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- PDB-5co1: Crystal Structure of Zebrafish Protocadherin-19 EC3-4 -

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Basic information

Entry
Database: PDB / ID: 5co1
TitleCrystal Structure of Zebrafish Protocadherin-19 EC3-4
ComponentsProtocadherin-19 isoform 1
KeywordsCELL ADHESION / adhesion / epilepsy
Function / homology
Function and homology information


regulation of neuronal action potential / neural tube formation / brain morphogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / excitatory postsynaptic potential / visual perception / cell-cell adhesion / postsynapse / cell adhesion / cadherin binding ...regulation of neuronal action potential / neural tube formation / brain morphogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / excitatory postsynaptic potential / visual perception / cell-cell adhesion / postsynapse / cell adhesion / cadherin binding / calcium ion binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Protocadherin-19 / Cadherin, N-terminal / Cadherin-like / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like ...Protocadherin-19 / Cadherin, N-terminal / Cadherin-like / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protocadherin-19 isoform 1 / Protocadherin-19
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsCooper, S.R. / Jontes, J.D. / Sotomayor, M.
CitationJournal: Elife / Year: 2016
Title: Structural determinants of adhesion by Protocadherin-19 and implications for its role in epilepsy.
Authors: Cooper, S.R. / Jontes, J.D. / Sotomayor, M.
History
DepositionJul 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 31, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protocadherin-19 isoform 1
B: Protocadherin-19 isoform 1
C: Protocadherin-19 isoform 1
D: Protocadherin-19 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,33120
Polymers97,6894
Non-polymers64116
Water88349
1
A: Protocadherin-19 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5835
Polymers24,4221
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protocadherin-19 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5835
Polymers24,4221
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protocadherin-19 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5835
Polymers24,4221
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protocadherin-19 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5835
Polymers24,4221
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.355, 86.631, 132.583
Angle α, β, γ (deg.)90.00, 122.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protocadherin-19 isoform 1


Mass: 24422.326 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pcdh19 / Plasmid: pET21a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: C4P340, UniProt: F8W3X3*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 100 mM Sodium Cacodylate pH 6.1, 100 mM Calcium Acetate, 25% MPD

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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: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.51→50 Å / Num. obs: 47847 / % possible obs: 98 % / Redundancy: 4.4 % / Net I/σ(I): 16.59
Reflection shellResolution: 2.51→2.55 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 2.21 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4aqe_A

Resolution: 2.51→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 21.276 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23943 2360 4.9 %RANDOM
Rwork0.18837 ---
obs0.19091 45487 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å20.1 Å2
2---0.07 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6464 0 16 49 6529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196574
X-RAY DIFFRACTIONr_bond_other_d0.0010.026270
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9688953
X-RAY DIFFRACTIONr_angle_other_deg0.74314456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.035825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.00326.113319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.289151109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5341528
X-RAY DIFFRACTIONr_chiral_restr0.0990.21061
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0217519
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021385
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_it6.265.7823318
X-RAY DIFFRACTIONr_mcbond_other6.2615.783317
X-RAY DIFFRACTIONr_mcangle_it9.7088.6384137
X-RAY DIFFRACTIONr_mcangle_other9.7078.6414138
X-RAY DIFFRACTIONr_scbond_it6.5496.4443256
X-RAY DIFFRACTIONr_scbond_other6.5456.4413254
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.2439.3684816
X-RAY DIFFRACTIONr_long_range_B_refined14.15244.9076780
X-RAY DIFFRACTIONr_long_range_B_other14.15344.9116777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.514→2.579 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 143 -
Rwork0.383 2966 -
obs--86.63 %
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)
10.6434-0.58780.64582.8766-0.83940.678-0.05740.03330.0981-0.108-0.0547-0.3086-0.01920.02580.1120.164-0.0165-0.01320.13890.06390.1748-32.7976-1.4263-10.9764
20.975-0.65251.29510.9371-1.4073.00970.04070.1670.1250.28260.0472-0.1179-0.00050.1351-0.08790.40170.115-0.18980.088-0.01290.1727-19.969-30.08723.9643
30.7788-0.9137-0.83172.82981.01690.905-0.05680.0336-0.1299-0.0557-0.07480.26480.012-0.0290.13160.1418-0.01620.02350.1436-0.04210.1825-40.2408-31.0331-11.4
41.0266-0.4648-0.87090.40840.7942.057-0.02560.01920.0053-0.0680.0398-0.0264-0.1057-0.1806-0.01420.17140.06740.11050.22310.0450.1039-57.8791-2.493821.0154
50.3299-0.30480.52852.2927-0.13620.9140.00330.04910.0164-0.01940.0061-0.23360.00230.0526-0.00940.0005-0.00450.00930.22170.02730.25514.8952-38.647355.5045
61.7448-1.20341.27151.2426-1.4832.03180.1577-0.0053-0.0683-0.2159-0.07870.20150.10810.1296-0.0790.16950.018-0.19580.0582-0.01430.2421-15.0638-10.137233.172
70.2022-0.433-0.41531.81330.37361.1966-0.00580.0619-0.05220.022-0.05950.23050.0002-0.08280.06520.0196-0.01330.04820.2312-0.01550.2393-10.5672-37.627459.409
80.48420.1013-0.90110.5290.19172.1056-0.08520.0258-0.0303-0.0719-0.0622-0.02750.1134-0.05030.14730.1816-0.03220.12280.1730.00180.169611.9035-65.648529.3047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A213 - 318
2X-RAY DIFFRACTION1A1001 - 1002
3X-RAY DIFFRACTION1A1004
4X-RAY DIFFRACTION2A319 - 423
5X-RAY DIFFRACTION2A1003
6X-RAY DIFFRACTION3B213 - 318
7X-RAY DIFFRACTION3B501 - 502
8X-RAY DIFFRACTION3B504
9X-RAY DIFFRACTION4B319 - 422
10X-RAY DIFFRACTION4B503
11X-RAY DIFFRACTION5C213 - 318
12X-RAY DIFFRACTION5C501 - 502
13X-RAY DIFFRACTION5C504
14X-RAY DIFFRACTION6C319 - 422
15X-RAY DIFFRACTION6C503
16X-RAY DIFFRACTION7D213 - 318
17X-RAY DIFFRACTION7D501 - 502
18X-RAY DIFFRACTION7D504
19X-RAY DIFFRACTION8D319 - 422
20X-RAY DIFFRACTION8D503

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