[English] 日本語
Yorodumi
- PDB-9kfd: Truncated Fzo1,GTP-bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kfd
TitleTruncated Fzo1,GTP-bound
ComponentsMitofusin FZO1
KeywordsHYDROLASE / Fzo1 / dynamin / mitofusin
Function / homology
Function and homology information


peroxisomal-mitochondrial contact site / peroxisome-mitochondrion membrane tether activity / mitochondrial outer membrane fusion / Factors involved in megakaryocyte development and platelet production / RHOT2 GTPase cycle / mitochondrial inner membrane fusion / PINK1-PRKN Mediated Mitophagy / mitochondrion localization / mitochondrial fusion / intracellular distribution of mitochondria ...peroxisomal-mitochondrial contact site / peroxisome-mitochondrion membrane tether activity / mitochondrial outer membrane fusion / Factors involved in megakaryocyte development and platelet production / RHOT2 GTPase cycle / mitochondrial inner membrane fusion / PINK1-PRKN Mediated Mitophagy / mitochondrion localization / mitochondrial fusion / intracellular distribution of mitochondria / mitochondrial membrane / peroxisome / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitochondrial outer membrane / GTPase activity / GTP binding / mitochondrion
Similarity search - Function
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 FZO1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å
AuthorsYan, L.-M. / Gao, S. / Huang, S.-J.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371258 China
National Natural Science Foundation of China (NSFC)82341073 China
National Natural Science Foundation of China (NSFC)2320103002 China
National Natural Science Foundation of China (NSFC)82173098 China
CitationJournal: To Be Published
Title: A special latch in yeast mitofusin guarantees mitochondrial fusion by stabilizing self-assembly
Authors: Gao, S. / Huang, S.-J. / Yan, L.-M.
History
DepositionNov 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitofusin FZO1
B: Mitofusin FZO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5348
Polymers107,3932
Non-polymers1,1416
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-65 kcal/mol
Surface area37960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.404, 174.404, 127.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Mitofusin FZO1 / Transmembrane GTPase FZO1


Mass: 53696.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FZO1, YBR179C, YBR1241 / Production host: Escherichia coli (E. coli)
References: UniProt: P38297, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 72.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium chloride 0.1 M BIS-TRIS,pH 6.5 1.5 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97935 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.73→123.32 Å / Num. obs: 49576 / % possible obs: 97.8 % / Redundancy: 13.8 % / CC1/2: 0.978 / Net I/σ(I): 5.9
Reflection shellResolution: 2.73→2.87 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7355 / CC1/2: 0.904 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.19-4092refinement
autoPROCdata processing
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.73→66.46 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2628 2471 4.99 %
Rwork0.2328 --
obs0.2344 49533 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.73→66.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6763 0 68 20 6851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036919
X-RAY DIFFRACTIONf_angle_d0.6259318
X-RAY DIFFRACTIONf_dihedral_angle_d4.336891
X-RAY DIFFRACTIONf_chiral_restr0.0391082
X-RAY DIFFRACTIONf_plane_restr0.0051174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.780.36441180.35592669X-RAY DIFFRACTION100
2.78-2.840.39171400.33642640X-RAY DIFFRACTION100
2.84-2.90.37771600.32252641X-RAY DIFFRACTION100
2.9-2.970.39461340.31442690X-RAY DIFFRACTION100
2.97-3.040.41091460.31612653X-RAY DIFFRACTION100
3.04-3.120.38651390.31872654X-RAY DIFFRACTION100
3.12-3.210.34281420.29462662X-RAY DIFFRACTION100
3.21-3.320.32171160.26342663X-RAY DIFFRACTION100
3.32-3.420.30551230.26542384X-RAY DIFFRACTION99
3.46-3.570.26811210.25232245X-RAY DIFFRACTION100
3.57-3.740.25821280.24182525X-RAY DIFFRACTION94
3.74-3.930.25111390.22982503X-RAY DIFFRACTION94
3.93-4.180.22711220.21532669X-RAY DIFFRACTION100
4.18-4.50.22681460.19322683X-RAY DIFFRACTION100
4.5-4.950.1991410.18082699X-RAY DIFFRACTION100
4.95-5.670.19341670.21172665X-RAY DIFFRACTION100
5.67-7.140.27961440.24732680X-RAY DIFFRACTION100
7.15-66.460.23751450.19132737X-RAY DIFFRACTION100
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)
14.00141.8794-1.65924.4899-1.7941.64440.07690.34340.4795-0.0210.15580.015-0.08550.053-0.14440.57230.08090.09520.5124-0.01920.656323.54836.403-12.7693
23.56560.445-0.07482.41860.07533.3724-0.11260.2903-0.5069-0.18260.0350.18250.3004-0.140.07290.3801-0.02610.07340.3339-0.05570.589426.8024-19.2536-14.6627
35.349-0.88780.18810.7652-1.9746.3522-0.0758-0.2464-0.67140.48160.0220.59040.8354-0.45820.09410.5919-0.17150.11320.57880.1040.851823.926-22.98961.3543
42.0264-0.6244-0.42250.2976-0.38971.98720.2534-0.15420.12420.1185-0.2741-0.2726-0.0023-0.0057-0.03490.38130.0090.06850.519-0.03080.720119.44860.1114-5.3014
55.1511.3197-0.72523.7831-0.36073.88910.3496-0.01531.5587-0.21290.34151.0424-0.5645-0.1614-0.36860.57980.0640.08850.5096-0.00051.029617.252419.0114-8.9931
66.2937-1.58110.86645.2852-1.67342.542-0.0157-0.3910.8080.17060.0537-0.277-0.139-0.0842-0.08750.5436-0.08560.14710.5637-0.05920.617560.55697.1644-16.6915
72.92230.05920.19412.36790.27673.254-0.0238-0.4661-0.30470.3374-0.1231-0.2341-0.00610.30620.09980.43440.03440.01960.5930.12280.548558.5138-12.57590.6592
82.15590.3707-0.25173.4583-1.25631.6549-0.04160.04510.06460.3195-0.0824-0.3733-0.09450.11160.13560.42150.01080.06510.5268-0.02880.577163.7433-0.3916-19.3721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 82 through 184 )
2X-RAY DIFFRACTION2chain 'A' and (resid 185 through 392 )
3X-RAY DIFFRACTION3chain 'A' and (resid 393 through 442 )
4X-RAY DIFFRACTION4chain 'A' and (resid 443 through 816 )
5X-RAY DIFFRACTION5chain 'A' and (resid 817 through 855 )
6X-RAY DIFFRACTION6chain 'B' and (resid 85 through 184 )
7X-RAY DIFFRACTION7chain 'B' and (resid 185 through 392 )
8X-RAY DIFFRACTION8chain 'B' and (resid 393 through 853 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more