130.990.14999.9
7.2-8.056.2980.08817.6529800.9950.09799.7
8.05-9.37.0110.05627.6926200.9980.061100
9.3-11.387.0540.04234.4522410.9990.046100
11.38-16.16.2490.0434.9817090.9980.04499.7
16.1-49.1335.9990.03436.748960.9990.03894.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.6→49.133 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.62 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2523 2242 5 %
Rwork0.2435 42572 -
obs0.244 44814 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 403.87 Å2 / Biso mean: 146.1573 Å2 / Biso min: 63.25 Å2
Refinement stepCycle: final / Resolution: 3.6→49.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10322 0 8 0 10330
Biso mean--101.4 --
Num. residues----1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610502
X-RAY DIFFRACTIONf_angle_d0.97614182
X-RAY DIFFRACTIONf_chiral_restr0.0581617
X-RAY DIFFRACTIONf_plane_restr0.0061847
X-RAY DIFFRACTIONf_dihedral_angle_d16.2626500
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A637X-RAY DIFFRACTION17.07TORSIONAL
12B637X-RAY DIFFRACTION17.07TORSIONAL
21A1729X-RAY DIFFRACTION17.07TORSIONAL
22B1729X-RAY DIFFRACTION17.07TORSIONAL
31A0X-RAY DIFFRACTION17.07TORSIONAL
32B0X-RAY DIFFRACTION17.07TORSIONAL
41A889X-RAY DIFFRACTION17.07TORSIONAL
42B889X-RAY DIFFRACTION17.07TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6-3.67830.35151340.34952547268199
3.6783-3.76380.29471380.32426122750100
3.7638-3.85790.32241380.307926242762100
3.8579-3.96220.291370.291926082745100
3.9622-4.07870.29241390.285726372776100
4.0787-4.21030.28461380.275326242762100
4.2103-4.36070.25271390.251426352774100
4.3607-4.53520.28431390.251926342773100
4.5352-4.74140.25821390.229226462785100
4.7414-4.99120.23921390.228726432782100
4.9912-5.30350.22931400.23126622802100
5.3035-5.71250.26261400.255426612801100
5.7125-6.28630.31021420.271326872829100
6.2863-7.19350.28651430.278427192862100
7.1935-9.05380.20011440.205827382882100
9.0538-49.13790.19781530.18922895304899
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)
13.97730.27311.67732.6494-0.66414.0476-0.1805-0.68330.37210.34510.04170.4294-0.9973-0.2487-0.00360.94050.0312-0.07580.93940.07380.8467-102.505565.6927-16.3741
23.3637-2.64890.7423.55271.44115.11810.265-0.17150.5316-0.3267-0.2242-1.2379-1.2403-0.05970.0040.8318-0.04020.06911.4538-0.01231.5827.429546.723819.1837
32.40350.20270.01582.5735-0.45082.74840.08390.7843-0.1933-0.1661-0.24610.38080.4319-0.2706-0.00030.65310.1757-0.05651.4158-0.31430.9696-32.829919.9049-29.4821
40.5314-0.2003-1.26991.59721.14344.7732-0.1628-0.02640.06060.15260.11160.03460.33990.0638-0.00010.7809-0.0387-0.01730.9661-0.12920.8708-54.705929.73339.8708
55.8875-2.45590.0982.457-0.58881.34120.01750.09040.0761-0.17870.15190.05160.1009-0.02810.00130.544-0.0499-0.06370.8982-0.07330.596-53.18138.3981-9.0556
65.70970.739-0.22210.59010.09272.68650.13670.28690.21770.23440.0239-0.05140.14890.40550.00070.58130.0329-0.10860.8473-0.13580.7389-27.886836.835817.3392
72.5776-0.99210.69833.6209-1.88764.3242-0.00120.62450.081-0.3453-0.0865-1.031-1.10110.7653-0.00891.6436-0.1953-0.11481.02530.15921.2466-97.043487.3665-33.9959
80.7848-0.3880.73380.2866-1.01465.9470.58160.2764-0.11681.37210.7667-0.2951-2.5244-1.2879-0.05092.1383-0.12510.26081.70020.39414.012125.407168.945222.1761
90.1647-0.1468-0.12580.60860.08340.0907-0.80040.01191.97893.2410.69321.809-2.38110.2067-0.05074.2129-0.3396-1.07882.08940.2954.111941.953371.414932.4381
100.7452-0.23730.00610.1943-0.15270.1713-0.7788-0.43993.06842.86370.015-0.9597-2.01250.75260.00653.9669-0.1202-1.04122.1718-0.33874.093339.748275.892732.6993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 223:253 or resseq 879:910 or resseq 516:549)A223 - 253
2X-RAY DIFFRACTION1chain 'A' and (resseq 223:253 or resseq 879:910 or resseq 516:549)A879 - 910
3X-RAY DIFFRACTION1chain 'A' and (resseq 223:253 or resseq 879:910 or resseq 516:549)A516 - 549
4X-RAY DIFFRACTION2chain 'B' and (resseq 223:253 or resseq 879:911 or resseq 516:549)B223 - 253
5X-RAY DIFFRACTION2chain 'B' and (resseq 223:253 or resseq 879:911 or resseq 516:549)B879 - 911
6X-RAY DIFFRACTION2chain 'B' and (resseq 223:253 or resseq 879:911 or resseq 516:549)B516 - 549
7X-RAY DIFFRACTION3chain 'A' and (resseq 598:624 or resseq 710:820)A598 - 624
8X-RAY DIFFRACTION3chain 'A' and (resseq 598:624 or resseq 710:820)A710 - 820
9X-RAY DIFFRACTION4chain 'B' and (resseq 598:624 or resseq 710:820)B598 - 624
10X-RAY DIFFRACTION4chain 'B' and (resseq 598:624 or resseq 710:820)B710 - 820
11X-RAY DIFFRACTION5chain 'A' and (resseq 550:597 or resseq 625:709 or resseq 821:878)A550 - 597
12X-RAY DIFFRACTION5chain 'A' and (resseq 550:597 or resseq 625:709 or resseq 821:878)A625 - 709
13X-RAY DIFFRACTION5chain 'A' and (resseq 550:597 or resseq 625:709 or resseq 821:878)A821 - 878
14X-RAY DIFFRACTION6chain 'B' and (resseq 550:597 or resseq 625:709 or resseq 821:878)B550 - 597
15X-RAY DIFFRACTION6chain 'B' and (resseq 550:597 or resseq 625:709 or resseq 821:878)B625 - 709
16X-RAY DIFFRACTION6chain 'B' and (resseq 550:597 or resseq 625:709 or resseq 821:878)B821 - 878
17X-RAY DIFFRACTION7chain 'A' and (resseq 254:515)A254 - 515
18X-RAY DIFFRACTION8chain 'B' and (resseq 289:358 or resseq 505:515)B289 - 358
19X-RAY DIFFRACTION8chain 'B' and (resseq 289:358 or resseq 505:515)B505 - 515
20X-RAY DIFFRACTION9chain 'B' and (resseq 376:392 or resseq 407:423 or resseq 438:444 or resseq 468:490)B376 - 392
21X-RAY DIFFRACTION9chain 'B' and (resseq 376:392 or resseq 407:423 or resseq 438:444 or resseq 468:490)B407 - 423
22X-RAY DIFFRACTION9chain 'B' and (resseq 376:392 or resseq 407:423 or resseq 438:444 or resseq 468:490)B438 - 444
23X-RAY DIFFRACTION9chain 'B' and (resseq 376:392 or resseq 407:423 or resseq 438:444 or resseq 468:490)B468 - 490
24X-RAY DIFFRACTION10chain 'B' and (resseq 254:288 or resseq 359:375 or resseq 393:406 or resseq 424:437 or resseq 445:467 or resseq 491:504)B254 - 288
25X-RAY DIFFRACTION10chain 'B' and (resseq 254:288 or resseq 359:375 or resseq 393:406 or resseq 424:437 or resseq 445:467 or resseq 491:504)B359 - 375
26X-RAY DIFFRACTION10chain 'B' and (resseq 254:288 or resseq 359:375 or resseq 393:406 or resseq 424:437 or resseq 445:467 or resseq 491:504)B393 - 406
27X-RAY DIFFRACTION10chain 'B' and (resseq 254:288 or resseq 359:375 or resseq 393:406 or resseq 424:437 or resseq 445:467 or resseq 491:504)B445 - 467
28X-RAY DIFFRACTION10chain 'B' and (resseq 254:288 or resseq 359:375 or resseq 393:406 or resseq 424:437 or resseq 445:467 or resseq 491:504)B491 - 504

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