[English] 日本語
Yorodumi
- PDB-5tfm: Crystal Structure of Human Cadherin-23 EC6-8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tfm
TitleCrystal Structure of Human Cadherin-23 EC6-8
ComponentsCadherin-23
KeywordsCELL ADHESION / hearing / mechanotransduction / adhesion / calcium-binding protein
Function / homology
Function and homology information


cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / photoreceptor ribbon synapse / cell-cell adhesion via plasma-membrane adhesion molecules / stereocilium / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / photoreceptor cell maintenance ...cochlear hair cell ribbon synapse / kinocilium / equilibrioception / sensory perception of light stimulus / stereocilium tip / photoreceptor ribbon synapse / cell-cell adhesion via plasma-membrane adhesion molecules / stereocilium / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / photoreceptor cell maintenance / catenin complex / auditory receptor cell stereocilium organization / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / response to stimulus / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / regulation of cytosolic calcium ion concentration / visual perception / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / cadherin binding / centrosome / calcium ion binding / membrane
Similarity search - Function
Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsJaiganesh, A. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)DC012534 United States
CitationJournal: Structure / Year: 2018
Title: Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness.
Authors: Jaiganesh, A. / De-la-Torre, P. / Patel, A.A. / Termine, D.J. / Velez-Cortes, F. / Chen, C. / Sotomayor, M.
History
DepositionSep 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_volume / _citation.page_first / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7097
Polymers37,4861
Non-polymers2236
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.407, 93.407, 122.386
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-1014-

HOH

-
Components

#1: Protein Cadherin-23 / / Otocadherin


Mass: 37485.625 Da / Num. of mol.: 1 / Fragment: Cadherin domains 6-8, residues 557-886
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH23, KIAA1774, KIAA1812, UNQ1894/PRO4340 / Plasmid: pET-21a / Production host: Escherichia coli BL21 / Strain (production host): BL21 RIPL / References: UniProt: Q9H251
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 4.12 Å3/Da / Density % sol: 70.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 0.1 M MES pH 6.8, 1.2 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Cryo-jet crystal cryocoolers
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.92→80.89 Å / Num. obs: 13518 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.08
Reflection shellResolution: 2.92→2.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TFL

5tfl


Resolution: 2.92→80.89 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.912 / SU B: 34.236 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 0.557 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24635 648 4.8 %RANDOM
Rwork0.19773 ---
obs0.20006 12825 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 88.416 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å21.28 Å20 Å2
2--2.57 Å2-0 Å2
3----8.32 Å2
Refinement stepCycle: 1 / Resolution: 2.92→80.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 6 24 2506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022529
X-RAY DIFFRACTIONr_bond_other_d0.0020.022365
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9633454
X-RAY DIFFRACTIONr_angle_other_deg0.89535453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89124.867113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30515404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5381514
X-RAY DIFFRACTIONr_chiral_restr0.070.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02543
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5425.5671280
X-RAY DIFFRACTIONr_mcbond_other1.5415.5681279
X-RAY DIFFRACTIONr_mcangle_it2.5768.3491597
X-RAY DIFFRACTIONr_mcangle_other2.5768.3481598
X-RAY DIFFRACTIONr_scbond_it1.5365.7621249
X-RAY DIFFRACTIONr_scbond_other1.5355.7621250
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6338.5721856
X-RAY DIFFRACTIONr_long_range_B_refined4.11864.1122606
X-RAY DIFFRACTIONr_long_range_B_other4.09664.112605
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.921→2.996 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 46 -
Rwork0.333 939 -
obs--99.9 %
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)
12.25472.0895-2.07816.9277-5.487210.1776-0.1273-0.3641-0.27260.52980.0092-0.0027-0.5245-0.60580.11810.11280.0852-0.01870.16720.06270.29686.250317.714158.8874
20.96661.3645-3.27742.9413-4.117211.9931-0.20150.56190.0602-0.33920.55460.03430.3945-1.719-0.3530.1117-0.18560.0070.5247-0.03170.148611.259735.983815.6401
32.90230.7295-0.59593.8187-2.6278.45320.26770.25110.148-0.6146-0.4144-0.18140.3065-0.17550.14670.3799-0.0850.09810.3404-0.07960.252923.14451.2558-31.6852
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A534 - 642
2X-RAY DIFFRACTION1A902 - 903
3X-RAY DIFFRACTION2A643 - 749
4X-RAY DIFFRACTION2A901
5X-RAY DIFFRACTION2A904 - 905
6X-RAY DIFFRACTION3A750 - 858
7X-RAY DIFFRACTION3A906

+
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