[English] 日本語
Yorodumi
- PDB-9k9m: X-ray structure of FBB18 from Chlamydomonas reinhardtii. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9k9m
TitleX-ray structure of FBB18 from Chlamydomonas reinhardtii.
ComponentsFlagellar associated protein
KeywordsMOTOR PROTEIN / dynein
Function / homologyCilia- and flagella-associated protein 298 / Cilia- and flagella-associated protein 298 / regulation of cilium movement / Flagellar associated protein
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsSahashi, Y. / Tanaka, H. / Shimo-Kon, R. / Yamamoto, R. / Kurisu, G. / Kon, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP17H03665 Japan
Japan Society for the Promotion of Science (JSPS)JP17K15117 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Chlamydomonas FBB18 is a ubiquitin-like protein essential for the cytoplasmic preassembly of various ciliary dyneins.
Authors: Yamamoto, R. / Sahashi, Y. / Shimo-Kon, R. / Sakato-Antoku, M. / Suzuki, M. / Luo, L. / Tanaka, H. / Ishikawa, T. / Yagi, T. / King, S.M. / Kurisu, G. / Kon, T.
History
DepositionOct 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flagellar associated protein
C: Flagellar associated protein
B: Flagellar associated protein
D: Flagellar associated protein


Theoretical massNumber of molelcules
Total (without water)106,2334
Polymers106,2334
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.954, 152.093, 116.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein
Flagellar associated protein


Mass: 26558.154 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_16g688450v5 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K3CU42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 18% PEG8000, 100 mM HEPES (pH7.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 91792 / % possible obs: 98 % / Redundancy: 2.8 % / Biso Wilson estimate: 52.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.44 Å / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 14545 / CC1/2: 0.732

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→34.61 Å / SU ML: 0.3724 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.5764 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2506 3752 4.09 %
Rwork0.1982 87992 -
obs0.2003 91744 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6469 0 0 118 6587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00796581
X-RAY DIFFRACTIONf_angle_d0.95448896
X-RAY DIFFRACTIONf_chiral_restr0.05391004
X-RAY DIFFRACTIONf_plane_restr0.00731163
X-RAY DIFFRACTIONf_dihedral_angle_d4.18164072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.43631270.35753048X-RAY DIFFRACTION91
2.33-2.360.3941370.3473201X-RAY DIFFRACTION97.12
2.36-2.390.35541390.32923272X-RAY DIFFRACTION97.18
2.39-2.430.33711350.31873260X-RAY DIFFRACTION97.75
2.43-2.460.35291360.31363188X-RAY DIFFRACTION97.36
2.46-2.50.40371360.30443257X-RAY DIFFRACTION96.75
2.5-2.540.38411380.28463182X-RAY DIFFRACTION96.99
2.54-2.590.30761400.2663227X-RAY DIFFRACTION95.87
2.59-2.640.31541330.26183193X-RAY DIFFRACTION96.27
2.64-2.690.30471390.263214X-RAY DIFFRACTION97.22
2.69-2.740.33931390.25443279X-RAY DIFFRACTION98.19
2.74-2.80.26271390.24873265X-RAY DIFFRACTION98.87
2.8-2.870.40011460.23893321X-RAY DIFFRACTION99.34
2.87-2.940.2771420.23823294X-RAY DIFFRACTION99.48
2.94-3.020.26971400.23423280X-RAY DIFFRACTION99.45
3.02-3.10.28251460.23623321X-RAY DIFFRACTION99.4
3.1-3.210.31391390.21843299X-RAY DIFFRACTION99.57
3.21-3.320.2731440.22393337X-RAY DIFFRACTION99.6
3.32-3.450.30271410.21473299X-RAY DIFFRACTION99.42
3.45-3.610.23371400.1963345X-RAY DIFFRACTION99.01
3.61-3.80.25391420.19323219X-RAY DIFFRACTION98.74
3.8-4.040.21241400.16713271X-RAY DIFFRACTION98.67
4.04-4.350.21051400.16193299X-RAY DIFFRACTION98.65
4.35-4.790.15731420.14163210X-RAY DIFFRACTION97.24
4.79-5.470.20671380.16233274X-RAY DIFFRACTION97.91
5.47-6.890.2421350.17583316X-RAY DIFFRACTION99.68
6.89-34.610.19341390.14453321X-RAY DIFFRACTION99.68
Refinement TLS params.Method: refined / Origin x: 61.5561228032 Å / Origin y: 37.6811072045 Å / Origin z: -0.170861886489 Å
111213212223313233
T0.388585635386 Å2-0.00328676390672 Å2-0.0292355800824 Å2-0.426504455815 Å20.00236205354188 Å2--0.486949611701 Å2
L0.103907970327 °20.0765370772948 °2-0.0473914330421 °2-0.738228214812 °2-0.053092944305 °2--0.0218977275959 °2
S-0.073568336246 Å °0.0290831243898 Å °0.0309861645067 Å °0.0388462935351 Å °0.00735174475875 Å °-0.0301630071865 Å °-0.0671646147582 Å °0.0288639771435 Å °0.0737346147695 Å °
Refinement TLS groupSelection details: all

+
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