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- PDB-4aqt: Laminin gamma1 LN-LE1-2 structure -

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Basic information

Entry
Database: PDB / ID: 4aqt
TitleLaminin gamma1 LN-LE1-2 structure
ComponentsLAMININ SUBUNIT GAMMA-1
KeywordsCELL ADHESION
Function / homology
Function and homology information


laminin-1 complex / laminin-10 complex / tissue morphogenesis / hair follicle cell proliferation / regulation of basement membrane organization / hemidesmosome assembly / positive regulation of integrin-mediated signaling pathway / glycosphingolipid binding / tissue development / hair cell differentiation ...laminin-1 complex / laminin-10 complex / tissue morphogenesis / hair follicle cell proliferation / regulation of basement membrane organization / hemidesmosome assembly / positive regulation of integrin-mediated signaling pathway / glycosphingolipid binding / tissue development / hair cell differentiation / protein complex involved in cell-matrix adhesion / extracellular matrix structural constituent / hair follicle morphogenesis / positive regulation of muscle cell differentiation / basement membrane / positive regulation of cell adhesion / extracellular matrix disassembly / synaptic cleft / substrate adhesion-dependent cell spreading / animal organ morphogenesis / neuromuscular junction / neuron projection development / cell migration / gene expression / chromatin organization / protein-containing complex assembly / collagen-containing extracellular matrix / cell adhesion / extracellular region
Similarity search - Function
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-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. ...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-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 / Laminin / Galactose-binding domain-like / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Laminin subunit gamma-1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsCarafoli, F. / Hussain, S. / Hohenester, E.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structures of the Network-Forming Short-Arm Tips of the Laminin Beta1 and Gamma1 Chains.
Authors: Carafoli, F. / Hussain, S. / Hohenester, E.
History
DepositionApr 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 2.1Dec 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LAMININ SUBUNIT GAMMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8244
Polymers41,9761
Non-polymers8483
Water0
1
A: LAMININ SUBUNIT GAMMA-1
hetero molecules

A: LAMININ SUBUNIT GAMMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6488
Polymers83,9532
Non-polymers1,6966
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
Buried area4210 Å2
ΔGint-14 kcal/mol
Surface area34930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.010, 203.010, 93.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein LAMININ SUBUNIT GAMMA-1 / / LAMININ B2 CHAIN / LAMININ-1 SUBUNIT GAMMA / LAMININ-10 SUBUNIT GAMMA / LAMININ-11 SUBUNIT GAMMA / ...LAMININ B2 CHAIN / LAMININ-1 SUBUNIT GAMMA / LAMININ-10 SUBUNIT GAMMA / LAMININ-11 SUBUNIT GAMMA / LAMININ-2 SUBUNIT GAMMA / LAMININ-3 SUBUNIT GAMMA / LAMININ-4 SUBUNIT GAMMA / LAMININ-6 SUBUNIT GAMMA / LAMININ-7 SUBUNIT GAMMA / LAMININ-8 SUBUNIT GAMMA / LAMININ-9 SUBUNIT GAMMA / S-LAMININ SUBUNIT GAMMA / S-LAM GAMMA


Mass: 41976.402 Da / Num. of mol.: 1 / Fragment: LN-LE1-2 FRAGMENT, RESIDUES 33-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PCEP-PU / Cell line (production host): HEK293 C18 / Production host: HOMO SAPIENS (human) / References: UniProt: P02468
#2: 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.: 1
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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.: 1
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

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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: 4.43 Å3/Da / Density % sol: 72 %
Description: THE DIFFRACTION LIMIT OF THE CRYSTAL WAS ANISOTROPIC AND LIMITED TO 3.8 A ALONG THE C AXIS.
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: May 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.17→50 Å / Num. obs: 12556 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 83.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.6
Reflection shellResolution: 3.17→3.25 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y38

2y38


Resolution: 3.2→50 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
Details: BECAUSE OF THE ANISOTROPIC DIFFRACTION LIMIT, THE DATA WERE TRUNCATED AT 3.8 A ALONG THE C-AXIS AND AT 3.2 A ALONG THE A- AND B-AXES USING THE DIFFRACTION ANISOTROPY SERVER
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 1059 8.6 %RANDOM
Rwork0.2307 ---
obs0.2307 10269 83.4 %-
Solvent computationSolvent model: FLAT / Bsol: 18.1433 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 63.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.814 Å20 Å20 Å2
2---2.814 Å20 Å2
3---5.628 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 54 0 2742
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_deg1.5
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_it1.652
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it2.652.5
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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