[English] 日本語
Yorodumi
- PDB-1epf: CRYSTAL STRUCTURE OF THE TWO N-TERMINAL IMMUNOGLOBULIN DOMAINS OF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1epf
TitleCRYSTAL STRUCTURE OF THE TWO N-TERMINAL IMMUNOGLOBULIN DOMAINS OF THE NEURAL CELL ADHESION MOLECULE (NCAM)
ComponentsPROTEIN (NEURAL CELL ADHESION MOLECULE)
KeywordsCELL ADHESION / NCAM / IMMUNOGLOBULIN FOLD / GLYCOPROTEIN
Function / homology
Function and homology information


NCAM1 interactions / regulation of exocyst assembly / regulation of semaphorin-plexin signaling pathway / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / cellular response to molecule of bacterial origin / peripheral nervous system axon regeneration / LRR domain binding / homotypic cell-cell adhesion / NCAM signaling for neurite out-growth / Signal transduction by L1 ...NCAM1 interactions / regulation of exocyst assembly / regulation of semaphorin-plexin signaling pathway / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / cellular response to molecule of bacterial origin / peripheral nervous system axon regeneration / LRR domain binding / homotypic cell-cell adhesion / NCAM signaling for neurite out-growth / Signal transduction by L1 / : / thalamus development / fibroblast growth factor receptor binding / commissural neuron axon guidance / axonal fasciculation / negative regulation of programmed cell death / RAF/MAP kinase cascade / : / neuron development / epithelial to mesenchymal transition / phosphatase binding / animal organ regeneration / multicellular organismal response to stress / positive regulation of calcium-mediated signaling / positive regulation of cardiac muscle cell proliferation / cytoskeletal protein binding / response to cocaine / response to activity / calcium-mediated signaling / response to lead ion / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / neuron projection development / cell-cell junction / presynaptic membrane / heparin binding / growth cone / postsynaptic membrane / learning or memory / cell surface receptor signaling pathway / cell adhesion / response to xenobiotic stimulus / external side of plasma membrane / axon / neuronal cell body / glutamatergic synapse / cell surface / plasma membrane
Similarity search - Function
Neural cell adhesion / 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 ...Neural cell adhesion / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neural cell adhesion molecule 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsKasper, C. / Rasmussen, H. / Kastrup, J.S. / Ikemizu, S. / Jones, E.Y. / Berezin, V. / Bock, E. / Larsen, I.K.
Citation
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Expression, Crystallization and Preliminary X-Ray Analysis of the Two Amino-Terminal Ig Domains of the Neural Cell Adhesion Molecule (Ncam)
Authors: Kasper, C. / Rasmussen, H. / Berezin, V. / Bock, E. / Larsen, I.K.
History
DepositionMar 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (NEURAL CELL ADHESION MOLECULE)
B: PROTEIN (NEURAL CELL ADHESION MOLECULE)
C: PROTEIN (NEURAL CELL ADHESION MOLECULE)
D: PROTEIN (NEURAL CELL ADHESION MOLECULE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6695
Polymers85,6294
Non-polymers401
Water25,5451418
1
A: PROTEIN (NEURAL CELL ADHESION MOLECULE)
B: PROTEIN (NEURAL CELL ADHESION MOLECULE)


Theoretical massNumber of molelcules
Total (without water)42,8152
Polymers42,8152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PROTEIN (NEURAL CELL ADHESION MOLECULE)
D: PROTEIN (NEURAL CELL ADHESION MOLECULE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8553
Polymers42,8152
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.078, 122.505, 72.859
Angle α, β, γ (deg.)90.00, 98.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
PROTEIN (NEURAL CELL ADHESION MOLECULE) / NCAM


Mass: 21407.326 Da / Num. of mol.: 4 / Fragment: N-TERMINAL IG DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PHIL-S1 / Production host: Pichia pastoris (fungus) / References: UniProt: P13596
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1418 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: used macroseeding, Kasper, C., (1999) Acta Crystallogr., Sect.D, 55, 1598.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.5 mg/mlprotein1drop
210 mMHEPES1drop
315 mM1dropNaCl
412-13 %PEG40001reservoir
515 mM1reservoirCaCl2

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.855
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.855 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 64828 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 21.9
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.308 / % possible all: 90
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Num. measured all: 186351
Reflection shell
*PLUS
% possible obs: 90 % / Mean I/σ(I) obs: 3.4

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementResolution: 1.85→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3137 5 %RANDOM
Rwork0.201 ---
obs0.201 62119 89.3 %-
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6203 0 1 1418 7622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

+
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://pdbjlvh1.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