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- PDB-6eet: Crystal structure of mouse Protocadherin-15 EC9-MAD12 -

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Basic information

Entry
Database: PDB / ID: 6eet
TitleCrystal structure of mouse Protocadherin-15 EC9-MAD12
ComponentsProtocadherin-15
KeywordsCELL ADHESION / Mechanotransduction / calcium binding protein / hearing / stereocilia / tip link
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / inner ear auditory receptor cell differentiation / stereocilium / non-motile cilium assembly / photoreceptor cell maintenance ...detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / inner ear receptor cell stereocilium organization / righting reflex / detection of mechanical stimulus involved in sensory perception of sound / inner ear auditory receptor cell differentiation / stereocilium / non-motile cilium assembly / photoreceptor cell maintenance / auditory receptor cell stereocilium organization / adult walking behavior / startle response / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / visual perception / locomotory behavior / actin filament organization / morphogenesis of an epithelium / sensory perception of sound / multicellular organism growth / response to calcium ion / cell adhesion / synapse / calcium ion binding / extracellular space / membrane / plasma membrane / cytoplasm
Similarity search - Function
Extracellular cadherin domain / Protocadherin-15 / Extracellular Cadherin domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Protocadherin-15
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsNarui, Y. / 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
DepositionAug 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 7, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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
Revision 2.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,70511
Polymers52,9171
Non-polymers1,78810
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Multi-angle light scattering verified that the protein is a dimer in solution., gel filtration, Based upon the retention volume, the protein is likely to be a dimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint8 kcal/mol
Surface area23850 Å2
Unit cell
Length a, b, c (Å)129.507, 170.059, 91.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protocadherin-15 /


Mass: 52916.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 / Plasmid: pHis-N1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q99PJ1
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 4.77 Å3/Da / Density % sol: 74.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium salt, 30% (w/v) MPD, 5% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. obs: 16630 / % possible obs: 99.5 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.166 / Χ2: 1.027 / Net I/σ(I): 14.529
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 2.222 / Num. unique obs: 785 / Χ2: 1.091 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000v717data reduction
HKL-2000v717data scaling
PHASERv2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BXZ, 4XHZ

6bxz

4xhz


Resolution: 3.23→45.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 16.838 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.922 / ESU R Free: 0.367 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 790 4.8 %RANDOM
Rwork0.17568 ---
obs0.17854 15743 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 94.283 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å20 Å2-0 Å2
2--1.9 Å20 Å2
3----5.23 Å2
Refinement stepCycle: 1 / Resolution: 3.23→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3476 0 108 0 3584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0143658
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173305
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.7044983
X-RAY DIFFRACTIONr_angle_other_deg0.8091.6687768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2285442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25322.169189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.55415594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2871526
X-RAY DIFFRACTIONr_chiral_restr0.060.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
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_it5.9939.4261771
X-RAY DIFFRACTIONr_mcbond_other5.9749.4251770
X-RAY DIFFRACTIONr_mcangle_it8.76714.1382212
X-RAY DIFFRACTIONr_mcangle_other8.76614.1412213
X-RAY DIFFRACTIONr_scbond_it6.65910.0941884
X-RAY DIFFRACTIONr_scbond_other6.6510.0941884
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.23414.9532771
X-RAY DIFFRACTIONr_long_range_B_refined12.484068
X-RAY DIFFRACTIONr_long_range_B_other12.4864068
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.226→3.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 57 -
Rwork0.278 1065 -
obs--91.52 %

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