[English] 日本語
Yorodumi
- PDB-6wud: Human Calcium and Integrin Binding Protein 3 Bound to TMC1 Residu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wud
TitleHuman Calcium and Integrin Binding Protein 3 Bound to TMC1 Residues 303-347
Components
  • Calcium and integrin-binding family member 3
  • Transmembrane channel-like protein 1
KeywordsMETAL BINDING/TRANSPORT PROTEIN / EF-hand / Mechanotransduction / hearing / METAL BINDING PROTEIN / METAL BINDING-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


vestibular reflex / stereocilium tip / detection of mechanical stimulus involved in sensory perception of sound / auditory receptor cell development / regulation of calcium ion transmembrane transport / plasma membrane => GO:0005886 / voltage-gated calcium channel activity / calcium ion homeostasis / calcium ion transmembrane transport / external side of plasma membrane ...vestibular reflex / stereocilium tip / detection of mechanical stimulus involved in sensory perception of sound / auditory receptor cell development / regulation of calcium ion transmembrane transport / plasma membrane => GO:0005886 / voltage-gated calcium channel activity / calcium ion homeostasis / calcium ion transmembrane transport / external side of plasma membrane / calcium ion binding / magnesium ion binding
Similarity search - Function
TMC domain / Transmembrane channel-like protein / TMC domain / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Transmembrane channel-like protein 1 / Calcium and integrin-binding family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsShapiro, L. / Dionne, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)5R01DC016960-03 United States
CitationJournal: Neuron / Year: 2021
Title: CIB2 and CIB3 are auxiliary subunits of the mechanotransduction channel of hair cells.
Authors: Liang, X. / Qiu, X. / Dionne, G. / Cunningham, C.L. / Pucak, M.L. / Peng, G. / Kim, Y.H. / Lauer, A. / Shapiro, L. / Muller, U.
History
DepositionMay 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calcium and integrin-binding family member 3
B: Transmembrane channel-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6404
Polymers28,5912
Non-polymers492
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Proteins co-elute off of gel filtration column
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-22 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.650, 100.650, 49.723
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein Calcium and integrin-binding family member 3 / Kinase-interacting protein 3 / KIP 3


Mass: 22309.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CIB3, KIP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96Q77
#2: Protein Transmembrane channel-like protein 1 / Beethoven protein / Deafness protein / Transmembrane cochlear-expressed protein 1


Mass: 6281.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tmc1, Bth, dn / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R4P5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 25% PEG 3350 0.2M Magnesium Chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.77 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 1.838→87.17 Å / Num. obs: 23155 / % possible obs: 90.83 % / Redundancy: 17.8 % / Biso Wilson estimate: 27.65 Å2 / CC1/2: 0.999 / Net I/σ(I): 20.93
Reflection shellResolution: 1.838→1.904 Å / Num. unique obs: 1806 / CC1/2: 0.864 / % possible all: 72.18

-
Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WU7

6wu7


Resolution: 1.84→87.17 Å / SU ML: 0.1683 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.7705
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1876 3844 8.65 %
Rwork0.1635 40587 -
obs0.1656 44431 90.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.95 Å2
Refinement stepCycle: LAST / Resolution: 1.84→87.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 2 164 2046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151925
X-RAY DIFFRACTIONf_angle_d1.08772607
X-RAY DIFFRACTIONf_chiral_restr0.0628278
X-RAY DIFFRACTIONf_plane_restr0.0076343
X-RAY DIFFRACTIONf_dihedral_angle_d21.1158708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.860.3179990.2418989X-RAY DIFFRACTION61.05
1.86-1.890.241190.23971189X-RAY DIFFRACTION72.67
1.89-1.910.21831200.21791353X-RAY DIFFRACTION79.84
1.91-1.940.26571290.19471357X-RAY DIFFRACTION82.24
1.94-1.970.20621300.18431379X-RAY DIFFRACTION83.65
1.97-20.2061420.17831415X-RAY DIFFRACTION85.6
2-2.030.21361340.16741418X-RAY DIFFRACTION87.24
2.03-2.070.19771520.17311467X-RAY DIFFRACTION87.89
2.07-2.10.16451340.16591506X-RAY DIFFRACTION89.13
2.11-2.150.20831400.16671469X-RAY DIFFRACTION89.24
2.15-2.190.20631440.1621459X-RAY DIFFRACTION89.8
2.19-2.240.16791460.15691527X-RAY DIFFRACTION91.07
2.24-2.290.20961400.14461515X-RAY DIFFRACTION92.67
2.29-2.350.17031530.15591562X-RAY DIFFRACTION94.08
2.35-2.410.19161450.15961582X-RAY DIFFRACTION95.1
2.41-2.480.20941470.15381597X-RAY DIFFRACTION94.53
2.48-2.560.18361490.16571592X-RAY DIFFRACTION96.99
2.56-2.650.21591440.16811599X-RAY DIFFRACTION96.4
2.65-2.760.1711560.17451606X-RAY DIFFRACTION95.81
2.76-2.880.23771550.16111601X-RAY DIFFRACTION96.59
2.88-3.040.21491500.17471607X-RAY DIFFRACTION98.27
3.04-3.230.18751560.1761626X-RAY DIFFRACTION97.75
3.23-3.470.15951620.15491639X-RAY DIFFRACTION98.36
3.47-3.820.1481430.14841630X-RAY DIFFRACTION98.12
3.83-4.380.1681560.14091617X-RAY DIFFRACTION97.52
4.38-5.510.18071620.14481633X-RAY DIFFRACTION99.28
5.52-87.170.19321370.19351653X-RAY DIFFRACTION98.03

+
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