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- PDB-5uly: Crystal Structure of Human Protocadherin-15 EC2-3 -

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Basic information

Entry
Database: PDB / ID: 5uly
TitleCrystal Structure of Human Protocadherin-15 EC2-3
ComponentsProtocadherin-15
KeywordsCalcium-binding protein / hearing / mechanotransduction / adhesion
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: 2.64 Å
AuthorsWimalasena, L.N. / Sotomayor, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R00 DC012534 United States
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
DepositionJan 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: 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_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 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protocadherin-15
B: Protocadherin-15
C: Protocadherin-15
D: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,82412
Polymers117,5034
Non-polymers3218
Water2,360131
1
A: Protocadherin-15
C: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9126
Polymers58,7512
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protocadherin-15
D: Protocadherin-15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9126
Polymers58,7512
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.761, 147.625, 77.034
Angle α, β, γ (deg.)90.00, 101.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISAA128 - 36610 - 248
21HISHISBB128 - 36610 - 248
12THRTHRAA125 - 3667 - 248
22THRTHRCC125 - 3667 - 248
13THRTHRAA125 - 3667 - 248
23THRTHRDD125 - 3667 - 248
14HISHISBB128 - 36610 - 248
24HISHISCC128 - 36610 - 248
15HISHISBB128 - 36610 - 248
25HISHISDD128 - 36610 - 248
16THRTHRCC125 - 3667 - 248
26THRTHRDD125 - 3667 - 248

NCS ensembles :
IDDetails
11
22
33
44
55
66
DetailsDimer as determined by SEC and AUC

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Components

#1: Protein
Protocadherin-15 /


Mass: 29375.723 Da / Num. of mol.: 4 / Fragment: residues 143-390
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.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES (pH 7.5), 0.1 M KCl, 15% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: oxford cryo-jet
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 21, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 42598 / % possible obs: 96.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.625
Reflection shellResolution: 2.64→2.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.7 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4APX, 5T4M

4apx

5t4m


Resolution: 2.64→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.912 / SU B: 21.433 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.499 / ESU R Free: 0.288 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1962 4.8 %RANDOM
Rwork0.21523 ---
obs0.21671 39053 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.895 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å2-0 Å21.4 Å2
2---4.04 Å2-0 Å2
3---6.22 Å2
Refinement stepCycle: 1 / Resolution: 2.64→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7135 0 8 131 7274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197319
X-RAY DIFFRACTIONr_bond_other_d0.0020.026643
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.96910001
X-RAY DIFFRACTIONr_angle_other_deg1.028315478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1495882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88224.513359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8151148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6751547
X-RAY DIFFRACTIONr_chiral_restr0.0980.21153
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021389
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_it1.3083.0493561
X-RAY DIFFRACTIONr_mcbond_other1.3083.0493560
X-RAY DIFFRACTIONr_mcangle_it2.1334.5664432
X-RAY DIFFRACTIONr_mcangle_other2.1334.5664433
X-RAY DIFFRACTIONr_scbond_it1.4193.2043758
X-RAY DIFFRACTIONr_scbond_other1.4193.2043756
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.364.7445569
X-RAY DIFFRACTIONr_long_range_B_refined3.85734.3047114
X-RAY DIFFRACTIONr_long_range_B_other3.83434.2627098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A129620.08
12B129620.08
21A133100.09
22C133100.09
31A133660.08
32D133660.08
41B129180.09
42C129180.09
51B128080.08
52D128080.08
61C134520.08
62D134520.08
LS refinement shellResolution: 2.632→2.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 119 -
Rwork0.336 2719 -
obs--91.73 %
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)
13.69311.0673-0.10292.1351-0.00475.81240.2281-0.60470.0780.6361-0.09680.1127-0.3883-0.1381-0.13130.3650.0041-0.02420.30130.02810.120466.62125.0593109.8728
21.8546-0.5379-0.5271.7890.79533.5742-0.020.1790.0492-0.139-0.03930.07160.0572-0.08040.05930.1291-0.0245-0.05640.16490.04410.034574.112213.832766.9253
31.6199-0.34881.14232.10340.01766.0019-0.01470.547-0.1476-0.5304-0.0065-0.1102-0.0003-0.04520.02120.2818-0.0811-0.00160.4643-0.02850.107433.79374.565242.3353
42.06770.23860.44691.74680.7973.33450.0193-0.21880.10830.1016-0.07880.0902-0.137-0.10820.05950.1217-0.0111-0.02030.17890.01170.019141.293114.227184.5344
52.75940.0839-0.85965.92910.41121.22010.1474-0.2560.74520.0825-0.12010.2888-0.5162-0.0428-0.02730.40580.0006-0.09320.286-0.03220.342783.098143.344495.2358
61.9856-0.1493-0.11443.42111.21751.5073-0.07090.0589-0.26520.05580.0508-0.04480.14750.00120.02010.1624-0.0128-0.03480.15030.03690.06588.23380.929582.5978
71.0370.66650.42635.38480.06160.9490.0920.1222-0.6434-0.2242-0.1248-0.10660.5215-0.07450.03280.4759-0.00430.05610.3679-0.08140.588649.8152-17.99355.308
82.01410.20970.08183.81741.00421.4117-0.0092-0.02680.3178-0.05710.0290.0173-0.18970.0329-0.01990.14590.005-0.03370.17040.05480.085755.327427.108468.7206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A125 - 236
2X-RAY DIFFRACTION1A1001
3X-RAY DIFFRACTION2A237 - 366
4X-RAY DIFFRACTION2A1002
5X-RAY DIFFRACTION3B128 - 236
6X-RAY DIFFRACTION3B1001
7X-RAY DIFFRACTION4B237 - 366
8X-RAY DIFFRACTION4B1002
9X-RAY DIFFRACTION5C125 - 236
10X-RAY DIFFRACTION5C1001
11X-RAY DIFFRACTION6C237 - 366
12X-RAY DIFFRACTION6C1002
13X-RAY DIFFRACTION7D125 - 236
14X-RAY DIFFRACTION7D1001
15X-RAY DIFFRACTION8D237 - 366
16X-RAY DIFFRACTION8D1002

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