[English] 日本語
Yorodumi
- PDB-5aea: Crystal structure of human NCAM domain 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aea
TitleCrystal structure of human NCAM domain 1
ComponentsNEURAL CELL ADHESION MOLECULE 1Neural cell adhesion molecule
KeywordsCELL ADHESION / NCAM
Function / homology
Function and homology information


regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / NCAM signaling for neurite out-growth / Signal transduction by L1 / Interferon gamma signaling / virus receptor activity / RAF/MAP kinase cascade ...regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / NCAM signaling for neurite out-growth / Signal transduction by L1 / Interferon gamma signaling / virus receptor activity / RAF/MAP kinase cascade / collagen-containing extracellular matrix / cell adhesion / external side of plasma membrane / Golgi membrane / cell surface / extracellular region / membrane / plasma membrane / cytosol
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
CITRATE ANION / Neural cell adhesion molecule 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKvansakul, M. / Griffiths, K. / Foley, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: I-Bodies, Human Single Domain Antibodies that Antagonize Chemokine Receptor Cxcr4.
Authors: Griffiths, K. / Dolezal, O. / Cao, B. / Nilsson, S.K. / See, H.B. / Pfleger, K.D.G. / Roche, M. / Gorry, P.R. / Pow, A. / Viduka, K. / Lim, K. / Lu, B.G.C. / Chang, D.H.C. / Murray-Rust, T. ...Authors: Griffiths, K. / Dolezal, O. / Cao, B. / Nilsson, S.K. / See, H.B. / Pfleger, K.D.G. / Roche, M. / Gorry, P.R. / Pow, A. / Viduka, K. / Lim, K. / Lu, B.G.C. / Chang, D.H.C. / Murray-Rust, T. / Kvansakul, M. / Perugini, M.A. / Dogovski, C. / Doerflinger, M. / Zhang, Y. / Parisi, K. / Casey, J.L. / Nuttall, S.D. / Foley, M.
History
DepositionAug 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEURAL CELL ADHESION MOLECULE 1
B: NEURAL CELL ADHESION MOLECULE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0213
Polymers25,8322
Non-polymers1891
Water2,936163
1
A: NEURAL CELL ADHESION MOLECULE 1


Theoretical massNumber of molelcules
Total (without water)12,9161
Polymers12,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NEURAL CELL ADHESION MOLECULE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1052
Polymers12,9161
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.850, 107.327, 41.748
Angle α, β, γ (deg.)90.00, 99.57, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein NEURAL CELL ADHESION MOLECULE 1 / Neural cell adhesion molecule / N-CAM-1 / NCAM-1 / NCAM DOMAIN 1


Mass: 12915.902 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 20-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1 / References: UniProt: P13591
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 6.88 / Details: 1.45 M TRI-SODIUM CITRATE PH 6.88

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→38.44 Å / Num. obs: 16311 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 21.69 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZ1

1qz1


Resolution: 1.9→38.436 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 764 4.7 %
Rwork0.1723 --
obs0.1736 16292 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→38.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 13 163 1675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091547
X-RAY DIFFRACTIONf_angle_d1.0952105
X-RAY DIFFRACTIONf_dihedral_angle_d16.411566
X-RAY DIFFRACTIONf_chiral_restr0.055239
X-RAY DIFFRACTIONf_plane_restr0.005277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.04670.25581550.23683074X-RAY DIFFRACTION100
2.0467-2.25260.26911500.20653097X-RAY DIFFRACTION100
2.2526-2.57850.23431400.19223132X-RAY DIFFRACTION100
2.5785-3.24840.23181590.17843089X-RAY DIFFRACTION100
3.2484-38.44410.14641600.1413136X-RAY DIFFRACTION100
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)
11.7376-1.89340.40362.0726-0.44470.0967-0.5018-0.5710.63990.70740.21870.0723-0.55530.2464-0.09840.50070.00970.01620.2916-0.05790.2387-12.37972.757216.9735
20.1496-0.09620.03470.5599-0.04180.2368-0.1909-0.179-0.36670.6379-0.10470.39710.23250.13420.01380.2857-0.02010.06660.25870.00930.2391-10.401-11.7549.4699
31.07880.0674-0.20620.4018-0.67510.89650.2322-0.10440.19360.3899-0.31110.382-0.0995-0.27810.01140.15480.00640.05090.1932-0.05140.2171-12.20613.18778.7055
40.3240.50270.23660.97970.03510.3905-0.1255-0.06710.0366-0.33680.03620.0133-0.11160.0324-0.02740.14020.012-0.00880.1753-0.00480.1682-8.29392.46461.8337
50.4733-0.0071-0.07392.43-0.08530.04250.0373-0.03990.03710.0825-0.0655-0.58680.1632-0.03270.01120.1150.01160.0450.172-0.01960.1527-4.6315-4.12524.2461
60.85110.12120.11560.3322-0.46020.66090.1049-0.037-0.00080.0288-0.32470.3018-0.1776-0.1018-0.00270.3068-0.0198-0.06370.1903-0.01090.1619-6.0977-3.078211.0062
72.12581.59950.4531.9422-0.99974.08990.14630.2675-0.5186-0.19180.1587-0.30.13670.64890.06270.4441-0.14140.04580.4536-0.10740.33426.705211.8406-15.3947
81.2856-0.28550.54330.60690.10340.5846-0.07640.2172-0.2488-0.58760.25380.1556-0.04210.17530.04630.3261-0.0619-0.00840.2455-0.05520.15220.253215.599-11.677
90.5283-0.22740.03050.7861-0.45020.3548-0.0837-0.0299-0.0493-0.11170.15380.17640.0763-0.126-0.00020.2103-0.0272-0.00950.199-0.01490.2075-4.680417.3354-4.0314
100.72870.27540.71411.64980.41521.0324-0.06530.4444-1.2120.11440.1888-0.23880.59460.35170.11590.3230.05290.04920.2387-0.13620.52816.56598.2623-6.1744
110.8377-0.53850.32230.73690.03341.7371-0.35870.4622-0.0371-0.15550.094-0.0387-0.6482-0.1062-0.09230.2377-0.09590.03870.2056-0.02670.30784.827525.8564-7.6615
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 6 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 7 THROUGH 13 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 14 THROUGH 36 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 37 THROUGH 64 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 65 THROUGH 80 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 81 THROUGH 100 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 1 THROUGH 6 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 7 THROUGH 36 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 37 THROUGH 72 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 73 THROUGH 86 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 87 THROUGH 99 )

+
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