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- PDB-6wud: Human Calcium and Integrin Binding Protein 3 Bound to TMC1 Residu... -

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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 / auditory receptor cell development / detection of mechanical stimulus involved in sensory perception of sound / mechanosensitive monoatomic ion channel activity / stereocilium / regulation of calcium ion transmembrane transport / calcium ion homeostasis / voltage-gated calcium channel activity / calcium ion transmembrane transport ...vestibular reflex / stereocilium tip / auditory receptor cell development / detection of mechanical stimulus involved in sensory perception of sound / mechanosensitive monoatomic ion channel activity / stereocilium / regulation of calcium ion transmembrane transport / calcium ion homeostasis / voltage-gated calcium channel activity / calcium ion transmembrane transport / calcium channel activity / external side of plasma membrane / calcium ion binding / magnesium ion binding / plasma membrane
Similarity search - Function
TMC domain / Transmembrane channel-like protein / TMC domain / : / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...TMC domain / Transmembrane channel-like protein / TMC domain / : / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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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: 2.54 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

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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

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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

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