[English] 日本語
Yorodumi
- PDB-8xoq: Human Calcium and Integrin Binding Protein 2 (CIB2) Fusion to TMC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xoq
TitleHuman Calcium and Integrin Binding Protein 2 (CIB2) Fusion to TMC1 CBD-1 domain at 2.4 Angstroms resolution
ComponentsTransmembrane channel-like protein 1,Calcium and integrin-binding family member 2
KeywordsMETAL BINDING PROTEIN / CIB2
Function / homology
Function and homology information


vestibular reflex / muscle tendon junction / cuticular plate / stereocilium tip / detection of mechanical stimulus involved in sensory perception of sound / auditory receptor cell development / mechanosensitive monoatomic ion channel activity / stereocilium / regulation of calcium ion transmembrane transport / photoreceptor cell maintenance ...vestibular reflex / muscle tendon junction / cuticular plate / stereocilium tip / detection of mechanical stimulus involved in sensory perception of sound / auditory receptor cell development / mechanosensitive monoatomic ion channel activity / stereocilium / regulation of calcium ion transmembrane transport / photoreceptor cell maintenance / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / cellular response to ATP / photoreceptor outer segment / voltage-gated calcium channel activity / calcium ion homeostasis / photoreceptor inner segment / cell periphery / neuromuscular junction / sarcolemma / calcium channel activity / integrin binding / positive regulation of cytosolic calcium ion concentration / blood microparticle / external side of plasma membrane / calcium ion binding / magnesium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
TMC domain / Transmembrane channel-like protein / TMC domain / : / EF-hand domain pair / EF-hand, calcium binding motif / 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
Calcium and integrin-binding family member 2 / Transmembrane channel-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsLi, Y.H. / Chen, J.S. / Zhang, X. / Wang, C.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Commun Biol / Year: 2025
Title: Structural insights into calcium-dependent CIB2-TMC1 interaction in hair cell mechanotransduction.
Authors: Li, Y. / Chen, J. / Jiang, W. / Ye, J. / Zhang, X. / Wang, C.
History
DepositionJan 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transmembrane channel-like protein 1,Calcium and integrin-binding family member 2
B: Transmembrane channel-like protein 1,Calcium and integrin-binding family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4716
Polymers57,3742
Non-polymers974
Water1,58588
1
A: Transmembrane channel-like protein 1,Calcium and integrin-binding family member 2
hetero molecules

B: Transmembrane channel-like protein 1,Calcium and integrin-binding family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4716
Polymers57,3742
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1100 Å2
ΔGint-8 kcal/mol
Surface area26060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.065, 121.849, 62.208
Angle α, β, γ (deg.)90.00, 91.74, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Transmembrane channel-like protein 1,Calcium and integrin-binding family member 2 / Transmembrane cochlear-expressed protein 1 / Kinase-interacting protein 2 / KIP 2


Mass: 28686.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMC1, CIB2, KIP2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8TDI8, UniProt: O75838
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) Polyethylene glycol 3350, 0.1 M Tris (pH 8.5), 0.2 M Magnesium chloride hexahydrate.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 18424 / % possible obs: 99.4 % / Redundancy: 6.3 % / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.052 / Rrim(I) all: 0.134 / Χ2: 0.977 / Net I/σ(I): 7 / Num. measured all: 115387
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.445.40.2639460.9480.9870.1190.2890.81699.5
2.44-2.495.40.2549070.9480.9870.1160.280.87699.7
2.49-2.535.50.2669050.9110.9760.1230.2940.899.3
2.53-2.595.60.249310.950.9870.110.2640.95999.9
2.59-2.645.60.2319330.9620.990.1050.2540.92699.6
2.64-2.75.80.2259050.9660.9910.1010.2470.96999.2
2.7-2.775.50.2248710.9660.9910.1040.2481.07398.4
2.77-2.855.80.2299350.9650.9910.1060.2531.10599.2
2.85-2.936.30.219410.9740.9930.0910.2291.07399.9
2.93-3.026.50.2148890.9740.9930.0910.2331.00699.8
3.02-3.136.60.2079400.9790.9950.0880.2250.99299.5
3.13-3.266.60.1889190.9850.9960.0790.2041.03699.9
3.26-3.416.30.1559070.9810.9950.0660.1691.0799.5
3.41-3.586.80.1399440.9880.9970.0570.150.96299.6
3.58-3.817.10.1168980.9910.9980.0470.1250.92499.7
3.81-4.170.0979390.9930.9980.0390.1050.98599.7
4.1-4.526.60.0839190.9920.9980.0350.090.89998.4
4.52-5.177.10.0829230.9930.9980.0330.0890.90599.9
5.17-6.516.90.0889330.990.9970.0360.0961.00899.7
6.51-506.80.1119390.9750.9940.0460.121.09998.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→43.55 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.575 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.72 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24223 908 4.9 %RANDOM
Rwork0.20133 ---
obs0.20334 17492 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.379 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--0.49 Å20 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 2.41→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3806 0 4 88 3898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123889
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163752
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.865226
X-RAY DIFFRACTIONr_angle_other_deg0.4931.7918702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9165465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.341519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83310752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024427
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02837
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_it2.413.7591875
X-RAY DIFFRACTIONr_mcbond_other2.4093.7581875
X-RAY DIFFRACTIONr_mcangle_it3.7666.762335
X-RAY DIFFRACTIONr_mcangle_other3.7676.762336
X-RAY DIFFRACTIONr_scbond_it3.0094.0372014
X-RAY DIFFRACTIONr_scbond_other3.0094.0372015
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9087.2892892
X-RAY DIFFRACTIONr_long_range_B_refined6.41849.14311
X-RAY DIFFRACTIONr_long_range_B_other6.41849.164300
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.468 Å
RfactorNum. reflection% reflection
Rfree0.284 86 -
Rwork0.219 1259 -
obs--95.39 %

+
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