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- PDB-2wjs: Crystal structure of the LG1-3 region of the laminin alpha2 chain -

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Basic information

Entry
Database: PDB / ID: 2wjs
TitleCrystal structure of the LG1-3 region of the laminin alpha2 chain
ComponentsLAMININ SUBUNIT ALPHA-2
KeywordsCELL ADHESION / INTEGRIN / SECRETED / COILED COIL / GLYCOPROTEIN / LAMININ EGF-LIKE DOMAIN / EXTRACELLULAR MATRIX / LAMININ G-LIKE DOMAIN / DISULFIDE BOND / BASEMENT MEMBRANE
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 / tissue development / protein complex involved in cell-matrix adhesion / extracellular matrix structural constituent / positive regulation of muscle cell differentiation / regulation of embryonic development / positive regulation of cell adhesion ...regulation of basement membrane organization / Schwann cell differentiation / positive regulation of synaptic transmission, cholinergic / positive regulation of integrin-mediated signaling pathway / tissue development / protein complex involved in cell-matrix adhesion / extracellular matrix structural constituent / positive regulation of muscle cell differentiation / regulation of embryonic development / positive regulation of cell adhesion / basement membrane / synaptic cleft / regulation of cell migration / substrate adhesion-dependent cell spreading / animal organ morphogenesis / axon guidance / neuromuscular junction / sarcolemma / collagen-containing extracellular matrix / dendritic spine / signaling receptor binding / 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 N-terminal (Domain VI) ...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. / Jelly Rolls - #200 / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Laminin subunit alpha-2
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCarafoli, F. / Clout, N.J. / Hohenester, E.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structure of the Lg1-3 Region of the Laminin {Alpha}2 Chain.
Authors: Carafoli, F. / Clout, N.J. / Hohenester, E.
History
DepositionMay 28, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LAMININ SUBUNIT ALPHA-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1768
Polymers67,1711
Non-polymers1,0057
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)138.829, 138.829, 73.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein LAMININ SUBUNIT ALPHA-2 / LAMININ M CHAIN / MEROSIN HEAVY CHAIN / LAMININ ALPHA2 CHAIN


Mass: 67171.000 Da / Num. of mol.: 1 / Fragment: LG1-3,RESIDUES 2136-2475,2480-2565,2579-2746
Source method: isolated from a genetically manipulated source
Details: PROTEIN EXPRESSED IN PRESENCE OF KIFUNENSINE AND DIGESTED WITH ENDOGLYCOSIDASE H
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCEP-PU / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: Q60675
#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsN-ACETYLGLUCOSAMINE (NAG): COVALENTLY ATTACHED TO ASPARGINES 2236, 2356, 2431 AND 2554.
Sequence detailsTHE SEQUENCE OF THE CRYSTALLIZED PROTEIN ACTUALLY CORRESPONDS TO THE NCBI ENTRY NP_032507. VECTOR- ...THE SEQUENCE OF THE CRYSTALLIZED PROTEIN ACTUALLY CORRESPONDS TO THE NCBI ENTRY NP_032507. VECTOR-DERIVED N-TERMINAL APLA AND C-TERMINAL AAAHHHHHH. RESIDUES 2476-2479 (SMKA, EXON 53) MISSING. RESIDUES 2566- 2578 REPLACED BY G.IT IS A DELETION MUTATION.

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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: 3.62 Å3/Da / Density % sol: 65.76 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.045
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 19248 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.8 / % possible all: 89.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DYK

1dyk


Resolution: 2.8→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1894 9.4 %RANDOM
Rwork0.212 ---
obs0.212 19245 95.7 %-
Solvent computationSolvent model: FLAT / Bsol: 24.06 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.21 Å20 Å20 Å2
2--2.21 Å20 Å2
3----4.42 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 59 60 4056
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.812.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4CARBOHYDRATE.PARAM

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