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- PDB-5xau: Crystal structure of integrin binding fragment of laminin-511 -

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Basic information

Entry
Database: PDB / ID: 5xau
TitleCrystal structure of integrin binding fragment of laminin-511
Components(Laminin subunit ...) x 3
KeywordsCELL ADHESION / laminin / integrin / extracellular matrix protein
Function / homology
Function and homology information


laminin-5 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin-11 complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / extracellular matrix of synaptic cleft / L1CAM interactions ...laminin-5 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin-11 complex / laminin-1 complex / laminin-10 complex / regulation of basement membrane organization / extracellular matrix of synaptic cleft / L1CAM interactions / trunk neural crest cell migration / hemidesmosome assembly / postsynapse organization / cell adhesion mediator activity / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / morphogenesis of embryonic epithelium / morphogenesis of a polarized epithelium / Laminin interactions / Formation of the dystrophin-glycoprotein complex (DGC) / EGR2 and SOX10-mediated initiation of Schwann cell myelination / protein complex involved in cell-matrix adhesion / branching involved in salivary gland morphogenesis / endoderm development / negative regulation of cell adhesion / regulation of epithelial cell proliferation / odontogenesis / extracellular matrix structural constituent / skeletal system morphogenesis / MET activates PTK2 signaling / branching involved in ureteric bud morphogenesis / muscle organ development / positive regulation of muscle cell differentiation / maintenance of blood-brain barrier / endodermal cell differentiation / odontogenesis of dentin-containing tooth / regulation of embryonic development / basement membrane / Non-integrin membrane-ECM interactions / cilium assembly / extracellular matrix disassembly / hair follicle development / ECM proteoglycans / synaptic cleft / regulation of cell adhesion / Degradation of the extracellular matrix / embryo implantation / substrate adhesion-dependent cell spreading / positive regulation of cell adhesion / lung development / regulation of cell migration / positive regulation of epithelial cell proliferation / integrin-mediated signaling pathway / protein localization to plasma membrane / Post-translational protein phosphorylation / neuromuscular junction / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cell migration / : / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / cell adhesion / positive regulation of cell migration / receptor ligand activity / endoplasmic reticulum lumen / perinuclear region of cytoplasm / glutamatergic synapse / structural molecule activity / enzyme binding / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
: / LAMB1-4 helical domain / Laminin IV type B / Laminin IV type B domain / Laminin IV type A domain profile. / Laminin alpha, domain I / Laminin domain II / Laminin Domain I / Laminin Domain II / Laminin IV ...: / LAMB1-4 helical domain / Laminin IV type B / Laminin IV type B domain / Laminin IV type A domain profile. / 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/attractin EGF domain / 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. / TNFR/NGFR cysteine-rich region / Laminin G domain / Laminin G domain / Epidermal growth factor-like domain. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Laminin subunit alpha-5 / Laminin subunit beta-1 / Laminin subunit gamma-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsTakizawa, M. / Arimori, T. / Kitago, Y. / Takagi, J. / Sekiguchi, K.
CitationJournal: Sci Adv / Year: 2017
Title: Mechanistic basis for the recognition of laminin-511 by alpha 6 beta 1 integrin.
Authors: Takizawa, M. / Arimori, T. / Taniguchi, Y. / Kitago, Y. / Yamashita, E. / Takagi, J. / Sekiguchi, K.
History
DepositionMar 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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 / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Laminin subunit alpha-5
B: Laminin subunit beta-1
C: Laminin subunit gamma-1
D: Laminin subunit alpha-5
E: Laminin subunit beta-1
F: Laminin subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,95416
Polymers182,9016
Non-polymers2,05310
Water10,647591
1
A: Laminin subunit alpha-5
B: Laminin subunit beta-1
C: Laminin subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5798
Polymers91,4513
Non-polymers1,1285
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-75 kcal/mol
Surface area34540 Å2
MethodPISA
2
D: Laminin subunit alpha-5
E: Laminin subunit beta-1
F: Laminin subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3768
Polymers91,4513
Non-polymers9255
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-73 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.031, 121.618, 107.554
Angle α, β, γ (deg.)90.00, 127.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Laminin subunit ... , 3 types, 6 molecules ADBECF

#1: Protein Laminin subunit alpha-5


Mass: 73414.203 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2655-3327 / Mutation: I2723C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMA5, KIAA0533, KIAA1907 / Production host: Homo sapiens (human) / References: UniProt: O15230
#2: Protein Laminin subunit beta-1


Mass: 8552.753 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1714-1786
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMB1 / Production host: Homo sapiens (human) / References: UniProt: P07942
#3: Protein Laminin subunit gamma-1


Mass: 9483.724 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1528-1609 / Mutation: D1585C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMC1, LAMB2 / Production host: Homo sapiens (human) / References: UniProt: P11047

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Sugars , 2 types, 8 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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.: 7
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 , 2 types, 593 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate (pH 4.2), 19% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 164205 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.065 / Net I/σ(I): 29.08
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.47 / Rsym value: 1.14 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→49.41 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.081 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23726 8245 5 %RANDOM
Rwork0.20165 ---
obs0.20343 155954 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å2-0.15 Å2
2--1.4 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.8→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11248 0 128 591 11967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01911601
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210890
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9915705
X-RAY DIFFRACTIONr_angle_other_deg0.905325230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20951448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62223.728515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.152151954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9771593
X-RAY DIFFRACTIONr_chiral_restr0.0830.21775
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022350
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3262.5345828
X-RAY DIFFRACTIONr_mcbond_other1.3272.5345827
X-RAY DIFFRACTIONr_mcangle_it2.1973.7867264
X-RAY DIFFRACTIONr_mcangle_other2.1973.7867265
X-RAY DIFFRACTIONr_scbond_it1.7192.8755773
X-RAY DIFFRACTIONr_scbond_other1.7192.8755774
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8484.2118442
X-RAY DIFFRACTIONr_long_range_B_refined4.38129.99812272
X-RAY DIFFRACTIONr_long_range_B_other4.3829.99812273
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 596 -
Rwork0.32 11424 -
obs--98.88 %
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)
12.4305-2.92733.10743.6951-4.08794.7501-0.0717-0.10180.06490.07350.0543-0.083-0.1049-0.02890.01740.0597-0.0119-0.01710.07070.03560.112623.657953.026949.2972
20.3946-1.26561.27745.195-4.56064.33550.06320.0104-0.0651-0.12850.12680.0990.1613-0.0516-0.18990.01970.0199-0.00620.07340.05280.117327.564133.591158.4407
30.4321-0.95061.1022.1367-2.53213.2618-0.0038-0.0592-0.07790.00580.10830.1136-0.0215-0.0259-0.10460.03110.00490.01080.06210.04490.131522.968736.612460.3159
42.1279-2.0014.69362.3417-4.604610.4567-0.012-0.07050.0778-0.1409-0.1839-0.16570.0718-0.03370.19590.090.12580.04940.18520.07130.048320.94194.1011-27.16
50.5574-0.98882.33421.9725-3.898310.13370.10170.0196-0.0066-0.2375-0.14110.01770.3610.07570.03940.05710.09440.02160.21950.06820.032321.635188.1717-26.0874
60.7188-0.2341-0.27590.7691-1.76825.23510.25820.31760.03980.0288-0.04460.0661-0.3008-0.2464-0.21360.14050.11920.0250.26810.03730.013132.181482.4076-13.3113
70.19450.0305-0.00220.0103-0.02460.14720.0211-0.00370.0239-0.0013-0.01520.00750.03040.0195-0.00590.0624-0.00090.0140.07650.00280.073128.04977.679329.3186
80.51531.36-1.6438.038-4.06116.1742-0.3251-0.0363-0.01540.03810.2625-1.04180.50350.17650.06260.4190.1031-0.19790.1939-0.0080.289135.97813.6580.949
90.8074-0.08980.0910.29980.28990.62850.0513-0.0896-0.014-0.0782-0.0460.00980.0295-0.1237-0.00530.0624-0.03280.00090.0883-0.00980.0525-2.661364.473233.7263
101.13280.16860.64440.0460.07971.03040.0013-0.09950.0462-0.02510.01120.0027-0.00180.0115-0.01240.0373-0.01870.00140.0812-0.01280.065528.132581.307848.7905
111.20940.0324-0.03530.3319-0.32151.011-0.0611-0.03190.0540.07440.0223-0.022-0.0461-0.16640.03880.045-0.01370.02520.1174-0.0380.0512-6.488977.446661.8654
120.95250.28310.1020.50380.04220.1990.0640.154-0.05920.0254-0.03840.01330.04520.1142-0.02560.03930.0345-0.00490.1266-0.00910.031653.378175.202611.6084
130.9746-0.4198-0.16870.53470.03560.18380.00950.06910.08780.0184-0.01440.0357-0.00890.01180.00490.04510.00720.01350.05110.01190.088724.696598.531920.7
140.5728-0.0764-0.22380.66880.18810.6139-0.00270.09910.128-0.04070.0177-0.0175-0.1070.0736-0.0150.0426-0.0316-0.00350.13240.08550.069558.9136104.92778.37
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2705 - 2733
2X-RAY DIFFRACTION2B1716 - 1786
3X-RAY DIFFRACTION3C1535 - 1604
4X-RAY DIFFRACTION4D2673 - 2733
5X-RAY DIFFRACTION5E1715 - 1786
6X-RAY DIFFRACTION6F1553 - 1604
7X-RAY DIFFRACTION7A3501 - 3760
8X-RAY DIFFRACTION7B1801 - 1824
9X-RAY DIFFRACTION7C1701 - 1719
10X-RAY DIFFRACTION7D3501 - 3756
11X-RAY DIFFRACTION7E1801 - 1812
12X-RAY DIFFRACTION7F1701 - 1720
13X-RAY DIFFRACTION8A2676 - 2697
14X-RAY DIFFRACTION9A2734 - 2930
15X-RAY DIFFRACTION10A2931 - 3115
16X-RAY DIFFRACTION11A3116 - 3293
17X-RAY DIFFRACTION12D2734 - 2930
18X-RAY DIFFRACTION13D2931 - 3115
19X-RAY DIFFRACTION14D3116 - 3293

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