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- PDB-5ik8: Laminin A2LG45 I-form, G6/7 bound. -

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Basic information

Entry
Database: PDB / ID: 5ik8
TitleLaminin A2LG45 I-form, G6/7 bound.
ComponentsLaminin subunit alpha-2
KeywordsSTRUCTURAL PROTEIN / Extracellular Matrix / Ligand binding / LG domain
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 / basement membrane ...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 / basement membrane / positive regulation of cell adhesion / synaptic cleft / regulation of cell migration / axon guidance / animal organ morphogenesis / sarcolemma / neuromuscular junction / collagen-containing extracellular matrix / dendritic spine / cell adhesion / 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-type EGF-like (LE) domain profile. / Laminin G domain / 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
7-hydroxy-4-methyl-2H-chromen-2-one / CITRATE ANION / Laminin subunit alpha-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBriggs, D.C. / Hohenester, E. / Campbell, K.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101748/Z/13/Z United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural basis of laminin binding to the LARGE glycans on dystroglycan.
Authors: Briggs, D.C. / Yoshida-Moriguchi, T. / Zheng, T. / Venzke, D. / Anderson, M.E. / Strazzulli, A. / Moracci, M. / Yu, L. / Hohenester, E. / Campbell, K.P.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)85,53823
Polymers82,8102
Non-polymers2,72821
Water9,602533
1
A: Laminin subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,39511
Polymers41,4051
Non-polymers99010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Laminin subunit alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,14412
Polymers41,4051
Non-polymers1,73811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.540, 126.290, 144.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-4338-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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: 41405.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lama2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q60675

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Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D- ...alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 634.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-3DGlcpAb1-3DXylpa1-3DGlcpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122A-1b_1-5][a212h-1a_1-5]/1-2-1-2/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(3+1)][a-D-Xylp]{[(3+1)][b-D-GlcpA]{[(3+1)][a-D-Xylp]{}}}}LINUCSPDB-CARE
#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.: 2
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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Non-polymers , 5 types, 551 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-4MU / 7-hydroxy-4-methyl-2H-chromen-2-one / 4-methylumbelliferone / Hymecromone


Mass: 176.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 100mM Ammonium Citrate diabasic 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→55.77 Å / Num. obs: 68770 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.64 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DYK

1dyk


Resolution: 2→55.77 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.11
RfactorNum. reflection% reflection
Rfree0.2095 3436 5 %
Rwork0.177 --
obs0.1786 68768 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→55.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5755 0 175 533 6463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096073
X-RAY DIFFRACTIONf_angle_d0.6648203
X-RAY DIFFRACTIONf_dihedral_angle_d11.9123586
X-RAY DIFFRACTIONf_chiral_restr0.069933
X-RAY DIFFRACTIONf_plane_restr0.0031068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02740.36821430.28482585X-RAY DIFFRACTION100
2.0274-2.05640.30081480.27812569X-RAY DIFFRACTION100
2.0564-2.08710.32241460.26172573X-RAY DIFFRACTION100
2.0871-2.11970.27931270.24972599X-RAY DIFFRACTION100
2.1197-2.15440.25621410.22982563X-RAY DIFFRACTION100
2.1544-2.19160.27681330.22362622X-RAY DIFFRACTION100
2.1916-2.23140.26151390.21772561X-RAY DIFFRACTION100
2.2314-2.27430.24931340.20892612X-RAY DIFFRACTION100
2.2743-2.32080.23581360.2062591X-RAY DIFFRACTION100
2.3208-2.37120.28971240.20962586X-RAY DIFFRACTION100
2.3712-2.42640.24681170.20622612X-RAY DIFFRACTION100
2.4264-2.48710.25261360.1982602X-RAY DIFFRACTION100
2.4871-2.55430.2431240.192609X-RAY DIFFRACTION100
2.5543-2.62950.25441220.19282641X-RAY DIFFRACTION100
2.6295-2.71440.23441310.19652606X-RAY DIFFRACTION100
2.7144-2.81140.23291440.19642571X-RAY DIFFRACTION100
2.8114-2.92390.24681400.19692622X-RAY DIFFRACTION100
2.9239-3.0570.25151320.19212614X-RAY DIFFRACTION100
3.057-3.21810.26591250.18892631X-RAY DIFFRACTION100
3.2181-3.41970.20041350.17582625X-RAY DIFFRACTION100
3.4197-3.68370.16121500.1582633X-RAY DIFFRACTION100
3.6837-4.05430.17331560.14472607X-RAY DIFFRACTION100
4.0543-4.64080.15721480.12532652X-RAY DIFFRACTION100
4.6408-5.84590.18011540.14162674X-RAY DIFFRACTION100
5.8459-55.79170.20621510.19432772X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8617-0.77840.02591.39660.75860.9368-0.1463-0.23160.29320.1089-0.02950.3194-0.0119-0.19420.19070.40830.03140.07810.36440.02120.4995-30.54924.45345.2682
22.14670.61-0.21211.571-0.07852.29110.03390.17320.1737-0.00220.05440.0043-0.17-0.1168-0.08550.36540.06110.02450.27870.03880.348-3.661113.596824.4349
35.7194-0.99320.90542.93970.23742.6032-0.638-0.49910.82130.2140.0512-0.6968-0.32350.13070.33510.6201-0.0559-0.19160.43620.02160.7123-29.276876.311417.2087
43.4466-0.55651.10072.5209-0.42342.7027-0.1272-0.51960.22330.07850.13310.3556-0.5896-0.98150.14810.47950.2172-0.08190.7507-0.15770.4043-58.544473.53788.7945
53.13860.43260.85482.33830.15252.8841-0.187-0.09160.1565-0.03770.0290.2463-0.3155-0.75860.15590.40770.1275-0.0590.6556-0.08560.3646-59.330368.47562.0967
62.8395-0.89021.11280.4638-0.58972.0335-0.1844-0.06290.21060.1265-0.06150.0592-0.5708-0.71960.23260.52430.1266-0.06570.5716-0.12090.3514-42.264670.136718.1615
72.4575-1.04870.07552.63990.34932.0048-0.00770.0225-0.25170.2408-0.10170.04180.155-0.08050.08430.3575-0.0404-0.03220.3128-0.02450.3246-23.484850.90223.2802
82.8006-1.04730.5823.08020.14172.3520.09880.2469-0.1234-0.158-0.23420.3538-0.0332-0.41780.17980.3663-0.018-0.03130.4439-0.04750.3374-34.870358.395518.498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2738 through 2944 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2945 through 3118 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2741 through 2760 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2761 through 2790 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2791 through 2917 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2918 through 2947 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2948 through 3075 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3076 through 3118 )

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