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- PDB-5gof: Truncated mitofusin-1, GTP-bound -

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Basic information

Entry
Database: PDB / ID: 5gof
TitleTruncated mitofusin-1, GTP-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 / 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 / membrane / identical protein binding
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'-TRIPHOSPHATE / Mitofusin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.604 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 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)48,4294
Polymers47,8171
Non-polymers6133
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-13 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.579, 72.461, 95.344
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 1-369,UNP residues 696-741
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MFN1 / Production host: Escharinidae (invertebrata)
References: UniProt: Q8IWA4, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1mM ZnCl2, 100mM Tris-HCl (pH 8.0~9.0), 15~16% PEG 3350, 10~15% glycerol

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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: 1.6→44.66 Å / Num. obs: 426491 / % possible obs: 89.4 % / Redundancy: 7.1 % / Net I/σ(I): 25.54

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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: 1.604→29.105 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.46
RfactorNum. reflection% reflection
Rfree0.2145 2908 5.03 %
Rwork0.1793 --
obs0.1811 57847 89.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.604→29.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 34 427 3587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053329
X-RAY DIFFRACTIONf_angle_d0.8124510
X-RAY DIFFRACTIONf_dihedral_angle_d21.3182066
X-RAY DIFFRACTIONf_chiral_restr0.05503
X-RAY DIFFRACTIONf_plane_restr0.004579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6038-1.63010.27241630.23462836X-RAY DIFFRACTION99
1.6301-1.65820.26661580.2372892X-RAY DIFFRACTION100
1.6582-1.68830.27231520.21742894X-RAY DIFFRACTION100
1.6883-1.72080.29131530.22022902X-RAY DIFFRACTION100
1.7208-1.75590.25321270.21422885X-RAY DIFFRACTION100
1.7559-1.79410.23721550.2032892X-RAY DIFFRACTION100
1.7941-1.83580.25471600.21032882X-RAY DIFFRACTION100
1.8358-1.88170.28631540.26022796X-RAY DIFFRACTION97
1.8817-1.93260.34411270.29192124X-RAY DIFFRACTION99
1.9326-1.98940.2441130.1867285X-RAY DIFFRACTION95
1.9894-2.05360.26391370.19622905X-RAY DIFFRACTION100
2.0536-2.1270.21851540.18592918X-RAY DIFFRACTION100
2.127-2.21210.20061350.19212883X-RAY DIFFRACTION98
2.2121-2.31280.2586580.194940X-RAY DIFFRACTION33
2.3128-2.43470.21221460.17872919X-RAY DIFFRACTION99
2.4347-2.58710.21671550.17772917X-RAY DIFFRACTION100
2.5871-2.78670.19841810.17892922X-RAY DIFFRACTION100
2.7867-3.06690.22011410.17472975X-RAY DIFFRACTION100
3.0669-3.510.20891640.15682956X-RAY DIFFRACTION100
3.51-4.41970.17651400.14072632X-RAY DIFFRACTION88
4.4197-29.10970.18011350.17592584X-RAY DIFFRACTION82
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)
10.4337-0.22670.38422.2702-3.3074.94940.00810.01450.0242-0.00820.16110.1721-0.0396-0.2641-0.17040.13650.0061-0.00470.1536-0.00150.17718.630516.93811.0851
25.74010.84310.70963.45662.55057.93240.16790.3233-0.70630.2615-0.10220.54140.9931-0.3623-0.0830.28860.0309-0.05880.30710.03010.4856-2.7036-4.218820.2091
31.6209-0.5810.60472.3537-0.85751.89660.04890.1252-0.0491-0.0879-0.06250.01410.05090.07730.0150.1469-0.01550.01470.14480.01130.153419.0052-3.133624.7106
40.4899-0.13710.16762.4037-3.7137.2416-0.03470.04930.11330.2502-0.00260.0093-0.48340.08270.04150.149-0.013-0.01590.1199-0.01630.204415.39622.21645.2163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 156 )
3X-RAY DIFFRACTION3chain 'A' and (resid 157 through 284 )
4X-RAY DIFFRACTION4chain 'A' and (resid 285 through 736 )

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