[English] 日本語
Yorodumi
- PDB-8tri: Crystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tri
TitleCrystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A
ComponentsCadherin-23
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


kinocilium / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / inner ear receptor cell stereocilium organization / stereocilium tip / inner ear auditory receptor cell differentiation / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / stereocilium ...kinocilium / equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / inner ear receptor cell stereocilium organization / stereocilium tip / inner ear auditory receptor cell differentiation / photoreceptor ribbon synapse / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / stereocilium / photoreceptor cell maintenance / auditory receptor cell stereocilium organization / inner ear morphogenesis / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / cell adhesion / synapse / centrosome / calcium ion binding / plasma membrane
Similarity search - Function
Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.716 Å
AuthorsAshraf, Q. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 DC015271 United States
CitationJournal: To be published
Title: Crystal Structure of Mouse Cadherin-23 EC25-MAD28 F2894A
Authors: Ashraf, Q. / Sotomayor, M.
History
DepositionAug 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cadherin-23
B: Cadherin-23
C: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,43421
Polymers159,7133
Non-polymers72118
Water1629
1
A: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4787
Polymers53,2381
Non-polymers2406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4787
Polymers53,2381
Non-polymers2406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4787
Polymers53,2381
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.994, 164.657, 183.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Cadherin-23


Mass: 53237.551 Da / Num. of mol.: 3 / Fragment: residues 2603-3065 / Mutation: F2894A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q99PF4
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.96 Å3/Da / Density % sol: 82.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 1.25 M Lithium Acetate, 0.1 M MES pH 7.2, 25% glycerol (cryo)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 47174 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC1/2: 0.981 / CC star: 0.995 / Net I/σ(I): 11.5
Reflection shellResolution: 3.7→3.76 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 2309 / CC1/2: 0.56 / CC star: 0.847 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.716→49.563 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.187 / SU B: 22.316 / SU ML: 0.306 / Average fsc free: 0.9625 / Average fsc work: 0.9768 / Cross valid method: FREE R-VALUE / ESU R: 1.416 / ESU R Free: 0.422
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2294 2329 4.951 %
Rwork0.1871 44714 -
all0.189 --
obs-47043 98.678 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 124.855 Å2
Baniso -1Baniso -2Baniso -3
1-4.035 Å20 Å20 Å2
2--2.426 Å2-0 Å2
3----6.461 Å2
Refinement stepCycle: LAST / Resolution: 3.716→49.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10490 0 18 9 10517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01210687
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610158
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.65314566
X-RAY DIFFRACTIONr_angle_other_deg0.4991.57123283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.42851320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.794588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.336101751
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.87110552
X-RAY DIFFRACTIONr_chiral_restr0.0610.21681
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212850
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022482
X-RAY DIFFRACTIONr_nbd_refined0.2750.22424
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2380.210536
X-RAY DIFFRACTIONr_nbtor_refined0.1980.25176
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.26383
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2344
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0810.27
X-RAY DIFFRACTIONr_metal_ion_refined0.2660.264
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4220.226
X-RAY DIFFRACTIONr_nbd_other0.360.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.22
X-RAY DIFFRACTIONr_mcbond_it23.17911.9085298
X-RAY DIFFRACTIONr_mcbond_other23.16611.9095298
X-RAY DIFFRACTIONr_mcangle_it31.45621.4586612
X-RAY DIFFRACTIONr_mcangle_other31.45421.4596613
X-RAY DIFFRACTIONr_scbond_it27.75912.775389
X-RAY DIFFRACTIONr_scbond_other27.75712.775390
X-RAY DIFFRACTIONr_scangle_it36.62423.0717954
X-RAY DIFFRACTIONr_scangle_other36.62223.0717955
X-RAY DIFFRACTIONr_lrange_it40.939153.87444518
X-RAY DIFFRACTIONr_lrange_other40.939153.87344519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.716-3.8120.321330.29627590.29734680.9350.94783.3910.296
3.812-3.9150.341700.27632220.2834020.9330.95299.70610.276
3.915-4.0280.3081560.24830870.25132530.9360.96299.69260.248
4.028-4.1510.2771560.21930230.22231810.9480.9799.93710.219
4.151-4.2870.2741560.20529500.20831060.9480.9741000.205
4.287-4.4360.2511650.18828350.19130000.9580.9771000.188
4.436-4.6020.2531270.1727880.17329150.9590.9821000.17
4.602-4.7880.231140.15226620.15527760.9680.9861000.152
4.788-4.9990.1811430.13725390.1426820.980.9891000.137
4.999-5.240.1741330.13624540.13825870.9850.991000.136
5.24-5.520.221360.16323030.16724390.9760.9871000.163
5.52-5.850.2531100.17922210.18323310.9680.9851000.179
5.85-6.2480.2451090.1820720.18321830.9710.98599.90840.18
6.248-6.740.2181060.17719600.17920660.9780.9841000.177
6.74-7.370.218980.16218150.16519130.9790.9851000.162
7.37-8.2170.215900.14616430.14917350.9730.98799.88470.146
8.217-9.4450.176680.16414550.16515230.9850.9861000.164
9.445-11.4640.166660.1712720.1713380.9860.9861000.17
11.464-15.7950.19590.19110050.19110650.9820.98299.90610.191
15.795-49.5630.214340.2496490.2476830.9830.9741000.249

+
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