[English] 日本語
Yorodumi
- PDB-5mzh: Crystal structure of ODA16 from Chlamydomonas reinhardtii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mzh
TitleCrystal structure of ODA16 from Chlamydomonas reinhardtii
ComponentsDynein assembly factor with WDR repeat domains 1
KeywordsMOTOR PROTEIN / Intraflagellar transport / cilium / beta propeller / cargo adaptor
Function / homology
Function and homology information


outer dynein arm assembly / intraciliary transport / motile cilium / ciliary basal body / cilium / cytoplasm
Similarity search - Function
: / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Dynein assembly factor with WDR repeat domains 1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsLorentzen, E. / Taschner, M. / Basquin, J. / Mourao, A.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural basis of outer dynein arm intraflagellar transport by the transport adaptor protein ODA16 and the intraflagellar transport protein IFT46.
Authors: Taschner, M. / Mourao, A. / Awasthi, M. / Basquin, J. / Lorentzen, E.
History
DepositionJan 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Oct 17, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen
Item: _entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line ..._entity.formula_weight / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dynein assembly factor with WDR repeat domains 1
B: Dynein assembly factor with WDR repeat domains 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5635
Polymers100,2752
Non-polymers2883
Water5,134285
1
A: Dynein assembly factor with WDR repeat domains 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3303
Polymers50,1371
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dynein assembly factor with WDR repeat domains 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2332
Polymers50,1371
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.767, 62.767, 460.472
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Dynein assembly factor with WDR repeat domains 1 / Outer row dynein assembly protein 16


Mass: 50137.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: DAW1, ODA16 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3Y8L7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 300 mM ammonium sulfate and 100 mM Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49 Å / Num. obs: 39781 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rpim(I) all: 0.125 / Net I/σ(I): 7.3
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 0.8 / Num. unique all: 3718 / Rpim(I) all: 0.884 / % possible all: 82

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wjs
Resolution: 2.398→49.154 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2199 2011 5.06 %
Rwork0.1577 --
obs0.1609 39774 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.398→49.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6417 0 15 285 6717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086635
X-RAY DIFFRACTIONf_angle_d1.1089014
X-RAY DIFFRACTIONf_dihedral_angle_d14.2233898
X-RAY DIFFRACTIONf_chiral_restr0.0631031
X-RAY DIFFRACTIONf_plane_restr0.0071152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.31011070.24682663X-RAY DIFFRACTION95
2.46-2.52650.32161830.24662713X-RAY DIFFRACTION94
2.5265-2.60080.3381570.23662659X-RAY DIFFRACTION94
2.6008-2.68460.30141440.22232654X-RAY DIFFRACTION95
2.6846-2.78050.28921290.21472721X-RAY DIFFRACTION95
2.7805-2.89170.30571600.19922666X-RAY DIFFRACTION94
2.8917-3.02320.26091370.18612747X-RAY DIFFRACTION95
3.0232-3.18230.25131430.16772694X-RAY DIFFRACTION95
3.1823-3.38140.21261620.15942675X-RAY DIFFRACTION94
3.3814-3.64190.19741300.14472713X-RAY DIFFRACTION95
3.6419-4.00740.20631540.13422677X-RAY DIFFRACTION95
4.0074-4.5850.15021350.11392701X-RAY DIFFRACTION95
4.585-5.76790.17211440.11692721X-RAY DIFFRACTION95
5.7679-27.55570.16061260.14332723X-RAY DIFFRACTION96

+
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