[English] 日本語
Yorodumi
- PDB-7ok5: Crystal structure of mouse neurofascin 155 immunoglobulin domains -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ok5
TitleCrystal structure of mouse neurofascin 155 immunoglobulin domains
ComponentsNeurofascin 155
KeywordsCELL ADHESION / Dimer Glycoprotein Immunoglobulin cell adhesion protein Neural cell adhesion protein Horseshoe
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsChataigner, L.M.P. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Research Council (ERC) Netherlands
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into the contactin 1 - neurofascin 155 adhesion complex.
Authors: Chataigner, L.M.P. / Gogou, C. / den Boer, M.A. / Frias, C.P. / Thies-Weesie, D.M.E. / Granneman, J.C.M. / Heck, A.J.R. / Meijer, D.H. / Janssen, B.J.C.
History
DepositionMay 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Neurofascin 155
A: Neurofascin 155
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,5648
Polymers139,2612
Non-polymers5,3036
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint104 kcal/mol
Surface area61310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.604, 96.273, 238.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Neurofascin 155


Mass: 69630.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nfasc / Production host: Homo sapiens (human)
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% (w/v) PEG 8000 and 100 mM HEPES/Sodium hydroxide pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.97→79.54 Å / Num. obs: 37686 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 80.069 Å2 / CC1/2: 0.976 / Net I/σ(I): 6.2
Reflection shellResolution: 2.97→3.02 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1838 / CC1/2: 0.399 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P3Y

3p3y


Resolution: 2.97→74.92 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.269 1879 5 %
Rwork0.2214 35695 -
obs0.2238 37574 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 284.6 Å2 / Biso mean: 113.2317 Å2 / Biso min: 54.97 Å2
Refinement stepCycle: final / Resolution: 2.97→74.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9191 0 355 0 9546
Biso mean--151.22 --
Num. residues----1161
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.97-3.050.41951480.36862642279098
3.05-3.140.3631430.32482683282699
3.14-3.240.3581500.28292711286199
3.24-3.360.30041400.280727112851100
3.36-3.490.28971570.273126702827100
3.49-3.650.33111140.24527742888100
3.65-3.840.31821460.238727312877100
3.84-4.080.24821130.218127802893100
4.08-4.40.24941660.197527252891100
4.4-4.840.2381420.18332753289599
4.84-5.540.22431570.186127742931100
5.54-6.980.27741570.22628052962100
6.98-74.920.24131460.20082936308299
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)
12.82440.935-1.30757.6887-2.27239.5861-0.0114-0.0373-0.1595-0.2178-0.0053-0.32480.16390.0603-0.0140.63250.04170.07040.68450.09150.7848-12.0645-50.043663.9012
21.42790.6948-0.63612.9848-1.26943.0532-0.0808-0.01080.32960.02010.20840.7414-0.2687-0.3109-0.21370.82390.103-0.00760.8464-0.00950.8833-19.3247-22.447155.7292
34.14762.0201-0.58733.888-0.10591.71590.7026-0.11570.04411.3088-0.6762-1.13470.23610.3288-0.00061.9956-0.13980.06531.12190.23491.1129-5.3441-34.2834100.1314
443.51111.92493.18921.27192.11930.01620.51-1.58420.35390.8239-1.71890.16561.0421-0.52311.34820.02330.18341.6686-0.49122.054424.7997-14.647488.9188
51.6966-0.1971-0.1844.98842.83769.0490.0151-0.0917-0.2089-0.1715-0.1370.15290.3527-0.29250.0931.054-0.15340.23270.7391-0.07850.8592-0.511-50.133117.2097
60.6837-0.5145-0.18411.77821.64643.59690.0613-0.13940.1679-0.23090.4267-0.82430.25910.4258-0.57290.8477-0.03450.21040.7559-0.09671.03422.0976-36.918630.5489
71.76980.1105-1.58826.10541.75344.6483-0.1337-0.11420.3353-0.314-0.1445-0.4421-0.08620.02750.2591.22130.0773-0.03730.8196-0.05060.736313.4111-34.6476-18.1368
80.92821.32850.63245.93543.07232.3553-0.199-0.13020.1345-0.8907-0.00650.2172-0.9212-0.3530.25321.59570.0850.10020.9177-0.0360.926713.79021.1453-6.1328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 24 through 132)B24 - 132
2X-RAY DIFFRACTION2chain 'B' and (resid 133 through 436) or (chain 'B' and (resid 622 through 628))B0
3X-RAY DIFFRACTION3chain 'B' and (resid 437 through 530 ) or (chain 'B' and (resid 629 through 631 ))B0
4X-RAY DIFFRACTION4chain 'B' and (resid 531 through 621 ) or (chain 'B' and (resid 632 through 635 ))B0
5X-RAY DIFFRACTION5chain 'A' and (resid 24 through 132 )A24 - 132
6X-RAY DIFFRACTION6chain 'A' and (resid 133 through 436 ) or (chain 'A' and (resid 624 through 630 ))A0
7X-RAY DIFFRACTION7chain 'A' and (resid 437 through 530 ) or (chain 'A' and (resid 631 through 633 ))A0
8X-RAY DIFFRACTION8chain 'A' and (resid 531 through 623) or (chain 'A' and (resid 634 through 638 ))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://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