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- PDB-6eb5: Crystal Structure of Human Protocadherin-15 EC2-3 V250N -

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Basic information

Entry
Database: PDB / ID: 6eb5
TitleCrystal Structure of Human Protocadherin-15 EC2-3 V250N
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
PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like ...PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionAug 4, 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 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 6, 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
B: Protocadherin-15
A: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0228
Polymers58,7812
Non-polymers2406
Water72140
1
B: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5114
Polymers29,3911
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5114
Polymers29,3911
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.184, 31.945, 115.955
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 124 - 367 / Label seq-ID: 6 - 249

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein Protocadherin-15


Mass: 29390.691 Da / Num. of mol.: 2 / Mutation: V250N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCDH15, USH1F / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: Q96QU1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 0.1 M MES pH 5.9, 0.15 M MgCl2, 32% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 17491 / % possible obs: 95 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.194 / Net I/σ(I): 7.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.327 / Num. unique obs: 777 / % possible all: 89.2

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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: 5ULY

5uly


Resolution: 2.6→39.47 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.908 / SU B: 25.139 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 1.117 / ESU R Free: 0.349 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27039 778 4.7 %RANDOM
Rwork0.23201 ---
obs0.23393 15827 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.917 Å2
Baniso -1Baniso -2Baniso -3
1-4.12 Å2-0 Å2-1 Å2
2--0.68 Å20 Å2
3----3.59 Å2
Refinement stepCycle: 1 / Resolution: 2.6→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 6 40 3672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0143718
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173259
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.6735082
X-RAY DIFFRACTIONr_angle_other_deg0.7411.6237676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2115449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24923.204206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14415576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5011522
X-RAY DIFFRACTIONr_chiral_restr0.0520.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
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_it1.1332.7741820
X-RAY DIFFRACTIONr_mcbond_other1.1322.7741819
X-RAY DIFFRACTIONr_mcangle_it2.0254.142261
X-RAY DIFFRACTIONr_mcangle_other2.0244.142262
X-RAY DIFFRACTIONr_scbond_it0.9122.8231898
X-RAY DIFFRACTIONr_scbond_other0.912.8231896
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5924.2052821
X-RAY DIFFRACTIONr_long_range_B_refined3.34731.2273661
X-RAY DIFFRACTIONr_long_range_B_other3.33531.2263660
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6817 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.583→2.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 44 -
Rwork0.317 949 -
obs--75.8 %
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)
10.76750.2341-0.05911.9834-2.7395.0358-0.10210.08750.05570.03250.1992-0.0310.0153-0.3868-0.09710.0352-0.03470.00920.21090.05150.159449.1142.9562-0.4991
20.319-0.34780.57341.0924-1.62512.5752-0.03720.0360.0289-0.01430.012-0.01310.06140.01980.02520.076-0.02940.02430.06160.00790.226554.2389-22.648838.9044
30.6613-0.8879-0.51631.9542.10666.22420.0412-0.16410.1533-0.06870.22380.00850.1430.6027-0.26510.01880.0437-0.02470.2873-0.10050.188988.7983-12.522856.5541
40.66070.58081.10122.05962.03562.5794-0.0408-0.0578-0.01490.15170.04260.01430.0811-0.0352-0.00180.08580.03280.02230.0587-0.00470.206384.18-37.032116.2801
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A123 - 235
2X-RAY DIFFRACTION1A403
3X-RAY DIFFRACTION2A236 - 367
4X-RAY DIFFRACTION2A401 - 402
5X-RAY DIFFRACTION3B124 - 235
6X-RAY DIFFRACTION3B403
7X-RAY DIFFRACTION4B236 - 367
8X-RAY DIFFRACTION4B401 - 402

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