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- PDB-6n2e: Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370... -

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Basic information

Entry
Database: PDB / ID: 6n2e
TitleCrystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E
Components
  • Cadherin-23
  • Protocadherin-15
KeywordsCELL ADHESION / Mechanotransduction / Calcium-binding protein / stereocilia / hair cell / tip link
Function / homology
Function and homology information


equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / kinocilium / inner ear auditory receptor cell differentiation / calcium-dependent cell-cell adhesion / stereocilium ...equilibrioception / sensory perception of light stimulus / cochlear hair cell ribbon synapse / stereocilium tip / inner ear receptor cell stereocilium organization / photoreceptor ribbon synapse / kinocilium / inner ear auditory receptor cell differentiation / calcium-dependent cell-cell adhesion / stereocilium / photoreceptor cell maintenance / auditory receptor cell stereocilium organization / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / inner ear morphogenesis / homophilic cell-cell adhesion / inner ear development / cochlea development / photoreceptor outer segment / regulation of cytosolic calcium ion concentration / photoreceptor inner segment / locomotory behavior / sensory perception of sound / calcium ion transport / cell adhesion / calcium ion binding / synapse / centrosome / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin-like - #3430 / : / PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherins / Cadherin conserved site / Cadherin domain signature. ...Immunoglobulin-like - #3430 / : / 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
Protocadherin-15 / Protocadherin-15 / Cadherin-23
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChoudhary, D. / De-la-Torre, P. / Sotomayor, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 DC015271 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception.
Authors: Choudhary, D. / Narui, Y. / Neel, B.L. / Wimalasena, L.N. / Klanseck, C.F. / De-la-Torre, P. / Chen, C. / Araya-Secchi, R. / Tamilselvan, E. / Sotomayor, M.
History
DepositionNov 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 7, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.3Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 11, 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protocadherin-15
B: Protocadherin-15
C: Cadherin-23
D: Cadherin-23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,62922
Polymers133,9074
Non-polymers72118
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-103 kcal/mol
Surface area57200 Å2
Unit cell
Length a, b, c (Å)76.792, 65.397, 190.015
Angle α, β, γ (deg.)90.00, 99.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protocadherin-15


Mass: 43069.160 Da / Num. of mol.: 2 / Mutation: G16D, N369D, Q370N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH15 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: A0A087X1T6, UniProt: Q96QU1*PLUS
#2: Protein Cadherin-23 / Otocadherin


Mass: 23884.445 Da / Num. of mol.: 2 / Mutation: T15E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh23 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q99PF4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.52 Å3/Da / Density % sol: 65.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Imidazole pH 6.8, 46% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 41847 / % possible obs: 93.2 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.055 / Net I/σ(I): 12.33
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.4 % / Num. unique obs: 1806 / Rpim(I) all: 0.236 / % possible all: 86.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFO, 4AQ8

6mfo

4aq8


Resolution: 2.9→49.52 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.908 / SU B: 22.739 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25332 1909 4.9 %RANDOM
Rwork0.22464 ---
obs0.22605 37058 92.36 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 75.813 Å2
Baniso -1Baniso -2Baniso -3
1--7.42 Å2-0 Å2-49.81 Å2
2--63.34 Å20 Å2
3----55.93 Å2
Refinement stepCycle: 1 / Resolution: 2.9→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8699 0 18 62 8779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138902
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178048
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.65512172
X-RAY DIFFRACTIONr_angle_other_deg1.281.57218738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.35851091
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55323.084509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.887151409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8971560
X-RAY DIFFRACTIONr_chiral_restr0.0750.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0210005
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021767
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_it0.2350.4594388
X-RAY DIFFRACTIONr_mcbond_other0.2350.4594387
X-RAY DIFFRACTIONr_mcangle_it0.4330.6875471
X-RAY DIFFRACTIONr_mcangle_other0.4330.6875472
X-RAY DIFFRACTIONr_scbond_it0.2460.4684514
X-RAY DIFFRACTIONr_scbond_other0.2460.4684512
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4170.6976701
X-RAY DIFFRACTIONr_long_range_B_refined2.7838.81834156
X-RAY DIFFRACTIONr_long_range_B_other2.7428.76734128
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.891→2.966 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 125 -
Rwork0.299 2375 -
obs--79.24 %
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)
12.90390.25522.60680.6287-0.3933.9007-0.09091.1178-0.1009-0.35440.1007-0.0186-0.02870.2664-0.00981.1359-0.0638-0.03271.91530.05210.8618-0.954712.19499.7283
21.20830.0660.21750.7141-0.19697.2301-0.01110.67610.0387-0.2727-0.028-0.120.02380.09770.03910.7029-0.00810.03080.46730.02940.707612.523112.706755.5623
31.5693-0.12640.22790.92370.04324.3956-0.1748-0.340.03370.1762-0.0520.03650.0157-0.24330.22680.6998-0.01630.05790.09270.01060.68313.461417.8278104.8923
42.9505-0.46412.15341.2221-0.3233.95770.18630.8556-0.2918-0.2126-0.02320.11710.07530.0798-0.16310.732-0.0150.04760.8268-0.15230.7633-45.5745-9.666737.5133
55.98941.80312.32130.76040.88151.23190.09550.06020.03530.0371-0.05520.13560.0826-0.2119-0.04040.7542-0.13170.04240.2302-0.00720.7078-9.6248-2.681270.8682
62.3617-0.02370.34542.89670.65142.75140.0862-0.01360.00430.5250.0753-0.50220.46350.2865-0.16150.78630.0412-0.0210.03230.01020.750432.19773.864596.8403
73.2830.33952.88031.23431.0414.78220.03050.90440.2656-0.19750.0251-0.2229-0.38530.2882-0.05560.9232-0.02540.09051.40590.15190.9772-36.2432.708926.8178
85.2302-1.64614.04560.8583-1.31963.25440.05510.1727-0.7448-0.07440.44720.3143-0.0579-0.2621-0.50240.9412-0.0835-0.01881.7668-0.01321.0856-14.3315-0.439813.3216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 119
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2A120 - 238
4X-RAY DIFFRACTION2A403 - 404
5X-RAY DIFFRACTION3A239 - 368
6X-RAY DIFFRACTION3A405
7X-RAY DIFFRACTION4B5 - 119
8X-RAY DIFFRACTION4B401 - 402
9X-RAY DIFFRACTION5B120 - 238
10X-RAY DIFFRACTION5B403
11X-RAY DIFFRACTION5B405
12X-RAY DIFFRACTION6B239 - 369
13X-RAY DIFFRACTION6B404
14X-RAY DIFFRACTION7C2 - 198
15X-RAY DIFFRACTION7C301 - 303
16X-RAY DIFFRACTION8D2 - 198
17X-RAY DIFFRACTION8D301 - 303

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