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- PDB-6cv7: Mouse Protocadherin-15 Extracellular Cadherin Domains 1 through 3 -

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Basic information

Entry
Database: PDB / ID: 6cv7
TitleMouse Protocadherin-15 Extracellular Cadherin Domains 1 through 3
ComponentsProtocadherin-15
KeywordsCELL ADHESION / SIGNALING PROTEIN / Cadherin / Hair Cells / Hearing / Dimer
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 / adult walking behavior / auditory receptor cell stereocilium organization / 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: 1.692 Å
AuthorsDionne, G. / Shapiro, L.
CitationJournal: Neuron / Year: 2018
Title: Mechanotransduction by PCDH15 Relies on a Novel cis-Dimeric Architecture.
Authors: Dionne, G. / Qiu, X. / Rapp, M. / Liang, X. / Zhao, B. / Peng, G. / Katsamba, P.S. / Ahlsen, G. / Rubinstein, R. / Potter, C.S. / Carragher, B. / Honig, B. / Muller, U. / Shapiro, L.
History
DepositionMar 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 1.2Jun 23, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 4, 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)44,88819
Polymers42,8131
Non-polymers2,07518
Water8,791488
1
A: Protocadherin-15
hetero molecules

A: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,77638
Polymers85,6262
Non-polymers4,15036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_667-y+1,-x+1,-z+13/61
Unit cell
Length a, b, c (Å)114.444, 114.444, 172.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

21A-974-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protocadherin-15 /


Mass: 42812.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q99PJ1

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Sugars , 2 types, 8 molecules

#4: 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.: 5
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
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 498 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 3.8 Å3/Da / Density % sol: 67.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 35% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.692→99.111 Å / Num. obs: 73884 / % possible obs: 99.26 % / Redundancy: 18.2 % / Biso Wilson estimate: 29.23 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1154 / Rrim(I) all: 0.1186 / Net I/σ(I): 20.19
Reflection shellResolution: 1.692→1.753 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.97 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 6959 / CC1/2: 0.362 / % possible all: 92.5

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4APX

4apx


Resolution: 1.692→99.111 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.64
RfactorNum. reflection% reflection
Rfree0.1876 3694 5 %
Rwork0.1689 --
obs0.1699 73872 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.692→99.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 122 488 3510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0623187
X-RAY DIFFRACTIONf_angle_d1.6454293
X-RAY DIFFRACTIONf_dihedral_angle_d13.0621155
X-RAY DIFFRACTIONf_chiral_restr0.1515
X-RAY DIFFRACTIONf_plane_restr0.01558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6924-1.71460.38251130.40682141X-RAY DIFFRACTION81
1.7146-1.73810.37981410.36232683X-RAY DIFFRACTION100
1.7381-1.7630.33621400.31492671X-RAY DIFFRACTION100
1.763-1.78930.30831410.26882674X-RAY DIFFRACTION100
1.7893-1.81720.26261400.24792664X-RAY DIFFRACTION100
1.8172-1.8470.24551430.23572701X-RAY DIFFRACTION100
1.847-1.87890.20211400.21422668X-RAY DIFFRACTION100
1.8789-1.91310.22331410.20162680X-RAY DIFFRACTION100
1.9131-1.94990.19781410.19182669X-RAY DIFFRACTION100
1.9499-1.98970.18681410.18342687X-RAY DIFFRACTION100
1.9897-2.03290.25331410.17512690X-RAY DIFFRACTION100
2.0329-2.08020.18971410.17262683X-RAY DIFFRACTION100
2.0802-2.13220.20941430.17032709X-RAY DIFFRACTION100
2.1322-2.18990.23481410.16722675X-RAY DIFFRACTION100
2.1899-2.25430.19761420.15912706X-RAY DIFFRACTION100
2.2543-2.32710.17381430.16092713X-RAY DIFFRACTION100
2.3271-2.41030.1711420.15792708X-RAY DIFFRACTION100
2.4103-2.50680.20281440.16252712X-RAY DIFFRACTION100
2.5068-2.62090.18641420.16322717X-RAY DIFFRACTION100
2.6209-2.75910.19571440.16972742X-RAY DIFFRACTION100
2.7591-2.9320.19771450.16942732X-RAY DIFFRACTION100
2.932-3.15840.1661440.16882752X-RAY DIFFRACTION100
3.1584-3.47620.18711450.16432766X-RAY DIFFRACTION100
3.4762-3.97920.18521470.16262796X-RAY DIFFRACTION100
3.9792-5.01340.14981490.13452822X-RAY DIFFRACTION100
5.0134-99.28180.16161600.16043017X-RAY DIFFRACTION100
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)
14.4132-2.2988-1.56552.91431.06551.724-0.1129-0.10240.01470.16780.1167-0.1192-0.06090.2293-0.00160.24050.02770.00110.24960.00110.1593103.3567-28.4187178.6365
21.461-2.1783-0.78435.39751.33810.9855-0.1471-0.0493-0.06350.26880.08360.1650.1008-0.04930.06160.22810.01470.00840.1926-0.00410.194569.92866.8701185.171
31.9497-2.3103-0.57774.28490.85961.2932-0.2105-0.14070.06580.39080.14480.2271-0.1038-0.17690.06810.28550.06470.03520.2618-0.00180.253543.933446.0669197.9977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 121 )
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 239 )
3X-RAY DIFFRACTION3chain 'A' and (resid 240 through 366 )

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