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- PDB-5goe: Truncated mitofusin-1, GDP-bound -

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Basic information

Entry
Database: PDB / ID: 5goe
TitleTruncated mitofusin-1, GDP-bound
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 / Factors involved in megakaryocyte development and platelet production / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / Factors involved in megakaryocyte development and platelet production / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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
GUANOSINE-5'-DIPHOSPHATE / Mitofusin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 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 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Structure summary
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2602
Polymers47,8171
Non-polymers4431
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-6 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.420, 72.910, 94.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 47816.508 Da / Num. of mol.: 1 / Fragment: UNP residues 696-741 / Mutation: T109A
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.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.75 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium citrate tribasic and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→44.7 Å / Num. obs: 86503 / % possible obs: 98.9 % / Redundancy: 7.9 % / Net I/σ(I): 25.08

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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: 1.801→44.693 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.66
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2042 4335 5.01 %
Rwork0.177 --
obs0.1784 86503 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.801→44.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 28 273 3378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063232
X-RAY DIFFRACTIONf_angle_d0.7634374
X-RAY DIFFRACTIONf_dihedral_angle_d21.5831993
X-RAY DIFFRACTIONf_chiral_restr0.048490
X-RAY DIFFRACTIONf_plane_restr0.004562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8005-1.8210.24811190.25562669X-RAY DIFFRACTION94
1.821-1.84240.25871580.24522738X-RAY DIFFRACTION100
1.8424-1.86490.29351180.23892764X-RAY DIFFRACTION100
1.8649-1.88850.26381490.22812774X-RAY DIFFRACTION100
1.8885-1.91330.24251480.22832791X-RAY DIFFRACTION100
1.9133-1.93950.27491490.21762749X-RAY DIFFRACTION100
1.9395-1.96720.26791700.20742743X-RAY DIFFRACTION100
1.9672-1.99660.25331270.20742815X-RAY DIFFRACTION100
1.9966-2.02780.17161390.19362782X-RAY DIFFRACTION100
2.0278-2.0610.22111520.19522716X-RAY DIFFRACTION100
2.061-2.09660.23531480.19052780X-RAY DIFFRACTION100
2.0966-2.13470.19291320.17922793X-RAY DIFFRACTION100
2.1347-2.17580.18711400.18262770X-RAY DIFFRACTION100
2.1758-2.22020.2781280.17672780X-RAY DIFFRACTION100
2.2202-2.26840.19541700.17642764X-RAY DIFFRACTION100
2.2684-2.32120.241580.18282728X-RAY DIFFRACTION100
2.3212-2.37930.21351600.17692760X-RAY DIFFRACTION100
2.3793-2.44360.21171340.17542795X-RAY DIFFRACTION100
2.4436-2.51550.17711370.17672784X-RAY DIFFRACTION100
2.5155-2.59670.19891490.18122776X-RAY DIFFRACTION100
2.5967-2.68950.22871650.17282724X-RAY DIFFRACTION100
2.6895-2.79710.19391690.18622768X-RAY DIFFRACTION100
2.7971-2.92440.19511520.18222723X-RAY DIFFRACTION100
2.9244-3.07860.27631130.18332823X-RAY DIFFRACTION100
3.0786-3.27140.19421410.17362743X-RAY DIFFRACTION100
3.2714-3.52390.20971590.16572770X-RAY DIFFRACTION100
3.5239-3.87830.16761580.15442756X-RAY DIFFRACTION100
3.8783-4.43910.17481390.14672743X-RAY DIFFRACTION99
4.4391-5.59110.20241510.15492637X-RAY DIFFRACTION95
5.5911-44.70630.18231030.2092210X-RAY DIFFRACTION79
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)
11.0282-0.53661.32992.3169-2.69586.7154-0.0030.0970.0362-0.02070.16070.1686-0.0239-0.3209-0.19520.1725-0.00560.00030.22260.03490.2768.086822.646-6.2158
25.3791-0.77310.9622.6402-0.03513.5150.0394-0.0909-0.4513-0.01330.11430.91720.2508-0.5081-0.13340.21340.0080.01260.23610.05530.42240.8749-1.109421.825
33.3465-1.21310.95443.9224-1.56513.27370.12690.2054-0.1683-0.1435-0.1361-0.0580.24390.2417-0.01130.2270.00980.0390.2060.01990.192120.6465-3.941124.9901
40.6958-0.1644-0.06012.6554-3.52426.2291-0.030.04920.13250.2563-0.0601-0.0248-0.41830.13880.06290.1639-0.0182-0.00950.1342-0.01260.221715.367622.3325.1523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 166 )
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 284 )
4X-RAY DIFFRACTION4chain 'A' and (resid 285 through 735 )

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