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- PDB-6e8f: Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1 -

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Basic information

Entry
Database: PDB / ID: 6e8f
TitleCrystal Structure of Human Protocadherin-15 EC3-5 CD2-1
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 / calcium ion binding / synapse / extracellular space / extracellular region / plasma membrane
Similarity search - Function
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: 2.99 Å
AuthorsChoudhary, D. / Tamilselvan, E. / 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
DepositionJul 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 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 ...citation / citation_author / pdbx_struct_conn_angle / 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 / _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.pdbx_dist_value / _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
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
Revision 1.4Oct 9, 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
A: Protocadherin-15
C: Protocadherin-15
B: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,78717
Polymers121,2433
Non-polymers54414
Water1448
1
A: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5986
Polymers40,4141
Non-polymers1835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5755
Polymers40,4141
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6156
Polymers40,4141
Non-polymers2005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.735, 95.906, 258.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Protocadherin-15


Mass: 40414.297 Da / Num. of mol.: 3
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 / Variant (production host): RIPL / References: UniProt: Q96QU1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 5.14 Å3/Da / Density % sol: 76.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 40% MPD, 0.2 M Lithium Chloride, 0.01 M Adenosine triphosphate disodium

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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: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.768
11-K, -H, -L20.232
ReflectionResolution: 2.99→50 Å / Num. obs: 48387 / % possible obs: 99.9 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.208 / Net I/σ(I): 9.31
Reflection shellResolution: 3→3.05 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2.44 / Num. unique obs: 2333 / % possible all: 99.1

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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: 5T4M

5t4m


Resolution: 2.99→47.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 16.245 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.058 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 2321 4.8 %RANDOM
Rwork0.17397 ---
obs0.17583 45968 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 85.679 Å2
Baniso -1Baniso -2Baniso -3
1-16.44 Å20 Å20 Å2
2---67.51 Å2-0 Å2
3---51.07 Å2
Refinement stepCycle: 1 / Resolution: 2.99→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7966 0 14 8 7988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0148161
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177267
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.66711188
X-RAY DIFFRACTIONr_angle_other_deg0.7621.61817094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.15451014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77123.729413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.738151260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1211540
X-RAY DIFFRACTIONr_chiral_restr0.0540.21147
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021359
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_it2.546.2184077
X-RAY DIFFRACTIONr_mcbond_other2.546.2174076
X-RAY DIFFRACTIONr_mcangle_it4.2159.3135084
X-RAY DIFFRACTIONr_mcangle_other4.2159.3135085
X-RAY DIFFRACTIONr_scbond_it2.2886.3334084
X-RAY DIFFRACTIONr_scbond_other2.2886.3334085
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8149.4426105
X-RAY DIFFRACTIONr_long_range_B_refined6.25471.8318196
X-RAY DIFFRACTIONr_long_range_B_other6.25471.8368196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.99→3.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 131 -
Rwork0.234 2673 -
obs--78.04 %
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)
11.3241-0.1202-0.272.6243-0.44140.1494-0.19110.0936-0.11620.12610.1407-0.16180.0303-0.12160.05040.0437-0.08550.00220.5192-0.06280.2726-3.6167-21.3476-33.7716
21.5844-0.23510.90430.0441-0.10880.9392-0.04090.24750.00280.0327-0.03080.03220.04280.15610.07170.172-0.0251-0.00660.4229-0.05420.2604-45.4978-6.8166-43.7183
32.0473-0.49490.17820.3135-0.08140.70940.0057-0.0020.05420.09520.07940.0055-0.0452-0.0881-0.08510.0572-0.01420.00420.441-0.00330.3451-93.58330.0157-54.1512
41.18540.2004-0.2760.50030.01870.1381-0.20180.0275-0.1245-0.02710.1802-0.0984-0.09910.0330.02160.3945-0.08760.01990.1703-0.03440.2992-27.9845-45.4187-28.2938
50.0663-0.0261-0.23342.33150.20180.9199-0.02730.03610.0040.25320.0945-0.00220.05220.0064-0.06720.3510.0094-0.02790.2494-0.02160.2158-44.1456-3.1144-18.2157
60.44880.163-0.47212.51210.11710.6479-0.00930.08120.12790.0552-0.01380.04150.0677-0.13130.02310.38870.0252-0.0320.1733-0.05850.2614-52.519345.3475-10.1446
70.6316-0.8316-0.10212.3896-0.41560.2835-0.0652-0.01340.02220.15450.1292-0.0486-0.06580.0103-0.06410.2810.00730.010.2706-0.01560.272-48.6178-76.1337-91.1276
80.8676-0.7967-1.30710.83240.95683.29060.1427-0.28290.3435-0.24110.2713-0.25580.11320.0054-0.41390.2214-0.00830.07640.3824-0.16680.3477-67.2374-41.0801-67.0319
90.348-0.8616-0.29132.57621.88243.6650.176-0.22290.1808-0.28020.5282-0.51820.10280.4782-0.70420.1395-0.2120.16070.5311-0.49260.4841-77.0446-14.8802-29.1941
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A242 - 366
2X-RAY DIFFRACTION2A367 - 486
3X-RAY DIFFRACTION2A701
4X-RAY DIFFRACTION2A703
5X-RAY DIFFRACTION2A705
6X-RAY DIFFRACTION3A487 - 594
7X-RAY DIFFRACTION3A702
8X-RAY DIFFRACTION3A704
9X-RAY DIFFRACTION4B242 - 366
10X-RAY DIFFRACTION5B367 - 486
11X-RAY DIFFRACTION5B705
12X-RAY DIFFRACTION5B701
13X-RAY DIFFRACTION5B703
14X-RAY DIFFRACTION6B487 - 595
15X-RAY DIFFRACTION6B702
16X-RAY DIFFRACTION6B704
17X-RAY DIFFRACTION7C242 - 366
18X-RAY DIFFRACTION8C367 - 486
19X-RAY DIFFRACTION8C701
20X-RAY DIFFRACTION8C704
21X-RAY DIFFRACTION9C487 - 589
22X-RAY DIFFRACTION9C702 - 703

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