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Basic information

Entry
Database: PDB / ID: 5yew
TitleStructural basis for GTP hydrolysis and conformational change of mitofusin 1 in mediating mitochondrial fusion
Components(Mitofusin-1,Mitofusin-1 fusion ...) x 2
KeywordsHYDROLASE / Mitochondria / Fusion / MFN1
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
BERYLLIUM TRIFLUORIDE ION / GUANOSINE-5'-DIPHOSPHATE / : / Mitofusin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYan, L. / Qi, Y. / Huang, X. / Yu, C.
Funding support China, 3items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31700659 China
the National Natural Science Foundation of China31225006 China
the National Natural Science Foundation of China81322023 China
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural basis for GTP hydrolysis and conformational change of MFN1 in mediating membrane fusion
Authors: Yan, L. / Qi, Y. / Huang, X. / Yu, C. / Lan, L. / Guo, X. / Rao, Z. / Hu, J. / Lou, Z.
History
DepositionSep 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 6, 2024Group: 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_struct_conn_angle / refine_hist / software / struct_conn / struct_ncs_dom_lim
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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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 / _refine_hist.d_res_low / _software.classification / _software.name / _struct_conn.pdbx_dist_value / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitofusin-1,Mitofusin-1 fusion protein
B: Mitofusin-1,Mitofusin-1 fusion protein
C: Mitofusin-1,Mitofusin-1 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,90915
Polymers142,1923
Non-polymers1,71812
Water0
1
A: Mitofusin-1,Mitofusin-1 fusion protein
B: Mitofusin-1,Mitofusin-1 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,94410
Polymers94,7992
Non-polymers1,1458
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-45 kcal/mol
Surface area35340 Å2
MethodPISA
2
C: Mitofusin-1,Mitofusin-1 fusion protein
hetero molecules

C: Mitofusin-1,Mitofusin-1 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,93110
Polymers94,7862
Non-polymers1,1458
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area5750 Å2
ΔGint-45 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.942, 207.942, 107.893
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA6 - 7356 - 415
21PROPROBB6 - 7356 - 415
12LEULEUAA6 - 7346 - 414
22LEULEUCC6 - 7346 - 414
13SERSERBB6 - 7366 - 416
23SERSERCC6 - 7366 - 416

NCS ensembles :
ID
1
2
3

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Components

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Mitofusin-1,Mitofusin-1 fusion ... , 2 types, 3 molecules ABC

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


Mass: 47405.887 Da / Num. of mol.: 1 / Fragment: UNP residues 1-364,UNP residues 694-741 / Mutation: T138V, V139N
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: Protein Mitofusin-1,Mitofusin-1 fusion protein / Fzo homolog / Transmembrane GTPase MFN1


Mass: 47392.887 Da / Num. of mol.: 2 / Fragment: UNP residues 1-364,UNP residues 694-741
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

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Non-polymers , 4 types, 12 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 4.74 Å3/Da / Density % sol: 74.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 160mM potassium thiocyanate, 16% PEG3350, 1% tacsimate (pH 7.0), 20mM HEPES, 2% PEG5000, 4% 1-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 44371 / % possible obs: 100 % / Redundancy: 19.7 % / Net I/σ(I): 14.33

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.88 / SU B: 20.02 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 2.73 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25733 1941 4.8 %RANDOM
Rwork0.22265 ---
obs0.22429 38433 90.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.655 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9329 0 102 0 9431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0199587
X-RAY DIFFRACTIONr_bond_other_d0.0020.029274
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.96512929
X-RAY DIFFRACTIONr_angle_other_deg1.017321360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99451157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14525.098459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.235151794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4651548
X-RAY DIFFRACTIONr_chiral_restr0.0930.21469
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022168
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4567.6544655
X-RAY DIFFRACTIONr_mcbond_other5.4527.6544654
X-RAY DIFFRACTIONr_mcangle_it8.39811.4735803
X-RAY DIFFRACTIONr_mcangle_other8.39811.4745804
X-RAY DIFFRACTIONr_scbond_it5.7798.0544932
X-RAY DIFFRACTIONr_scbond_other5.778.0584921
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.01411.9267111
X-RAY DIFFRACTIONr_long_range_B_refined13.28339564
X-RAY DIFFRACTIONr_long_range_B_other13.27939531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A237840.13
12B237840.13
21A242960.11
22C242960.11
31B238480.13
32C238480.13
LS refinement shellResolution: 3.203→3.286 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 122 -
Rwork0.381 2411 -
obs--77.72 %

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