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- PDB-6jfm: Mitofusin2 (MFN2)_T111D -

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Basic information

Entry
Database: PDB / ID: 6jfm
TitleMitofusin2 (MFN2)_T111D
ComponentsMitofusin-2,Mitofusin-2
KeywordsMEMBRANE PROTEIN / mitochondriral fusion / GTPase activity / CMT2A
Function / homology
Function and homology information


: / RHOT2 GTPase cycle / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / mitochondrion localization / protein localization to phagophore assembly site / camera-type eye morphogenesis / negative regulation of Ras protein signal transduction / protein targeting to mitochondrion / blastocyst formation / mitochondrial membrane organization ...: / RHOT2 GTPase cycle / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / mitochondrion localization / protein localization to phagophore assembly site / camera-type eye morphogenesis / negative regulation of Ras protein signal transduction / protein targeting to mitochondrion / blastocyst formation / mitochondrial membrane organization / mitochondrial fusion / positive regulation of vascular associated smooth muscle cell apoptotic process / response to unfolded protein / aerobic respiration / positive regulation of vascular associated smooth muscle cell proliferation / PINK1-PRKN Mediated Mitophagy / negative regulation of smooth muscle cell proliferation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule cytoskeleton / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / mitochondrial outer membrane / membrane => GO:0016020 / GTPase activity / apoptotic process / ubiquitin protein ligase binding / GTP binding / mitochondrion / cytosol
Similarity search - Function
Mitofusin-2 / Fzo/mitofusin HR2 domain / fzo-like conserved region / Mitofusin family / 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
ACETATE ION / Mitofusin-2 / Mitofusin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLi, Y.J. / Cao, Y.L. / Feng, J.X. / Qi, Y.B. / Meng, S.X. / Yang, J.F. / Zhong, Y.T. / Kang, S.S. / Chen, X.X. / Lan, L. ...Li, Y.J. / Cao, Y.L. / Feng, J.X. / Qi, Y.B. / Meng, S.X. / Yang, J.F. / Zhong, Y.T. / Kang, S.S. / Chen, X.X. / Lan, L. / Luo, L. / Yu, B. / Chen, S.D. / Chan, D.C. / Hu, J.J. / Gao, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: Nat Commun / Year: 2019
Title: Structural insights of human mitofusin-2 into mitochondrial fusion and CMT2A onset.
Authors: Li, Y.J. / Cao, Y.L. / Feng, J.X. / Qi, Y. / Meng, S. / Yang, J.F. / Zhong, Y.T. / Kang, S. / Chen, X. / Lan, L. / Luo, L. / Yu, B. / Chen, S. / Chan, D.C. / Hu, J. / Gao, S.
History
DepositionFeb 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitofusin-2,Mitofusin-2
B: Mitofusin-2,Mitofusin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9277
Polymers99,6892
Non-polymers2385
Water4,828268
1
A: Mitofusin-2,Mitofusin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0435
Polymers49,8451
Non-polymers1984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-6 kcal/mol
Surface area20650 Å2
MethodPISA
2
B: Mitofusin-2,Mitofusin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8852
Polymers49,8451
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-4 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.437, 126.563, 79.972
Angle α, β, γ (deg.)90.00, 102.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitofusin-2,Mitofusin-2 / Transmembrane GTPase MFN2


Mass: 49844.508 Da / Num. of mol.: 2 / Mutation: T111D,T111D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Macaca mulatta (Rhesus monkey)
Gene: MFN2, CPRP1, KIAA0214, MFN2, EGK_00242 / Production host: Escherichia coli (E. coli)
References: UniProt: O95140, UniProt: G7MGV9, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.16 M Calcium acetate 0.08 M Sodium cacodylate PH 6.5 14.4% (W/V) PEG 8000 20% (V/V) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.09→126.6 Å / Num. obs: 50379 / % possible obs: 98.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 2.09→2.14 Å / Rmerge(I) obs: 0.573 / Num. unique obs: 3741 / Rrim(I) all: 0.743

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JFK

6jfk


Resolution: 2.09→31.641 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.57
RfactorNum. reflection% reflection
Rfree0.2293 2467 4.9 %
Rwork0.1758 --
obs0.1784 50316 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.09→31.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6759 0 11 268 7038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086951
X-RAY DIFFRACTIONf_angle_d0.9439367
X-RAY DIFFRACTIONf_dihedral_angle_d12.1315951
X-RAY DIFFRACTIONf_chiral_restr0.0481032
X-RAY DIFFRACTIONf_plane_restr0.0061229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.13020.25661200.21852688X-RAY DIFFRACTION99
2.1302-2.17370.28161270.22162650X-RAY DIFFRACTION99
2.1737-2.22090.27351480.21782713X-RAY DIFFRACTION100
2.2209-2.27260.26511520.21832610X-RAY DIFFRACTION99
2.2726-2.32940.29571650.2052639X-RAY DIFFRACTION99
2.3294-2.39230.27411430.20472596X-RAY DIFFRACTION98
2.3923-2.46270.23291390.20952619X-RAY DIFFRACTION97
2.4627-2.54220.26131310.20022626X-RAY DIFFRACTION98
2.5422-2.6330.24951320.19082703X-RAY DIFFRACTION99
2.633-2.73840.25291480.19182656X-RAY DIFFRACTION100
2.7384-2.86290.23321530.18492676X-RAY DIFFRACTION100
2.8629-3.01370.28611210.18922663X-RAY DIFFRACTION99
3.0137-3.20240.2461360.18382703X-RAY DIFFRACTION99
3.2024-3.44940.24831310.17882645X-RAY DIFFRACTION98
3.4494-3.7960.22841520.15882573X-RAY DIFFRACTION97
3.796-4.34410.18681140.14762716X-RAY DIFFRACTION99
4.3441-5.46850.20021250.14472685X-RAY DIFFRACTION99
5.4685-31.64440.17571300.17032688X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -7.2694 Å / Origin y: -12.3214 Å / Origin z: 16.5388 Å
111213212223313233
T0.2389 Å2-0.0035 Å2-0.0221 Å2-0.1982 Å20.0147 Å2--0.2652 Å2
L0.2519 °2-0.0858 °20.2375 °2-0.2332 °2-0.1248 °2--0.8423 °2
S-0.0214 Å °0.0117 Å °0.0159 Å °0.0162 Å °-0.0025 Å °-0.0705 Å °-0.0793 Å °-0.0228 Å °0.0328 Å °
Refinement TLS groupSelection details: all

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