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- PDB-4xhz: Crystal Structure of Human Protocadherin-15 EC8-10 -

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Basic information

Entry
Database: PDB / ID: 4xhz
TitleCrystal Structure of Human Protocadherin-15 EC8-10
ComponentsProtocadherin-15
KeywordsCELL ADHESION / hearing / mechanotransduction / adhesion / calcium-binding protein
Function / homology
Function and homology information


equilibrioception / sensory perception of light stimulus / stereocilium / photoreceptor cell maintenance / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / sensory perception of sound ...equilibrioception / sensory perception of light stimulus / stereocilium / photoreceptor cell maintenance / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / homophilic cell adhesion via plasma membrane adhesion molecules / inner ear development / photoreceptor outer segment / sensory perception of sound / cell adhesion / synapse / calcium ion binding / extracellular space / extracellular region / plasma membrane
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 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)K99/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
DepositionJan 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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
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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)37,5865
Polymers37,4301
Non-polymers1564
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.929, 157.929, 142.898
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2101-

HOH

21A-2117-

HOH

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Components

#1: Protein Protocadherin-15 /


Mass: 37430.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH15, USH1F / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q96QU1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.76 Å3/Da / Density % sol: 81.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES (pH6.5), 1.6M NaCl

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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-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→136.77 Å / Num. obs: 26222 / % possible obs: 99.41 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 73.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 24.95
Reflection shellResolution: 2.803→2.876 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 4.09 / % possible all: 99.68

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UBH, 1EDH, 3Q2W

3ubh

1edh

3q2w


Resolution: 2.803→136.77 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 14.63 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19954 1270 4.8 %RANDOM
Rwork0.17003 ---
obs0.17145 24952 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.383 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å2-0 Å2
2--0.08 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.803→136.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 4 68 2664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192654
X-RAY DIFFRACTIONr_ext_dist_refined_d0.2480.01189
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.9733633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1735332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93424.53117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35815415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.371514
X-RAY DIFFRACTIONr_chiral_restr0.0720.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0222035
X-RAY DIFFRACTIONr_nbd_refined0.2380.31080
X-RAY DIFFRACTIONr_nbtor_refined0.3370.51868
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.5148
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other0.1120.511
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.330
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.54
X-RAY DIFFRACTIONr_mcbond_it5.3195.4021331
X-RAY DIFFRACTIONr_mcangle_it7.3748.0951662
X-RAY DIFFRACTIONr_scbond_it7.4435.6821322
X-RAY DIFFRACTIONr_scangle_it9.6178.3531971
X-RAY DIFFRACTIONr_lrange_it11.58551.74411199
LS refinement shellResolution: 2.803→2.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 95 -
Rwork0.356 1800 -
obs--99.89 %
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)
11.3762-1.21721.98512.5581-1.82912.9487-0.0594-0.0128-0.2522-0.17780.37030.1699-0.01750.0455-0.31090.09950.0003-0.0060.16990.03880.2171181.6435315.6607129.9337
22.5587-1.32150.79761.21890.1680.8786-0.19570.0253-0.0046-0.11870.07140.1058-0.30790.09330.12430.23590.0671-0.01920.15350.04150.0791219.1037287.8975139.1693
31.55440.6844-0.14020.37820.44523.57590.22460.07210.05090.07110.0634-0.028-0.0790.0118-0.2880.1462-0.0372-0.02540.1329-0.07710.1546244.4357287.4404165.7406
40.11130.6257-0.28043.9016-1.69240.75260.1569-0.0360.01160.7346-0.08690.1822-0.36070.1247-0.070.2732-0.1632-0.01540.4626-0.01820.0435242.5591292.0895198.6684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A795 - 898
2X-RAY DIFFRACTION1A2002 - 2003
3X-RAY DIFFRACTION2A899 - 1009
4X-RAY DIFFRACTION2A2001
5X-RAY DIFFRACTION3A1010 - 1112
6X-RAY DIFFRACTION4A1113 - 1127

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