[English] 日本語
Yorodumi
- PDB-5e52: Crystal structure of human CNTN5 FN1-FN3 domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5.0E+52
TitleCrystal structure of human CNTN5 FN1-FN3 domains
ComponentsContactin-5
KeywordsCELL ADHESION / Neural cell adhesion molecule / Fibronectin type III domains
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / cell-cell adhesion mediator activity / presynapse assembly / side of membrane / axon guidance / sensory perception of sound / cell-cell adhesion / GABA-ergic synapse / presynaptic membrane / axon ...Post-translational modification: synthesis of GPI-anchored proteins / cell-cell adhesion mediator activity / presynapse assembly / side of membrane / axon guidance / sensory perception of sound / cell-cell adhesion / GABA-ergic synapse / presynaptic membrane / axon / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily ...Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Contactin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.685 Å
AuthorsNikolaienko, R.M. / Bouyain, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088806 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues.
Authors: Nikolaienko, R.M. / Hammel, M. / Dubreuil, V. / Zalmai, R. / Hall, D.R. / Mehzabeen, N. / Karuppan, S.J. / Harroch, S. / Stella, S.L. / Bouyain, S.
History
DepositionOct 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Contactin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6022
Polymers32,5071
Non-polymers951
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.770, 154.518, 90.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Contactin-5 / Neural recognition molecule NB-2 / hNB-2


Mass: 32507.084 Da / Num. of mol.: 1 / Fragment: FN domains 1-3, UNP residues 671-969
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNTN5 / Plasmid: pT7HMP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O94779
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.51 Å3/Da / Density % sol: 72.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1M NH4H2PO4, 10% (v/v) Tacsimate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2013
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.685→50 Å / Num. obs: 14285 / % possible obs: 85.7 % / Redundancy: 12 % / Biso Wilson estimate: 63.98 Å2 / Rmerge(I) obs: 0.112 / Χ2: 1.035 / Net I/av σ(I): 17.35 / Net I/σ(I): 14 / Num. measured all: 171135
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.685-2.85.90.4189261.07156.3
2.8-2.917.70.38110151.12762.5
2.91-3.049.60.30711211.05868.4
3.04-3.210.70.25413211.09880.5
3.2-3.411.90.21414841.04389.3
3.4-3.6612.70.18116231.03198.8
3.66-4.03140.14516700.94199.9
4.03-4.6214.30.10516661.03999.9
4.62-5.8114.20.08916911.049100
5.81-5013.40.08617681.02199.2

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
Coot0.8.1model building
PDB_EXTRACT3.15data extraction
PHASER2.5.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EQ4

5eq4


Resolution: 2.685→38.63 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 1398 10.13 %
Rwork0.194 12409 -
obs0.198 13807 82.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.11 Å2 / Biso mean: 95.0442 Å2 / Biso min: 47.33 Å2
Refinement stepCycle: final / Resolution: 2.685→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 5 19 2282
Biso mean--122.95 69.13 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092320
X-RAY DIFFRACTIONf_angle_d1.1343164
X-RAY DIFFRACTIONf_chiral_restr0.042349
X-RAY DIFFRACTIONf_plane_restr0.006412
X-RAY DIFFRACTIONf_dihedral_angle_d16.41838
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.685-2.78080.331810.269365073145
2.7808-2.89210.346880.248185093857
2.8921-3.02360.27381100.2451966107665
3.0236-3.1830.29141260.22741093121975
3.183-3.38230.23511470.21971281142886
3.3823-3.64330.2741590.20761452161197
3.6433-4.00950.24261700.20051494166499
4.0095-4.58890.22311650.170115061671100
4.5889-5.77850.17531720.158815261698100
5.7785-38.63350.2291800.19791591177199
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)
15.30162.93481.18653.69821.88116.6383-1.01161.28420.0191-0.75120.19010.7113-1.5522-0.62890.71730.8560.1512-0.21451.1488-0.23680.62913.441248.569645.4593
26.2195-0.90562.87133.81191.13357.1686-0.6712.2313-0.6303-0.13430.5386-0.2182-0.74541.36340.11720.5314-0.36940.10711.1414-0.130.4550.052845.895458.0961
31.7978-1.6955-2.32017.8046.46535.10740.04520.44230.1726-1.2455-0.3670.5606-1.3985-0.65330.35041.1956-0.0067-0.22510.9954-0.03050.566551.238371.959278.1507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 671 through 774 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 775 through 869 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 870 through 969 )A0

+
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