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- PDB-5gom: Truncated mitofusin-1, transition-like state -

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Basic information

Entry
Database: PDB / ID: 5gom
TitleTruncated mitofusin-1, transition-like state
ComponentsMitofusin-1
KeywordsHYDROLASE / mitochondrial fusion
Function / homology
Function and homology information


RHOT2 GTPase cycle / outer mitochondrial membrane protein complex / mitochondrion localization / GTP metabolic process / positive regulation of mitochondrial membrane potential / mitochondrial fusion / PINK1-PRKN Mediated Mitophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Factors involved in megakaryocyte development and platelet production / mitochondrial outer membrane ...RHOT2 GTPase cycle / outer mitochondrial membrane protein complex / mitochondrion localization / GTP metabolic process / positive regulation of mitochondrial membrane potential / mitochondrial fusion / PINK1-PRKN Mediated Mitophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Factors involved in megakaryocyte development and platelet production / mitochondrial outer membrane / GTPase activity / GTP binding / mitochondrion / identical protein binding / membrane
Similarity search - Function
Fzo/mitofusin HR2 domain / fzo-like conserved region / Mitofusin family / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / GUANOSINE-5'-DIPHOSPHATE / Mitofusin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsCao, Y.L. / Gao, S.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology of the People's Republic of China2013CB910500 China
National Natural Science Foundation of China31200553 China
Ministry of Education of the People's Republic of ChinaNCET-12-0567 China
CitationJournal: Nature / Year: 2017
Title: MFN1 structures reveal nucleotide-triggered dimerization critical for mitochondrial fusion
Authors: Cao, Y.L. / Meng, S. / Chen, Y. / Feng, J.X. / Gu, D.D. / Yu, B. / Li, Y.J. / Yang, J.Y. / Liao, S. / Chan, D.C. / Gao, S.
History
DepositionJul 27, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 20, 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

Downloads & links

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Assembly

Deposited unit
A: Mitofusin-1
B: Mitofusin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6745
Polymers95,6332
Non-polymers1,0413
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-16 kcal/mol
Surface area39210 Å2
Unit cell
Length a, b, c (Å)146.108, 45.982, 146.180
Angle α, β, γ (deg.)90.00, 92.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mitofusin-1 / Fzo homolog / Transmembrane GTPase MFN1


Mass: 47816.508 Da / Num. of mol.: 2 / Fragment: UNP residues 1-362,UNP residues 696-741
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MFN1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IWA4, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: 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: 2.57 Å3/Da / Density % sol: 52.05 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100mM MES (pH 6.0), 240mM NaCl, 36% pentaerythriol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.8016→48.697 Å / Num. obs: 181542 / % possible obs: 99.1 % / Redundancy: 7.4 % / Net I/σ(I): 20.55

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.802→48.69 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 32.86 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.259 2360 5.09 %
Rwork0.1889 --
obs0.1926 46389 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.802→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6484 0 64 4 6552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076667
X-RAY DIFFRACTIONf_angle_d0.9488993
X-RAY DIFFRACTIONf_dihedral_angle_d19.8334068
X-RAY DIFFRACTIONf_chiral_restr0.0461011
X-RAY DIFFRACTIONf_plane_restr0.0051150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8016-2.85880.32291050.27162454X-RAY DIFFRACTION92
2.8588-2.92090.37381310.24892561X-RAY DIFFRACTION99
2.9209-2.98880.39111310.22862610X-RAY DIFFRACTION100
2.9888-3.06360.32851080.23582749X-RAY DIFFRACTION100
3.0636-3.14640.30171250.23512516X-RAY DIFFRACTION100
3.1464-3.2390.39691510.24112634X-RAY DIFFRACTION100
3.239-3.34350.27641220.2272627X-RAY DIFFRACTION100
3.3435-3.4630.27871600.22792582X-RAY DIFFRACTION100
3.463-3.60160.33591590.22592596X-RAY DIFFRACTION100
3.6016-3.76540.29341500.21552561X-RAY DIFFRACTION100
3.7654-3.96390.27531370.20532599X-RAY DIFFRACTION100
3.9639-4.21210.28941460.18242653X-RAY DIFFRACTION100
4.2121-4.53710.22561400.15722627X-RAY DIFFRACTION100
4.5371-4.99330.18771460.15082557X-RAY DIFFRACTION100
4.9933-5.71480.23081420.1692611X-RAY DIFFRACTION100
5.7148-7.19630.26231470.19872597X-RAY DIFFRACTION100
7.1963-48.6970.21221600.152495X-RAY DIFFRACTION96
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)
19.40591.8053-6.01234.2184-0.96894.5564-0.103-1.0528-1.63640.1447-0.4087-1.4021-0.15931.73150.46410.79980.1240.06991.9230.08410.822823.546220.42736.5172
26.5940.5826-0.02293.2838-0.22764.55590.2437-0.2383-0.18440.081-0.2232-0.0852-0.2204-0.0736-0.02880.53570.20830.15830.44740.12690.3448-11.105518.630826.2366
35.47131.3051-4.14812.8054-0.80284.15540.03141.23150.2775-0.03730.1844-0.8669-0.2980.1306-0.15830.61120.0430.04611.1648-0.05310.601417.15125.50731.221
41.6034-0.4033-1.52511.87320.95533.393-0.3735-0.2074-0.1397-0.22540.0495-0.2551-0.7966-0.8395-0.50670.56360.20860.25623.285-0.46320.2282-64.014533.917871.1612
55.7787-0.588-0.84593.3868-1.19835.80870.0545-0.1740.83780.1839-0.11790.6464-1.2356-1.17520.06020.79670.24990.0391.1734-0.21480.6769-44.438626.217341.0945
63.48790.0133-0.56542.7225-0.1816.36060.2044-1.3972-0.09030.127-0.4063-0.1343-0.26460.13240.22660.5194-0.01020.07981.28120.08830.4402-28.41814.104647.877
72.1167-1.5614-3.11820.42951.84683.6174-0.307-0.9387-0.35110.3379-0.00240.04850.4512-0.19960.27770.7328-0.03540.18522.7091-0.3710.5848-58.612625.429575.0645
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 309 )
3X-RAY DIFFRACTION3chain 'A' and (resid 310 through 735 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 73 )
5X-RAY DIFFRACTION5chain 'B' and (resid 74 through 200 )
6X-RAY DIFFRACTION6chain 'B' and (resid 201 through 309 )
7X-RAY DIFFRACTION7chain 'B' and (resid 310 through 736 )

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