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- PDB-8afo: Structure of fibronectin 2 and 3 of L1CAM at 2.0 Angstrom -

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Basic information

Entry
Database: PDB / ID: 8afo
TitleStructure of fibronectin 2 and 3 of L1CAM at 2.0 Angstrom
ComponentsNeural cell adhesion molecule L1
KeywordsCELL ADHESION / fibronectin / glycans / L1CAM
Function / homology
Function and homology information


L1CAM interactions / axon guidance receptor activity / Interaction between L1 and Ankyrins / Basigin interactions / axon development / homophilic cell adhesion via plasma membrane adhesion molecules / Recycling pathway of L1 / positive regulation of axon extension / axonal growth cone / cell-matrix adhesion ...L1CAM interactions / axon guidance receptor activity / Interaction between L1 and Ankyrins / Basigin interactions / axon development / homophilic cell adhesion via plasma membrane adhesion molecules / Recycling pathway of L1 / positive regulation of axon extension / axonal growth cone / cell-matrix adhesion / Signal transduction by L1 / axon guidance / synapse organization / neuron projection development / chemotaxis / cell migration / nervous system development / collagen-containing extracellular matrix / cell adhesion / axon / protein domain specific binding / focal adhesion / dendrite / neuronal cell body / cell surface / plasma membrane
Similarity search - Function
Neurofascin/L1/NrCAM, C-terminal domain / Bravo-like intracellular region / 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. ...Neurofascin/L1/NrCAM, C-terminal domain / Bravo-like intracellular region / 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
Similarity search - Domain/homology
Neural cell adhesion molecule L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsGuedez, G. / Loew, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Faseb J. / Year: 2023
Title: X-ray structure and function of fibronectin domains two and three of the neural cell adhesion molecule L1.
Authors: Guedez, G. / Loers, G. / Jeffries, C.M. / Kozak, S. / Meijers, R. / Svergun, D.I. / Schachner, M. / Low, C.
History
DepositionJul 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neural cell adhesion molecule L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6866
Polymers24,3771
Non-polymers1,3095
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.083, 96.749, 105.853
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Neural cell adhesion molecule L1 / N-CAM-L1 / NCAM-L1


Mass: 24377.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L1CAM, CAML1, MIC5 / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: P32004
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 150 mM sodium citrate pH 5.5, 10.6% PEG 20.000, 10 mM sodium potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 18884 / % possible obs: 94.02 % / Redundancy: 12.4 % / Biso Wilson estimate: 43.43 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.08 / Net I/σ(I): 17.8
Reflection shellResolution: 1.99→2.1 Å / Num. unique obs: 1022 / CC1/2: 0.69 / Rrim(I) all: 1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→48.52 Å / SU ML: 0.185 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4086
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 938 4.97 %
Rwork0.1927 17946 -
obs0.1949 18884 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.62 Å2
Refinement stepCycle: LAST / Resolution: 1.99→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 84 168 1818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931696
X-RAY DIFFRACTIONf_angle_d1.1582318
X-RAY DIFFRACTIONf_chiral_restr0.0896265
X-RAY DIFFRACTIONf_plane_restr0.0097295
X-RAY DIFFRACTIONf_dihedral_angle_d31.3142250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.10.3281880.29111679X-RAY DIFFRACTION62.79
2.1-2.230.2991400.24542625X-RAY DIFFRACTION97.74
2.23-2.40.30881340.23942638X-RAY DIFFRACTION97.61
2.4-2.640.25631420.22952694X-RAY DIFFRACTION99.79
2.64-3.020.25581420.21592718X-RAY DIFFRACTION99.83
3.02-3.810.27471430.1892738X-RAY DIFFRACTION99.9
3.81-48.520.19261490.16452854X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: -17.7962692944 Å / Origin y: -24.4805560412 Å / Origin z: 10.7070149513 Å
111213212223313233
T0.340661729476 Å20.029637397916 Å20.065533916947 Å2-0.371814179239 Å20.0383485172331 Å2--0.386959951046 Å2
L0.298325950236 °20.317934041121 °20.629872725937 °2-1.05680754634 °2-1.33957831343 °2--2.7275582332 °2
S-0.0338407847081 Å °-0.0312575298504 Å °-0.0775165844335 Å °-0.106430709217 Å °0.0832415400272 Å °-0.0254404588581 Å °0.145760788587 Å °-0.0898796172727 Å °4.66116479377E-5 Å °
Refinement TLS groupSelection details: all

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