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- PDB-7ok5: Crystal structure of mouse neurofascin 155 immunoglobulin domains -

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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
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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