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- PDB-4yep: L4b Domain of Human Laminin alpha-2 -

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Basic information

Entry
Database: PDB / ID: 4yep
TitleL4b Domain of Human Laminin alpha-2
ComponentsLaminin subunit alpha-2
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding fold / laminin / extracellular matrix / ephrin receptor
Function / homology
Function and homology information


regulation of basement membrane organization / Schwann cell differentiation / positive regulation of synaptic transmission, cholinergic / positive regulation of integrin-mediated signaling pathway / Laminin interactions / EGR2 and SOX10-mediated initiation of Schwann cell myelination / protein complex involved in cell-matrix adhesion / MET activates PTK2 signaling / muscle organ development / positive regulation of muscle cell differentiation ...regulation of basement membrane organization / Schwann cell differentiation / positive regulation of synaptic transmission, cholinergic / positive regulation of integrin-mediated signaling pathway / Laminin interactions / EGR2 and SOX10-mediated initiation of Schwann cell myelination / protein complex involved in cell-matrix adhesion / MET activates PTK2 signaling / muscle organ development / positive regulation of muscle cell differentiation / maintenance of blood-brain barrier / regulation of embryonic development / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / synaptic cleft / regulation of cell migration / positive regulation of cell adhesion / axon guidance / neuromuscular junction / sarcolemma / collagen-containing extracellular matrix / dendritic spine / cell adhesion / signaling receptor binding / structural molecule activity / extracellular region
Similarity search - Function
Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin, N-terminal / : ...Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV / Laminin B (Domain IV) / Laminin IV type A domain profile. / Laminin B domain / Laminin, N-terminal / : / Laminin N-terminal (Domain VI) / Laminin N-terminal domain profile. / Laminin N-terminal domain (domain VI) / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Laminin subunit alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.19 Å
AuthorsToot, M. / Gat, Y. / Fass, D.
Funding support Israel, 2items
OrganizationGrant numberCountry
European Research Council under the European Union Seventh Framework Programme310649 Israel
Kimmel Center for Macromolecular Assemblies Israel
CitationJournal: Febs J. / Year: 2015
Title: Laminin L4 domain structure resembles adhesion modules in ephrin receptor and other transmembrane glycoproteins.
Authors: Moran, T. / Gat, Y. / Fass, D.
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2May 8, 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: Laminin subunit alpha-2
B: Laminin subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,36117
Polymers43,4302
Non-polymers93115
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint41 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.710, 131.510, 44.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1501-

HOH

21A-1642-

HOH

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Components

#1: Protein Laminin subunit alpha-2 / Laminin M chain / Laminin-12 subunit alpha / Laminin-2 subunit alpha / Laminin-4 subunit alpha / ...Laminin M chain / Laminin-12 subunit alpha / Laminin-2 subunit alpha / Laminin-4 subunit alpha / Merosin heavy chain


Mass: 21715.029 Da / Num. of mol.: 2 / Fragment: L4b domain, UNP residues 1181-1362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMA2, LAMM / Plasmid: pMal-c2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24043
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG 3350, 20% ethylene glycol, 50 mM sodium phosphate pH 8.0
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.919 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 1.19→52.85 Å / Num. obs: 110147 / % possible obs: 99.9 % / Redundancy: 13 % / Net I/σ(I): 12.2
Reflection shellResolution: 1.19→1.232 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 1.19→52.846 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1619 7756 7.04 %random
Rwork0.1267 ---
obs0.1291 110147 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.19→52.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 60 480 3602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0223454
X-RAY DIFFRACTIONf_angle_d1.9044707
X-RAY DIFFRACTIONf_dihedral_angle_d13.2761367
X-RAY DIFFRACTIONf_chiral_restr0.128516
X-RAY DIFFRACTIONf_plane_restr0.012595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.20350.26022500.23933369X-RAY DIFFRACTION100
1.2035-1.21760.28972370.23963392X-RAY DIFFRACTION100
1.2176-1.23250.24872540.22713342X-RAY DIFFRACTION100
1.2325-1.24810.2532600.21923388X-RAY DIFFRACTION100
1.2481-1.26450.24892670.20773371X-RAY DIFFRACTION100
1.2645-1.28180.25872290.20233417X-RAY DIFFRACTION100
1.2818-1.30020.25382750.20133297X-RAY DIFFRACTION100
1.3002-1.31960.22552880.19043399X-RAY DIFFRACTION100
1.3196-1.34020.25032470.18073337X-RAY DIFFRACTION100
1.3402-1.36220.21552360.16833420X-RAY DIFFRACTION100
1.3622-1.38560.22452350.1653402X-RAY DIFFRACTION100
1.3856-1.41080.20612350.15853415X-RAY DIFFRACTION100
1.4108-1.4380.20622640.15213384X-RAY DIFFRACTION100
1.438-1.46730.20942440.13933379X-RAY DIFFRACTION100
1.4673-1.49920.18472360.13013427X-RAY DIFFRACTION100
1.4992-1.53410.17352540.11883374X-RAY DIFFRACTION100
1.5341-1.57250.15022720.10923380X-RAY DIFFRACTION100
1.5725-1.6150.16762410.1133427X-RAY DIFFRACTION100
1.615-1.66250.15112700.10463411X-RAY DIFFRACTION100
1.6625-1.71620.15352710.10373368X-RAY DIFFRACTION100
1.7162-1.77750.15332850.10173384X-RAY DIFFRACTION100
1.7775-1.84870.15242750.10363403X-RAY DIFFRACTION100
1.8487-1.93290.13942500.10313446X-RAY DIFFRACTION100
1.9329-2.03480.14022730.09763427X-RAY DIFFRACTION100
2.0348-2.16230.12142520.0963420X-RAY DIFFRACTION100
2.1623-2.32920.13472900.09933418X-RAY DIFFRACTION100
2.3292-2.56360.13192520.10213472X-RAY DIFFRACTION100
2.5636-2.93450.13312690.11183503X-RAY DIFFRACTION100
2.9345-3.69710.14812760.1123518X-RAY DIFFRACTION100
3.6971-52.89780.13912690.13183701X-RAY DIFFRACTION100

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