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- PDB-5kj4: Crystal Structure of Mouse Protocadherin-15 EC9-10 -

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Basic information

Entry
Database: PDB / ID: 5kj4
TitleCrystal Structure of Mouse Protocadherin-15 EC9-10
ComponentsProtocadherin-15
KeywordsCalcium-binding protein / hearing / mechanotransduction / adhesion
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / inner ear receptor cell stereocilium organization / righting reflex / inner ear auditory receptor cell differentiation / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior ...detection of mechanical stimulus involved in equilibrioception / inner ear receptor cell stereocilium organization / righting reflex / inner ear auditory receptor cell differentiation / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior / startle response / homophilic cell-cell adhesion / inner ear development / actin filament bundle assembly / photoreceptor outer segment / visual perception / actin filament organization / morphogenesis of an epithelium / locomotory behavior / sensory perception of sound / response to calcium ion / multicellular organism growth / calcium ion binding / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...: / PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsAraya-Secchi, R. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R00 DC012534 United States
CitationJournal: Nat Commun / Year: 2016
Title: An elastic element in the protocadherin-15 tip link of the inner ear.
Authors: Araya-Secchi, R. / Neel, B.L. / Sotomayor, M.
History
DepositionJun 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protocadherin-15
B: Protocadherin-15
C: Protocadherin-15
D: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,36616
Polymers103,8854
Non-polymers48112
Water45025
1
A: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0914
Polymers25,9711
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0914
Polymers25,9711
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0914
Polymers25,9711
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0914
Polymers25,9711
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.541, 143.541, 95.599
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA898 - 11251 - 228
21GLUGLUBB898 - 11251 - 228
12ASPASPAA898 - 11181 - 221
22ASPASPCC898 - 11181 - 221
13ASPASPAA898 - 11181 - 221
23ASPASPDD898 - 11181 - 221
14ASPASPBB898 - 11181 - 221
24ASPASPCC898 - 11181 - 221
15ASPASPBB898 - 11181 - 221
25ASPASPDD898 - 11181 - 221
16HISHISCC898 - 11191 - 222
26HISHISDD898 - 11191 - 222

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Protocadherin-15


Mass: 25971.160 Da / Num. of mol.: 4 / Fragment: Cadherin 9 and 10, residues 924-1149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21 / References: UniProt: Q99PJ1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 5.71 Å3/Da / Density % sol: 78.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.095M HEPES (pH7.5), 0.19M CaCl2, 26.6% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: oxford cryo-jet crystal cryocoolers
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.258
11-K, -H, -L20.244
11-h,-k,l30.244
11K, H, -L40.254
ReflectionResolution: 3.35→50 Å / Num. obs: 31590 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 69.9 Å2 / CC1/2: 0.91 / Rmerge(I) obs: 0.256 / Net I/σ(I): 6.96
Reflection shellResolution: 3.35→3.41 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 2.03 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XHZ

4xhz


Resolution: 3.35→46.98 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.889 / SU B: 16.758 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.068 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 1367 4.3 %RANDOM
Rwork0.15789 ---
obs0.15943 30204 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.308 Å2
Baniso -1Baniso -2Baniso -3
1-6.01 Å20 Å20 Å2
2--6.01 Å20 Å2
3----12.02 Å2
Refinement stepCycle: LAST / Resolution: 3.35→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6986 0 12 25 7023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197140
X-RAY DIFFRACTIONr_bond_other_d0.0020.026758
X-RAY DIFFRACTIONr_angle_refined_deg1.0781.9719766
X-RAY DIFFRACTIONr_angle_other_deg0.688315576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92624.259324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.094151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1131552
X-RAY DIFFRACTIONr_chiral_restr0.060.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021514
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_it1.5974.9943596
X-RAY DIFFRACTIONr_mcbond_other1.5974.9933595
X-RAY DIFFRACTIONr_mcangle_it2.6827.4874488
X-RAY DIFFRACTIONr_mcangle_other2.6827.4884489
X-RAY DIFFRACTIONr_scbond_it1.3485.0993544
X-RAY DIFFRACTIONr_scbond_other1.3485.0993545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3097.6115279
X-RAY DIFFRACTIONr_long_range_B_refined6.01595.91928626
X-RAY DIFFRACTIONr_long_range_B_other6.01595.91928627
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A139800.08
12B139800.08
21A136980.07
22C136980.07
31A136140.08
32D136140.08
41B139060.06
42C139060.06
51B139100.06
52D139100.06
61C138520.06
62D138520.06
LS refinement shellResolution: 3.354→3.441 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 106 -
Rwork0.215 2257 -
obs--99.54 %
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)
10.539-0.4474-0.03890.39950.04090.0141-0.2668-0.3641-0.08060.30350.2691-0.02750.05440.0516-0.00230.60820.0211-0.09760.46770.19210.461611.515532.442116.1228
21.00131.3458-0.83884.4841-1.00021.16290.03280.0651-0.1962-0.47070.0267-0.3607-0.143-0.2187-0.05960.15290.04020.06980.07570.03390.2332-10.541315.1988-10.4764
30.7548-0.7954-0.6871.42261.92753.1281-0.3127-0.19080.03510.1505-0.1340.2325-0.0836-0.53070.44660.47980.04480.0260.3136-0.16230.4064-10.408553.138114.6756
42.34181.70990.4912.23311.12910.7334-0.13040.1239-0.2102-0.17810.2362-0.185-0.0390.1471-0.10580.2355-0.03190.01870.04880.00350.223912.728368.666-11.7257
51.4691.0778-1.04310.8249-0.70990.90120.08340.14320.2290.03030.15360.0625-0.18470.1413-0.2370.4485-0.02870.03420.49520.06910.519610.340949.6391-53.9602
63.1263-4.0191-1.10975.53021.64411.6875-0.0826-0.0893-0.00380.21830.2112-0.05560.01170.01-0.12860.14560.0241-0.02010.0427-0.03920.1436-9.524666.1447-26.4288
71.47880.70921.78320.59371.2033.0382-0.07160.05990.00410.0025-0.16860.28540.3171-0.41790.24020.5305-0.0743-0.03110.3701-0.09710.3882-10.57229.6403-51.7138
83.7828-3.22480.23024.0774-0.13490.92640.0426-0.06580.01020.12220.16030.0313-0.06260.108-0.20290.11170.002-0.05010.0262-0.00120.19312.149115.824-25.3439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A898 - 1006
2X-RAY DIFFRACTION1A2001
3X-RAY DIFFRACTION2A1007 - 1125
4X-RAY DIFFRACTION2A2002 - 2003
5X-RAY DIFFRACTION3B898 - 1006
6X-RAY DIFFRACTION3B2001
7X-RAY DIFFRACTION4B1007 - 1125
8X-RAY DIFFRACTION4B2002 - 2003
9X-RAY DIFFRACTION5C898 - 1006
10X-RAY DIFFRACTION5C2001
11X-RAY DIFFRACTION6C1007 - 1119
12X-RAY DIFFRACTION6C2002 - 2003
13X-RAY DIFFRACTION7D898 - 1006
14X-RAY DIFFRACTION7D2001
15X-RAY DIFFRACTION8D1007 - 1119
16X-RAY DIFFRACTION8D2002 - 2003

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