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- PDB-5mc9: Crystal structure of the heterotrimeric integrin-binding region o... -

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Basic information

Entry
Database: PDB / ID: 5mc9
TitleCrystal structure of the heterotrimeric integrin-binding region of laminin-111
Components
  • Laminin subunit alpha-1
  • Laminin subunit beta-1
  • Laminin subunit gamma-1
KeywordsCELL ADHESION / Extracellular matrix / coiled coil / laminin G-like domain
Function / homology
Function and homology information


laminin-3 complex / laminin complex / laminin-2 complex / laminin-8 complex / laminin-1 complex / laminin-10 complex / tissue morphogenesis / hair follicle cell proliferation / regulation of basement membrane organization / retinal blood vessel morphogenesis ...laminin-3 complex / laminin complex / laminin-2 complex / laminin-8 complex / laminin-1 complex / laminin-10 complex / tissue morphogenesis / hair follicle cell proliferation / regulation of basement membrane organization / retinal blood vessel morphogenesis / morphogenesis of an epithelial sheet / hemidesmosome assembly / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / tissue development / hair cell differentiation / protein complex involved in cell-matrix adhesion / branching involved in salivary gland morphogenesis / negative regulation of cell adhesion / establishment of epithelial cell apical/basal polarity / odontogenesis / extracellular matrix structural constituent / hair follicle morphogenesis / positive regulation of muscle cell differentiation / epithelial tube branching involved in lung morphogenesis / regulation of embryonic development / basement membrane / extracellular matrix disassembly / synaptic cleft / embryo implantation / extracellular matrix / positive regulation of cell adhesion / regulation of cell migration / neuromuscular junction / neuron projection development / integrin binding / cell-cell junction / cell migration / chromatin organization / retina development in camera-type eye / protein-containing complex assembly / : / gene expression / learning or memory / cell surface receptor signaling pathway / cell adhesion / positive regulation of cell migration / protein phosphorylation / signaling receptor binding / perinuclear region of cytoplasm / enzyme binding / extracellular space / extracellular region / nucleus / membrane
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 / Laminin B (Domain 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 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 / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Laminin subunit gamma-1 / Laminin subunit beta-1 / Laminin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsPulido, D. / Hohenester, E.
CitationJournal: Structure / Year: 2017
Title: Crystal Structure of the Heterotrimeric Integrin-Binding Region of Laminin-111.
Authors: Pulido, D. / Hussain, S.A. / Hohenester, E.
History
DepositionNov 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Laminin subunit alpha-1
B: Laminin subunit beta-1
C: Laminin subunit gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1625
Polymers83,0823
Non-polymers802
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-76 kcal/mol
Surface area33310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.760, 98.360, 135.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Laminin subunit alpha-1 / Laminin A chain / Laminin-1 subunit alpha / Laminin-3 subunit alpha / S-laminin subunit alpha / S-LAM alpha


Mass: 69451.078 Da / Num. of mol.: 1 / Fragment: UNP residues 2079-2707
Source method: isolated from a genetically manipulated source
Details: mouse laminin alpha1 chain, residues with disordered side chains are alanine
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lama1, Lama, Lama-1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P19137
#2: Protein Laminin subunit beta-1 / Laminin B1 chain / Laminin-1 subunit beta / Laminin-10 subunit beta / Laminin-12 subunit beta / ...Laminin B1 chain / Laminin-1 subunit beta / Laminin-10 subunit beta / Laminin-12 subunit beta / Laminin-2 subunit beta / Laminin-6 subunit beta / Laminin-8 subunit beta


Mass: 6451.335 Da / Num. of mol.: 1 / Fragment: UNP residues 1735-1786
Source method: isolated from a genetically manipulated source
Details: mouse laminin beta1 chain, residues with disordered side chains are alanine
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lamb1, Lamb-1, Lamb1-1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P02469
#3: 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: 7179.124 Da / Num. of mol.: 1 / Fragment: UNP residues 1548-1607
Source method: isolated from a genetically manipulated source
Details: mouse laminin gamma1 chain, residues with disordered side chains are alanine
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lamc1, Lamb-2, Lamc-1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P02468
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.02 M magnesium chloride hexahydrate, 0.1 M Na-HEPES (pH 7.5), 22% w/v poly(acrylic acid sodium salt) 5100

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.13→56.9 Å / Num. obs: 47309 / % possible obs: 99.4 % / Redundancy: 4.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.5
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.628 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WJS

2wjs


Resolution: 2.13→56.9 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.19
RfactorNum. reflection% reflection
Rfree0.2378 2306 4.88 %
Rwork0.2103 --
obs0.2117 47240 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.13→56.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5321 0 2 294 5617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045421
X-RAY DIFFRACTIONf_angle_d0.6987325
X-RAY DIFFRACTIONf_dihedral_angle_d11.2142004
X-RAY DIFFRACTIONf_chiral_restr0.032843
X-RAY DIFFRACTIONf_plane_restr0.003947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1301-2.17640.31481320.28842795X-RAY DIFFRACTION100
2.1764-2.2270.29231400.27912789X-RAY DIFFRACTION100
2.227-2.28270.29271450.2762754X-RAY DIFFRACTION99
2.2827-2.34440.30721500.26482782X-RAY DIFFRACTION99
2.3444-2.41340.29661730.26712761X-RAY DIFFRACTION99
2.4134-2.49130.30841510.27342763X-RAY DIFFRACTION99
2.4913-2.58040.27571430.24132784X-RAY DIFFRACTION100
2.5804-2.68370.30311470.24672782X-RAY DIFFRACTION100
2.6837-2.80580.3081210.2412841X-RAY DIFFRACTION100
2.8058-2.95370.29541210.23692838X-RAY DIFFRACTION100
2.9537-3.13880.27761290.23532824X-RAY DIFFRACTION99
3.1388-3.38110.26481560.22052753X-RAY DIFFRACTION98
3.3811-3.72130.23691440.19372786X-RAY DIFFRACTION98
3.7213-4.25960.18171310.17072841X-RAY DIFFRACTION98
4.2596-5.36610.16881570.15452838X-RAY DIFFRACTION99
5.3661-56.90.20811660.19343003X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.8846 Å / Origin y: -16.7014 Å / Origin z: -15.4714 Å
111213212223313233
T0.2626 Å2-0.0278 Å20.0029 Å2-0.2293 Å20.0334 Å2--0.2442 Å2
L0.7767 °2-0.0862 °20.2031 °2-0.2663 °20.0708 °2--0.67 °2
S0.025 Å °0.0468 Å °-0.0218 Å °-0.0043 Å °-0.0021 Å °0.0283 Å °0.0531 Å °0.0009 Å °-0.0092 Å °
Refinement TLS groupSelection details: all

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