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- PDB-2yvc: Crystal structure of the Radixin FERM domain complexed with the N... -

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Basic information

Entry
Database: PDB / ID: 2yvc
TitleCrystal structure of the Radixin FERM domain complexed with the NEP cytoplasmic tail
Components
  • Neprilysin
  • Radixin
KeywordsCELL ADHESION / Protein-peptide complex
Function / homology
Function and homology information


Physiological factors / neuropeptide processing / neprilysin / creatinine metabolic process / stereocilium base / regulation of actin filament bundle assembly / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / oligopeptidase activity ...Physiological factors / neuropeptide processing / neprilysin / creatinine metabolic process / stereocilium base / regulation of actin filament bundle assembly / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / oligopeptidase activity / positive regulation of early endosome to late endosome transport / microvillus assembly / Metabolism of Angiotensinogen to Angiotensins / negative regulation of adherens junction organization / regulation of Rap protein signal transduction / Recycling pathway of L1 / negative regulation of homotypic cell-cell adhesion / substance P catabolic process / cellular response to UV-A / positive regulation of protein localization to early endosome / cell tip / regulation of postsynaptic neurotransmitter receptor diffusion trapping / protein kinase A signaling / peptide metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / barbed-end actin filament capping / stereocilium / cardiolipin binding / neuron projection terminus / negative regulation of cell size / apical protein localization / cellular response to thyroid hormone stimulus / establishment of endothelial barrier / positive regulation of neurogenesis / cellular response to UV-B / cortical actin cytoskeleton / protein kinase A binding / phosphatidylserine binding / cellular response to cytokine stimulus / microvillus / amyloid-beta clearance / brush border / cleavage furrow / replicative senescence / amyloid-beta metabolic process / positive regulation of G1/S transition of mitotic cell cycle / angiotensin maturation / cellular response to platelet-derived growth factor stimulus / ruffle / metallocarboxypeptidase activity / sensory perception of pain / Neutrophil degranulation / T-tubule / peptide binding / placenta development / positive regulation of long-term synaptic potentiation / filopodium / adherens junction / kidney development / trans-Golgi network / lung development / establishment of protein localization / protein catabolic process / metalloendopeptidase activity / response to estrogen / metallopeptidase activity / positive regulation of protein catabolic process / apical part of cell / synaptic vesicle / peptidase activity / lamellipodium / myelin sheath / regulation of cell shape / actin binding / ATPase binding / midbody / learning or memory / early endosome / ciliary basal body / positive regulation of cell migration / apical plasma membrane / membrane raft / protein domain specific binding / axon / focal adhesion / neuronal cell body / synapse / dendrite / centrosome / positive regulation of gene expression / protein homodimerization activity / proteolysis / extracellular region / zinc ion binding / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Neprilysin-like (M13) protease domain profile. / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal ...Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Neprilysin-like (M13) protease domain profile. / 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 / 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. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Metallopeptidase, catalytic domain superfamily / Band 4.1 domain / Band 4.1 homologues / 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 / Neprilysin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTerawaki, S. / Kitano, K. / Hakoshima, T.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Structural basis for type II membrane protein binding by ERM proteins revealed by the radixin-neutral endopeptidase 24.11 (NEP) complex
Authors: Terawaki, S. / Kitano, K. / Hakoshima, T.
#1: Journal: Embo J. / Year: 2000
Title: Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain
Authors: Hamada, K. / Shimizu, T. / Matsui, T. / Tsukita, S. / Hakoshima, T.
#2: Journal: Embo J. / Year: 2003
Title: Structural basis of adhesion-molecule recognition by ERM proteins revealed by the crystal structure of the radixin-ICAM-2 complex
Authors: Hamada, K. / Shimizu, T. / Yonemura, S. / Tsukita, S. / Tsukita, S. / Hakoshima, T.
#3: Journal: Structure / Year: 2006
Title: Structural basis for NHERF recognition by ERM proteins
Authors: Terawaki, S. / Maesaki, R. / Hakoshima, T.
History
DepositionApr 11, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
A: Radixin
B: Radixin
C: Radixin
D: Neprilysin
E: Neprilysin
F: Neprilysin


Theoretical massNumber of molelcules
Total (without water)118,3756
Polymers118,3756
Non-polymers00
Water00
1
A: Radixin
D: Neprilysin


Theoretical massNumber of molelcules
Total (without water)39,4582
Polymers39,4582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area16240 Å2
MethodPISA
2
B: Radixin
E: Neprilysin


Theoretical massNumber of molelcules
Total (without water)39,4582
Polymers39,4582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-2 kcal/mol
Surface area16540 Å2
MethodPISA
3
C: Radixin
F: Neprilysin


Theoretical massNumber of molelcules
Total (without water)39,4582
Polymers39,4582
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-5 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.790, 116.838, 141.884
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 Radixin / ESP10


Mass: 36924.559 Da / Num. of mol.: 3 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P26043
#2: Protein/peptide Neprilysin / Neutral endopeptidase 24.11 / Neutral endopeptidase / NEP / Enkephalinase / Atriopeptidase / CD10 antigen


Mass: 2533.902 Da / Num. of mol.: 3 / Fragment: cytoplasmic tail / Source method: obtained synthetically / Details: This sequence occurs naturally in mouse. / References: UniProt: Q61391

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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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.2M DL-maleic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2005
RadiationMonochromator: rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→29.71 Å / Num. obs: 30656 / % possible obs: 99.7 %
Reflection shellResolution: 3.2→3.31 Å / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GC7

1gc7


Resolution: 3.2→29.71 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.876 / SU B: 45.646 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26712 1542 5.1 %RANDOM
Rwork0.23264 ---
obs0.2344 28899 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.391 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--0.19 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7607 0 0 0 7607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227789
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.96110503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0455907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.68224.419396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.287151474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1881549
X-RAY DIFFRACTIONr_chiral_restr0.0780.21111
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025897
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.23555
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.25323
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3831.54690
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.39327399
X-RAY DIFFRACTIONr_scbond_it1.87733524
X-RAY DIFFRACTIONr_scangle_it3.154.53104
X-RAY DIFFRACTIONr_rigid_bond_restr1.50738214
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded0.65837612
LS refinement shellResolution: 3.195→3.277 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 101 -
Rwork0.351 1978 -
obs--95.45 %

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