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- PDB-6bxz: Crystal Structure of Pig Protocadherin-15 EC10-MAD12 -

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Basic information

Entry
Database: PDB / ID: 6bxz
TitleCrystal Structure of Pig Protocadherin-15 EC10-MAD12
ComponentsProtocadherin related 15
KeywordsCELL ADHESION / HEARING / MECHANOTRANSDUCTION / ADHESION / CALCIUM-BINDING PROTEIN
Function / homologyProtocadherin-15 / Extracellular Cadherin domain / stereocilium / plasma membrane => GO:0005886 / inner ear development / sensory perception of sound / cell adhesion / Protocadherin related 15
Function and homology information
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsDe-la-Torre, P. / Araya-Secchi, R. / Choudhary, D. / Sotomayor, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01 DC015271 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R00 DC012534 United States
CitationJournal: Biophys. J. / Year: 2018
Title: A Mechanically Weak Extracellular Membrane-Adjacent Domain Induces Dimerization of Protocadherin-15.
Authors: De-la-Torre, P. / Choudhary, D. / Araya-Secchi, R. / Narui, Y. / Sotomayor, M.
History
DepositionDec 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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
C: Protocadherin related 15
A: Protocadherin related 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2658
Polymers80,0252
Non-polymers2406
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size exclusion chromatography and AUC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-27 kcal/mol
Surface area32890 Å2
Unit cell
Length a, b, c (Å)92.284, 49.246, 108.253
Angle α, β, γ (deg.)90.00, 92.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 1011 - 1340 / Label seq-ID: 6 - 335

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

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Components

#1: Protein Protocadherin related 15


Mass: 40012.348 Da / Num. of mol.: 2 / Fragment: residues 942-1288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: PCDH15 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Rosetta / References: UniProt: F1SD06
#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 / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 20 % v/v Jeffamine M-600

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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: 2.09→108.18 Å / Num. obs: 57228 / % possible obs: 97.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.2
Reflection shellResolution: 2.09→2.14 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.45 / Num. unique obs: 2452 / % possible all: 85.3

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XHZ

4xhz


Resolution: 2.09→108.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.017 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.15 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21708 2786 5 %RANDOM
Rwork0.18735 ---
obs0.18883 53041 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å2-0.17 Å2
2---0.08 Å20 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 2.09→108.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5127 0 6 260 5393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195277
X-RAY DIFFRACTIONr_bond_other_d0.0010.024991
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9737162
X-RAY DIFFRACTIONr_angle_other_deg0.989311591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3365664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0724.472246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33615932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5911535
X-RAY DIFFRACTIONr_chiral_restr0.0930.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021043
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_it0.8092.1232617
X-RAY DIFFRACTIONr_mcbond_other0.812.1222616
X-RAY DIFFRACTIONr_mcangle_it1.283.1773270
X-RAY DIFFRACTIONr_mcangle_other1.283.1783271
X-RAY DIFFRACTIONr_scbond_it1.1952.2532660
X-RAY DIFFRACTIONr_scbond_other1.1942.2542661
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9183.3273885
X-RAY DIFFRACTIONr_long_range_B_refined5.08325.1225687
X-RAY DIFFRACTIONr_long_range_B_other5.02924.8355641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19652 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1C
2A
LS refinement shellResolution: 2.093→2.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 149 -
Rwork0.238 2932 -
obs--72.48 %
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)
10.2419-0.05110.48810.4795-1.17266.98970.0336-0.14250.12140.058-0.08180.08210.1772-0.15140.04820.56240.01280.05750.53670.06040.2456-16.7454-5.6977-72.0719
21.9251-0.08450.30991.9398-0.46575.4804-0.07640.2943-0.0601-0.34540.0256-0.11280.17930.21860.05080.0747-0.00180.00470.11740.00980.1522-14.3745-15.9161-21.3243
33.5776-1.0329-0.2224.06130.64521.33340.0014-0.04520.1080.07660.0237-0.283-0.04250.2543-0.02510.0233-0.0065-0.04790.1305-0.00210.1116-8.05972.6232-5.6063
41.40730.1458-1.65031.8136-0.74636.88910.08720.76430.1376-0.5532-0.05410.113-0.4863-0.3203-0.03310.72460.1003-0.00950.67450.1120.2344-31.69516.6828-63.0678
51.6735-0.0254-0.55482.2826-1.39986.3290.04390.09330.0281-0.1643-0.0046-0.0278-0.17970.1138-0.03930.0288-0.0007-0.00940.0149-0.02180.0848-33.51054.9624-16.4538
62.619-1.9888-0.67063.91490.79481.20760.02180.0577-0.10420.0058-0.0720.2080.1202-0.16240.05020.0183-0.0186-0.00750.02310.00310.1111-40.0284-18.0733-10.324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1009 - 1117
2X-RAY DIFFRACTION2C1118 - 1224
3X-RAY DIFFRACTION3C1225 - 1342
4X-RAY DIFFRACTION4A1011 - 1117
5X-RAY DIFFRACTION5A1118 - 1224
6X-RAY DIFFRACTION6A1225 - 1340

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