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- PDB-3x23: Radixin complex -

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Basic information

Entry
Database: PDB / ID: 3x23
TitleRadixin complex
Components
  • Peptide from Matrix metalloproteinase-14
  • Radixin
KeywordsCELL INVASION / FERM domain / Cell adhesion / Adhesion receptors
Function / homology
Function and homology information


membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / stereocilium base / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / microvillus assembly / response to odorant / chondrocyte proliferation / head development ...membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / stereocilium base / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / microvillus assembly / response to odorant / chondrocyte proliferation / head development / TGFBR3 PTM regulation / Recycling pathway of L1 / astrocyte cell migration / tissue remodeling / negative regulation of focal adhesion assembly / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of protein processing / endochondral ossification / actin filament capping / stereocilium / apical protein localization / intermediate filament cytoskeleton / embryonic cranial skeleton morphogenesis / cellular response to thyroid hormone stimulus / endothelial cell proliferation / zymogen activation / positive regulation of B cell differentiation / cortical actin cytoskeleton / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / Activation of Matrix Metalloproteinases / endodermal cell differentiation / metalloaminopeptidase activity / Collagen degradation / cleavage furrow / microvillus / collagen catabolic process / extracellular matrix disassembly / negative regulation of Notch signaling pathway / positive regulation of G1/S transition of mitotic cell cycle / regulation of protein localization to plasma membrane / response to mechanical stimulus / ovarian follicle development / ruffle / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / skeletal system development / filopodium / cell motility / lung development / establishment of protein localization / protein catabolic process / : / protein processing / metalloendopeptidase activity / Golgi lumen / response to estrogen / male gonad development / integrin binding / apical part of cell / melanosome / lamellipodium / myelin sheath / actin binding / positive regulation of cell growth / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cytoplasmic vesicle / angiogenesis / endopeptidase activity / response to oxidative stress / response to hypoxia / positive regulation of cell migration / protein domain specific binding / serine-type endopeptidase activity / focal adhesion / proteolysis / extracellular space / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / PGBD superfamily ...Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / PGBD superfamily / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-domain like / Metallopeptidase, catalytic domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Neutral zinc metallopeptidases, zinc-binding region signature. / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Radixin / Matrix metalloproteinase-14
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsTerawaki, S. / Kitano, K. / Aoyama, M. / Mori, T. / Hakoshima, T.
CitationJournal: Genes Cells / Year: 2015
Title: MT1-MMP recognition by ERM proteins and its implication in CD44 shedding
Authors: Terawaki, S. / Kitano, K. / Aoyama, M. / Mori, T. / Hakoshima, T.
History
DepositionDec 9, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Radixin
B: Peptide from Matrix metalloproteinase-14


Theoretical massNumber of molelcules
Total (without water)39,4002
Polymers39,4002
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area17160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.651, 122.651, 128.275
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Radixin / ESP10


Mass: 36924.559 Da / Num. of mol.: 1 / Fragment: FERM domain, UNP reisudes 1-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rdx / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P26043
#2: Protein/peptide Peptide from Matrix metalloproteinase-14


Mass: 2474.954 Da / Num. of mol.: 1 / Fragment: cytoplasmic tail, UNP residues 563-582 / Source method: obtained synthetically / Details: human / Source: (synth.) Homo sapiens (human) / References: UniProt: P50281
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12% polyethylene glycol 4000, 100mM MOPS (pH 7.0), 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2006
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.396→19.833 Å / Num. obs: 22917 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.045
Reflection shellResolution: 2.4→2.47 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GC7

1gc7


Resolution: 2.396→19.833 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1950 8.76 %Random
Rwork0.1891 ---
all0.1934 ---
obs0.1934 22248 97.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.396→19.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 0 179 2770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072653
X-RAY DIFFRACTIONf_angle_d1.0753576
X-RAY DIFFRACTIONf_dihedral_angle_d15.951026
X-RAY DIFFRACTIONf_chiral_restr0.047376
X-RAY DIFFRACTIONf_plane_restr0.005459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3961-2.45590.25531260.2051132890
2.4559-2.52220.29621330.1962135994
2.5222-2.59630.27271280.202138194
2.5963-2.67990.23441320.2014139195
2.6799-2.77540.28341370.2057138695
2.7754-2.88620.2931380.2424141397
2.8862-3.01710.33461410.2518145299
3.0171-3.17560.32971420.238146899
3.1756-3.37360.31121400.2129146899
3.3736-3.63270.23771420.1931148099
3.6327-3.99550.21111430.1791148699
3.9955-4.56750.18171450.14771517100
4.5675-5.73150.19711480.16811542100
5.7315-19.83320.21081550.1759162799
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)
13.38974.3578-4.90795.0395-6.04366.82040.3261-0.0885-0.04530.47130.08390.67830.1582-0.2402-0.51860.9139-0.3710.07920.5379-0.06570.5144-45.48124.6558.4272
21.21290.5081-0.25962.9898-1.51723.84320.1438-0.0913-0.15660.2831-0.16890.12090.7653-0.4049-0.00440.5156-0.20310.06680.381-0.04130.3298-37.066938.2988-3.5498
38.4045-0.15213.37317.37154.26544.0441-0.0516-0.15160.52180.0759-0.15480.3329-0.6481-1.23810.13050.3572-0.0240.06570.40510.09720.3786-39.679458.7566-15.7738
43.80091.13671.85613.42680.69695.32410.2849-0.2482-0.25650.4921-0.135-0.59610.98880.8961-0.07810.43230.05930.03490.5720.04160.4039-18.388242.21322.5243
57.6826-3.87773.88268.0157-5.9579.0620.2176-0.3990.0963-1.48360.42050.28360.9482-0.4696-0.72461.2542-0.4990.04871.0999-0.03650.5383-47.496524.98331.3063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 154 )
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 179 )
4X-RAY DIFFRACTION4chain 'A' and (resid 180 through 297 )
5X-RAY DIFFRACTION5chain 'B' and (resid 566 through 576 )

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