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- PDB-1jb3: The Laminin-Binding Domain of Agrin is structurally related to N-... -

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Basic information

Entry
Database: PDB / ID: 1jb3
TitleThe Laminin-Binding Domain of Agrin is structurally related to N-TIMP-1
ComponentsAgrin
KeywordsCELL ADHESION / neuromuscular junction / agrin / interaction coiled-doil proteins with globular proteins / OB-fold / TIMP
Function / homology
Function and homology information


acetylcholine receptor regulator activity / extracellular matrix of synaptic cleft / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / photoreceptor ribbon synapse / dystroglycan binding ...acetylcholine receptor regulator activity / extracellular matrix of synaptic cleft / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / photoreceptor ribbon synapse / dystroglycan binding / basal part of cell / transmembrane receptor protein tyrosine kinase activator activity / filopodium assembly / glycosaminoglycan binding / heparan sulfate proteoglycan binding / extracellular matrix binding / positive regulation of filopodium assembly / neuromuscular junction development / receptor clustering / basement membrane / laminin binding / positive regulation of GTPase activity / extracellular matrix / brain development / neuromuscular junction / nervous system development / heparin binding / signaling receptor activity / negative regulation of neuron projection development / actin cytoskeleton organization / cell differentiation / membrane raft / axon / synapse / calcium ion binding / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Laminin G domain / Laminin-type EGF-like (LE) domain profile. ...NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin EGF domain / : / Laminin-type EGF domain / SEA domain superfamily / Kazal-type serine protease inhibitor domain / Kazal-type serine protease inhibitor domain / SEA domain profile. / SEA domain / SEA domain / Laminin G domain profile. / Kazal type serine protease inhibitors / Laminin G domain / Laminin G domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Concanavalin A-like lectin/glucanase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsStetefeld, J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: The laminin-binding domain of agrin is structurally related to N-TIMP-1.
Authors: Stetefeld, J. / Jenny, M. / Schulthess, T. / Landwehr, R. / Schumacher, B. / Frank, S. / Ruegg, M.A. / Engel, J. / Kammerer, R.A.
History
DepositionJun 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agrin


Theoretical massNumber of molelcules
Total (without water)15,1311
Polymers15,1311
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.130, 49.460, 53.280
Angle α, β, γ (deg.)90.00, 116.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Agrin


Mass: 15131.321 Da / Num. of mol.: 1 / Fragment: Laminin-Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: Q90685, UniProt: P31696*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8125 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
20.1 Mcitrate1reservoir
320 %(w/v)PEG40001reservoir
420 %(w/v)2-propanol1reservoir
520 %(w/v)MPD1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95, 0.97842, 0.97928, 1.2
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
20.978421
30.979281
41.21
ReflectionResolution: 1.6→30 Å / Num. obs: 22609 / % possible obs: 94.3 % / Observed criterion σ(I): 5 / Redundancy: 2.3 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.06 / Net I/σ(I): 5
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 5 / Rsym value: 0.325
Reflection
*PLUS
Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 93.6 % / Rmerge(I) obs: 0.325

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1712138.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2135 9.9 %RANDOM
Rwork0.198 ---
obs0.198 21475 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 77 Å2 / ksol: 0.537 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.88 Å20 Å2-3.02 Å2
2---1.06 Å20 Å2
3----1.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 0 184 1210
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
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
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 333 9.9 %
Rwork0.285 3027 -
obs--86.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Rfactor Rfree: 0.309 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.285

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