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- PDB-8z3f: Complex structure of CIB2 and TMC1 CR1 -

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Basic information

Entry
Database: PDB / ID: 8z3f
TitleComplex structure of CIB2 and TMC1 CR1
Components
  • Calcium and integrin-binding family member 2
  • Transmembrane channel-like protein 1
KeywordsMETAL BINDING PROTEIN / Calcium binding
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 / cellular response to ATP / photoreceptor outer segment / voltage-gated calcium channel activity / calcium ion homeostasis / photoreceptor inner segment / neuromuscular junction / sarcolemma / calcium ion transmembrane transport / calcium channel activity / integrin binding / positive regulation of cytosolic calcium ion concentration / external side of plasma membrane / calcium ion binding / protein-containing complex binding / magnesium ion binding / protein homodimerization activity / plasma membrane / cytosol / 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
Transmembrane channel-like protein 1 / Calcium and integrin-binding family member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsWu, S. / Lin, L. / Lu, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Dev.Cell / Year: 2025
Title: Mechano-electrical transduction components TMC1-CIB2 undergo a Ca 2+ -induced conformational change linked to hearing loss.
Authors: Wu, S. / Lin, L. / Hu, Q. / Yao, X. / Wang, H. / Liu, S. / Liu, Q. / Xi, Y. / Lin, Y. / Gong, J. / Hu, R. / Zhan, W. / Luo, Y. / He, G. / Liu, Z. / Xiong, W. / Wang, Q. / Xu, Z. / Bai, F. / Lu, Q.
History
DepositionApr 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,2715
Polymers28,1512
Non-polymers1203
Water4,702261
1
A: Calcium and integrin-binding family member 2
hetero molecules

B: Transmembrane channel-like protein 1


Theoretical massNumber of molelcules
Total (without water)28,2715
Polymers28,1512
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1400 Å2
ΔGint-44 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.177, 36.225, 63.496
Angle α, β, γ (deg.)90.000, 98.869, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

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Components

#1: Protein Calcium and integrin-binding family member 2 / Kinase-interacting protein 2 / KIP 2


Mass: 22009.951 Da / Num. of mol.: 1 / Mutation: E141N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cib2, Kip2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z309
#2: Protein Transmembrane channel-like protein 1 / Beethoven protein / Deafness protein / Transmembrane cochlear-expressed protein 1


Mass: 6141.225 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8R4P5
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 2-Proranol, MES monohydrate Ph 6.0, PEG monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 25075 / % possible obs: 98.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 15.93 Å2 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.063 / Rrim(I) all: 0.142 / Χ2: 0.662 / Net I/σ(I): 3.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.74-1.774.80.68412100.731198.5
1.77-1.812470.6861
1.8-1.8412380.7961
1.84-1.8712510.841
1.87-1.9212720.8811
1.92-1.9612090.8881
1.96-2.0112690.9191
2.01-2.0612360.9381
2.06-2.1212600.9411
2.12-2.1912210.9531
2.19-2.2712650.9661
2.27-2.3612500.9721
2.36-2.4712580.9771
2.47-2.612650.9771
2.6-2.7612530.9851
2.76-2.9812310.9851
2.98-3.2712970.9881
3.27-3.7512550.9911
3.75-4.7212650.9931
4.72-5013230.9931

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→25.52 Å / SU ML: 0.1408 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.6271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 1269 5.06 %
Rwork0.1774 23805 -
obs0.1785 25074 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.85 Å2
Refinement stepCycle: LAST / Resolution: 1.74→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 3 261 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751885
X-RAY DIFFRACTIONf_angle_d1.09642541
X-RAY DIFFRACTIONf_chiral_restr0.0607281
X-RAY DIFFRACTIONf_plane_restr0.0062332
X-RAY DIFFRACTIONf_dihedral_angle_d5.5744243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.810.25281480.21672539X-RAY DIFFRACTION95.93
1.81-1.890.23231390.20612624X-RAY DIFFRACTION99.14
1.89-1.990.2241370.18482663X-RAY DIFFRACTION99.08
1.99-2.120.20971310.18422631X-RAY DIFFRACTION98.57
2.12-2.280.20661350.18272658X-RAY DIFFRACTION98.52
2.28-2.510.22851310.17212643X-RAY DIFFRACTION99.07
2.51-2.870.19651450.17862645X-RAY DIFFRACTION98.14
2.87-3.620.17091520.16762681X-RAY DIFFRACTION99.33
3.62-25.520.18551510.16752721X-RAY DIFFRACTION98.02

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