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- PDB-6mfo: Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N -

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Basic information

Entry
Database: PDB / ID: 6mfo
TitleCrystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N
ComponentsProtocadherin-15
KeywordsCELL ADHESION / Mechanotransduction / Calcium-binding protein / stereocilia / hair cell / tip link
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
Protocadherin-15 / Protocadherin-15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsChoudhary, D. / 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
DepositionSep 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Oct 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)43,2706
Polymers43,0691
Non-polymers2005
Water905
1
A: Protocadherin-15
hetero molecules

A: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,53912
Polymers86,1382
Non-polymers40110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)87.894, 116.516, 99.889
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: 43069.160 Da / Num. of mol.: 1 / 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 BL21 (bacteria) / Strain (production host): BL21 RIPL / References: UniProt: A0A087X1T6, UniProt: Q96QU1*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.97 Å3/Da / Density % sol: 58.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7 / Details: 0.1 M HEPES pH 7.7, 66% MPD, 4% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 9312 / % possible obs: 99.4 % / Redundancy: 9 % / Rmerge(I) obs: 0.362 / Rpim(I) all: 0.119 / Net I/σ(I): 6.8
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.384 / Num. unique obs: 460 / Rpim(I) all: 0.616 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4APX, 5ULY

4apx

5uly


Resolution: 3.15→49.99 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.869 / SU B: 44.508 / SU ML: 0.355 / Cross valid method: THROUGHOUT / ESU R Free: 0.505 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28841 442 4.8 %RANDOM
Rwork0.21454 ---
obs0.21806 8791 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 74.744 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å20 Å2
2---3.95 Å2-0 Å2
3---4.22 Å2
Refinement stepCycle: 1 / Resolution: 3.15→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 5 5 2639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0142686
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172384
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.6663662
X-RAY DIFFRACTIONr_angle_other_deg0.8171.635611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6735329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18723.067150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25215439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7281518
X-RAY DIFFRACTIONr_chiral_restr0.0580.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02446
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_it2.7816.2141328
X-RAY DIFFRACTIONr_mcbond_other2.786.2111327
X-RAY DIFFRACTIONr_mcangle_it4.529.3071653
X-RAY DIFFRACTIONr_mcangle_other4.529.311654
X-RAY DIFFRACTIONr_scbond_it2.8486.5721358
X-RAY DIFFRACTIONr_scbond_other2.8476.5751359
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7279.7482010
X-RAY DIFFRACTIONr_long_range_B_refined773.4352870
X-RAY DIFFRACTIONr_long_range_B_other773.4782870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.117→3.198 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 20 -
Rwork0.279 498 -
obs--75.84 %
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)
10.6149-1.25740.66453.9506-1.43051.04410.0340.0671-0.18360.01860.07120.1879-0.0992-0.0348-0.10530.05870.0251-0.05550.2569-0.0280.1088-33.7444-58.460234.9907
20.3511.0236-0.32083.0051-0.88710.73780.03770.00410.01220.12090.0780.02860.02710.0207-0.11580.0143-0.0089-0.01410.29660.01350.0252-34.8343-15.076513.5346
30.35770.4654-0.75326.4704-2.25941.9861-0.0037-0.0516-0.0133-0.0075-0.1129-0.1525-0.1480.0870.11670.2283-0.0022-0.09190.07150.00730.0409-23.479230.57742.1663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 120
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2A121 - 238
4X-RAY DIFFRACTION2A403
5X-RAY DIFFRACTION2A405
6X-RAY DIFFRACTION3A239 - 364
7X-RAY DIFFRACTION3A404

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