[English] 日本語
Yorodumi
- PDB-6l5h: Crystal structure of human rootletin 1108-1200 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l5h
TitleCrystal structure of human rootletin 1108-1200
ComponentsRootletin
KeywordsSTRUCTURAL PROTEIN / centrosome / rootletin / coiled-coil
Function / homology
Function and homology information


subapical part of cell / ciliary basal body organization / establishment of organelle localization / centriole-centriole cohesion / 9+2 motile cilium / protein localization to organelle / epithelial structure maintenance / positive regulation of protein localization to cilium / positive regulation of cilium assembly / cellular homeostasis ...subapical part of cell / ciliary basal body organization / establishment of organelle localization / centriole-centriole cohesion / 9+2 motile cilium / protein localization to organelle / epithelial structure maintenance / positive regulation of protein localization to cilium / positive regulation of cilium assembly / cellular homeostasis / photoreceptor cell maintenance / centrosome cycle / ciliary rootlet / kinesin binding / centriole / photoreceptor inner segment / establishment of localization in cell / structural constituent of cytoskeleton / protein localization / actin cytoskeleton / actin binding / centrosome / structural molecule activity / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsKim, J. / Choi, H.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2014R1A4A10052590 Korea, Republic Of
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Identification of a Structurally Dynamic Domain for Oligomer Formation in Rootletin.
Authors: Ko, D. / Kim, J. / Rhee, K. / Choi, H.J.
History
DepositionOct 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rootletin
B: Rootletin


Theoretical massNumber of molelcules
Total (without water)22,9252
Polymers22,9252
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-42 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.088, 32.162, 36.997
Angle α, β, γ (deg.)90.000, 96.170, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Rootletin / Ciliary rootlet coiled-coil protein


Mass: 11462.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CROCC, KIAA0445 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TZA2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 14% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 40235 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Χ2: 1.972 / Net I/σ(I): 14.6 / Num. measured all: 281721
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.325.90.53119990.940.2310.5810.99798.4
1.32-1.356.50.45819760.9460.1930.4980.99799.8
1.35-1.376.80.45620130.9610.1880.4941.052100
1.37-1.47.10.42219840.9720.1710.4561.081100
1.4-1.437.20.41819700.9590.1670.4511.09100
1.43-1.467.20.320180.9860.1210.3241.193100
1.46-1.57.20.11519920.9990.0470.1251.252100
1.5-1.547.20.14120420.9980.0570.1521.422100
1.54-1.597.20.15119680.9940.060.1631.528100
1.59-1.647.20.13420000.9950.0540.1441.719100
1.64-1.77.20.11920340.9960.0480.1291.778100
1.7-1.767.30.10420060.9960.0420.1131.874100
1.76-1.847.30.0919970.9970.0360.0972.125100
1.84-1.947.20.08520250.9960.0340.0922.516100
1.94-2.0670.07520220.9970.030.0813.115100
2.06-2.226.80.06120090.9970.0250.0673.382100
2.22-2.456.80.05820420.9970.0240.0623.582100
2.45-2.870.04820140.9980.0190.0513.125100
2.8-3.537.10.03420710.9990.0140.0372.514100
3.53-506.80.03320530.9990.0140.0362.92197.2

-
Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→22.087 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2044 1906 4.76 %
Rwork0.189 38151 -
obs0.1898 40057 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.17 Å2 / Biso mean: 23.9011 Å2 / Biso min: 10.03 Å2
Refinement stepCycle: final / Resolution: 1.3→22.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 0 183 1521
Biso mean---30.92 -
Num. residues----164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3005-1.3330.25381370.2592263397
1.333-1.3690.22311190.22162751100
1.369-1.40930.22751340.21972703100
1.4093-1.45480.23811450.21772720100
1.4548-1.50680.20221350.1989257896
1.5068-1.56710.19291430.1667271099
1.5671-1.63840.17561200.16152739100
1.6384-1.72470.1591580.16892707100
1.7247-1.83270.19381310.16862769100
1.8327-1.97420.16831300.18242731100
1.9742-2.17270.21041240.18062787100
2.1727-2.48670.17821430.17542751100
2.4867-3.13160.23721400.19922764100
3.1316-22.0870.20821470.1952280898

+
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://pdbjlvh1.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