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- PDB-2d10: Crystal structure of the Radixin FERM domain complexed with the N... -

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Basic information

Entry
Database: PDB / ID: 2d10
TitleCrystal structure of the Radixin FERM domain complexed with the NHERF-1 C-terminal tail peptide
Components
  • Ezrin-radixin-moesin binding phosphoprotein 50
  • Radixin
KeywordsCELL ADHESION / Protein-peptide complex
Function / homology
Function and homology information


renal phosphate ion absorption / regulation of renal phosphate excretion / renal sodium ion transport / stereocilium base / type 2 metabotropic glutamate receptor binding / regulation of actin filament bundle assembly / glutathione transport / dopamine receptor binding / regulation of organelle assembly / regulation of ruffle assembly ...renal phosphate ion absorption / regulation of renal phosphate excretion / renal sodium ion transport / stereocilium base / type 2 metabotropic glutamate receptor binding / regulation of actin filament bundle assembly / glutathione transport / dopamine receptor binding / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / cerebrospinal fluid circulation / negative regulation of sodium ion transport / positive regulation of early endosome to late endosome transport / microvillus assembly / negative regulation of adherens junction organization / bile acid secretion / maintenance of epithelial cell apical/basal polarity / import across plasma membrane / regulation of protein kinase activity / regulation of Rap protein signal transduction / gamma-aminobutyric acid import / Recycling pathway of L1 / stereocilium tip / plasma membrane organization / negative regulation of homotypic cell-cell adhesion / phospholipase C-activating dopamine receptor signaling pathway / cilium organization / channel activator activity / gland morphogenesis / positive regulation of protein localization to early endosome / cell tip / : / regulation of postsynaptic neurotransmitter receptor diffusion trapping / establishment of Golgi localization / fibroblast migration / intracellular phosphate ion homeostasis / plasma membrane protein complex / barbed-end actin filament capping / establishment of epithelial cell apical/basal polarity / stereocilium / type 3 metabotropic glutamate receptor binding / negative regulation of fibroblast migration / negative regulation of cell size / cellular response to thyroid hormone stimulus / establishment of endothelial barrier / auditory receptor cell stereocilium organization / chloride channel regulator activity / negative regulation of mitotic cell cycle / apical protein localization / beta-2 adrenergic receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / growth factor receptor binding / nuclear migration / protein kinase A binding / cortical actin cytoskeleton / regulation of cell size / renal absorption / microvillus membrane / microvillus / cleavage furrow / positive regulation of G1/S transition of mitotic cell cycle / phosphatase binding / transport across blood-brain barrier / positive regulation of intrinsic apoptotic signaling pathway / cellular response to platelet-derived growth factor stimulus / protein-membrane adaptor activity / ruffle / sperm midpiece / T-tubule / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endomembrane system / morphogenesis of an epithelium / cell periphery / protein localization to plasma membrane / filopodium / adherens junction / PDZ domain binding / establishment of protein localization / brush border membrane / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / apical part of cell / positive regulation of protein catabolic process / adenylate cyclase-activating dopamine receptor signaling pathway / myelin sheath / regulation of cell shape / lamellipodium / actin cytoskeleton / actin binding / ATPase binding / actin cytoskeleton organization / protein-containing complex assembly / midbody / vesicle / positive regulation of cell migration / apical plasma membrane
Similarity search - Function
EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / 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 ...EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / 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. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like (UB roll) / PH-like domain superfamily / Roll / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Na(+)/H(+) exchange regulatory cofactor NHE-RF1 / Radixin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTerawaki, S. / Maesaki, R. / Hakoshima, T.
Citation
Journal: Structure / Year: 2006
Title: Structural basis for NHERF recognition by ERM proteins
Authors: Terawaki, S. / Maesaki, R. / Hakoshima, T.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Crystallographic characterization of the radixin FERM domain bound to the C-terminal region of the human Na+/H+-exchanger regulatory factor (NHERF)
Authors: Terawaki, S. / Maesaki, R. / Okada, K. / Hakoshima, T.
#2: 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.
#3: 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.
History
DepositionAug 11, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: 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: Radixin
E: Ezrin-radixin-moesin binding phosphoprotein 50
F: Ezrin-radixin-moesin binding phosphoprotein 50
G: Ezrin-radixin-moesin binding phosphoprotein 50
H: Ezrin-radixin-moesin binding phosphoprotein 50


Theoretical massNumber of molelcules
Total (without water)161,3388
Polymers161,3388
Non-polymers00
Water11,115617
1
A: Radixin
E: Ezrin-radixin-moesin binding phosphoprotein 50


Theoretical massNumber of molelcules
Total (without water)40,3342
Polymers40,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-12 kcal/mol
Surface area16610 Å2
MethodPISA
2
B: Radixin
F: Ezrin-radixin-moesin binding phosphoprotein 50


Theoretical massNumber of molelcules
Total (without water)40,3342
Polymers40,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-12 kcal/mol
Surface area17030 Å2
MethodPISA
3
C: Radixin
G: Ezrin-radixin-moesin binding phosphoprotein 50


Theoretical massNumber of molelcules
Total (without water)40,3342
Polymers40,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-13 kcal/mol
Surface area17150 Å2
MethodPISA
4
D: Radixin
H: Ezrin-radixin-moesin binding phosphoprotein 50


Theoretical massNumber of molelcules
Total (without water)40,3342
Polymers40,3342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-10 kcal/mol
Surface area16770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.388, 146.277, 177.763
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.: 4 / Fragment: FERM domain (residues 3-312)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P26043
#2: Protein/peptide
Ezrin-radixin-moesin binding phosphoprotein 50 / Sodium-hydrogen exchanger regulatory factor 1 / EBP50 / Na+ / /H+ / exchange regulatory cofactor ...Sodium-hydrogen exchanger regulatory factor 1 / EBP50 / Na+ / /H+ / exchange regulatory cofactor NHE-RF / NHERF-1 / Regulatory cofactor of Na+ / /H+ / exchanger / Solute carrier family 9 isoform 3 regulatory factor 1


Mass: 3409.898 Da / Num. of mol.: 4 / Fragment: residues 331-358 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: O14745
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG4000, 5% Isopropanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 62668 / Num. obs: 62668 / % possible obs: 99.2 %
Reflection shellResolution: 2.5→2.64 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GC7

1gc7


Resolution: 2.5→29.93 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.894 / SU B: 9.601 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.464 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2675 1594 2.5 %RANDOM
Rwork0.22928 ---
obs0.23026 61240 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å20 Å20 Å2
2---0.3 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10408 0 0 617 11025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210660
X-RAY DIFFRACTIONr_angle_refined_deg0.9721.95414416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9251258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42724.522544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1151915
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3921563
X-RAY DIFFRACTIONr_chiral_restr0.0670.21534
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028155
X-RAY DIFFRACTIONr_nbd_refined0.1760.24676
X-RAY DIFFRACTIONr_nbtor_refined0.2980.27274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2667
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.219
X-RAY DIFFRACTIONr_mcbond_it0.3971.56541
X-RAY DIFFRACTIONr_mcangle_it0.708210209
X-RAY DIFFRACTIONr_scbond_it0.76534750
X-RAY DIFFRACTIONr_scangle_it1.3044.54207
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 97 -
Rwork0.275 4474 -
obs--100 %

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