[English] 日本語
Yorodumi
- PDB-5iu9: Crystal Structure of Zebrafish Protocadherin-19 EC1-4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iu9
TitleCrystal Structure of Zebrafish Protocadherin-19 EC1-4
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 / visual perception / excitatory postsynaptic potential / 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 / visual perception / excitatory postsynaptic potential / cell-cell adhesion / postsynapse / cell adhesion / cadherin binding / calcium ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Protocadherin-19 / Cadherin, N-terminal / Cadherin-like / : / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like ...Protocadherin-19 / Cadherin, N-terminal / Cadherin-like / : / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / 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 / MOLECULAR REPLACEMENT / Resolution: 3.59 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
DepositionMar 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.source / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 21, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.4Sep 27, 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 / 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_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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,16422
Polymers95,3972
Non-polymers76720
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.390, 59.776, 165.925
Angle α, β, γ (deg.)90.00, 94.39, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 423
2114B1 - 423

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999964, -0.005555, 0.006389), (-0.007707, 0.285143, -0.958454), (0.003503, -0.958469, -0.285175)134.62387, 33.32614, 43.61848

-
Components

#1: Protein Protocadherin-19 isoform 1


Mass: 47698.289 Da / Num. of mol.: 2 / Fragment: residues 20-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pcdh19 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / 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.: 18 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 200 mM Sodium Chloride, 100 mM TrisHCl pH 8.1, 8% PEG 20,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 3.59→50 Å / Num. obs: 15416 / % possible obs: 94.8 % / Redundancy: 2.7 % / Net I/σ(I): 4.9
Reflection shellResolution: 3.59→3.66 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.1 / % possible all: 86

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CO1

5co1


Resolution: 3.59→50 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.845 / SU B: 107.439 / SU ML: 0.666 / Cross valid method: THROUGHOUT / ESU R Free: 0.775 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30498 652 4.5 %RANDOM
Rwork0.24588 ---
obs0.24851 13943 93.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 89.717 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å2-0 Å20.47 Å2
2---0.23 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 3.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 20 15 6500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196574
X-RAY DIFFRACTIONr_bond_other_d0.0020.026242
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9688950
X-RAY DIFFRACTIONr_angle_other_deg0.985314403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.525836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.82725.884311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.381151110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5881534
X-RAY DIFFRACTIONr_chiral_restr0.0830.21053
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217543
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021379
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 6254 / Type: medium positional / Rms dev position: 0.79 Å / Weight position: 0.5
LS refinement shellResolution: 3.59→3.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 33 -
Rwork0.413 832 -
obs--75.68 %
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)
14.9141-0.6093-3.04124.6278-1.55462.87330.56180.4381-0.1969-0.2001-0.3840.5858-0.4538-0.1581-0.17780.24980.1285-0.09280.4242-0.26860.246722.197519.074680.9313
24.5859-3.6775-2.58083.62061.27452.59770.3405-0.08470.79810.05860.2007-0.6751-0.4158-0.0158-0.54110.24480.0613-0.04350.1048-0.13850.341556.47457.418556.9955
37.9964-3.4476-2.30453.45021.49250.97230.009-0.1417-0.3154-0.00550.00660.06030.03720.0257-0.01560.0944-0.0124-0.0970.1259-0.02170.138693.6589-21.164637.9875
42.6227-0.9112-1.5372.3033-0.42661.4374-0.33870.4339-0.4539-0.32490.0775-0.17850.5142-0.2250.26120.32150.0146-0.1210.3955-0.41770.5891133.1686-41.173418.4965
57.5127-4.3513-1.50894.23781.97121.61880.0122-0.6729-0.08950.21560.2005-0.09160.17010.2989-0.21270.1466-0.0255-0.10210.2096-0.02870.0927113.5025-39.87951.4719
67.1976-2.3292-4.7771.94380.44075.16950.03960.11860.1523-0.1464-0.047-0.09550.1414-0.28430.00740.115-0.0082-0.08060.0689-0.0170.09378.5009-20.018920.8274
77.1757-1.3356-4.43851.71781.35453.73250.2243-0.0348-0.0852-0.0317-0.06990.0502-0.14080.0124-0.15440.13780.0016-0.12310.1491-0.02410.174641.1742-9.617553.3216
84.2424-3.1369-2.61574.54682.17131.6410.0139-0.04980.2190.43830.1091-0.03010.0210.0061-0.1230.17580.0846-0.0620.4381-0.09420.12221.89242.880778.9642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION1A1001 - 1002
3X-RAY DIFFRACTION2A102 - 210
4X-RAY DIFFRACTION2A1003 - 1005
5X-RAY DIFFRACTION3A211 - 318
6X-RAY DIFFRACTION3A1006 - 1008
7X-RAY DIFFRACTION3A1010
8X-RAY DIFFRACTION4A319 - 422
9X-RAY DIFFRACTION4A1009
10X-RAY DIFFRACTION5B2 - 101
11X-RAY DIFFRACTION5B1001 - 1002
12X-RAY DIFFRACTION6B102 - 210
13X-RAY DIFFRACTION6B1003 - 1005
14X-RAY DIFFRACTION7B211 - 318
15X-RAY DIFFRACTION7B1006 - 1008
16X-RAY DIFFRACTION7B1010
17X-RAY DIFFRACTION8B319 - 423
18X-RAY DIFFRACTION8B1009

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more