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- PDB-2d11: Crystal structure of the Radixin FERM domain complexed with the N... -

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Basic information

Entry
Database: PDB / ID: 2d11
TitleCrystal structure of the Radixin FERM domain complexed with the NHERF-2 C-terminal tail peptide
Components
  • Na(+)/H(+) exchange regulatory cofactor NHE-RF2
  • Radixin
KeywordsCELL ADHESION / Protein-peptide complex
Function / homology
Function and homology information


stereocilium base / type 2 metabotropic glutamate receptor binding / regulation of actin filament bundle assembly / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / positive regulation of early endosome to late endosome transport / microvillus assembly / negative regulation of adherens junction organization / regulation of Rap protein signal transduction ...stereocilium base / type 2 metabotropic glutamate receptor binding / regulation of actin filament bundle assembly / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / positive regulation of early endosome to late endosome transport / microvillus assembly / negative regulation of adherens junction organization / regulation of Rap protein signal transduction / Recycling pathway of L1 / negative regulation of homotypic cell-cell adhesion / positive regulation of protein localization to early endosome / cell tip / : / regulation of postsynaptic neurotransmitter receptor diffusion trapping / barbed-end actin filament capping / stereocilium / type 3 metabotropic glutamate receptor binding / negative regulation of cell size / cellular response to thyroid hormone stimulus / establishment of endothelial barrier / apical protein localization / protein kinase A binding / cortical actin cytoskeleton / microvillus / cleavage furrow / positive regulation of G1/S transition of mitotic cell cycle / phosphatase binding / cellular response to platelet-derived growth factor stimulus / ruffle / protein-membrane adaptor activity / T-tubule / endomembrane system / protein localization to plasma membrane / adherens junction / filopodium / establishment of protein localization / beta-catenin binding / apical part of cell / positive regulation of protein catabolic process / myelin sheath / regulation of cell shape / lamellipodium / actin binding / ATPase binding / protein-containing complex assembly / midbody / positive regulation of cell migration / apical plasma membrane / cadherin binding / signaling receptor binding / protein domain specific binding / focal adhesion / positive regulation of gene expression / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol
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
Radixin / Na(+)/H(+) exchange regulatory cofactor NHE-RF2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Na(+)/H(+) exchange regulatory cofactor NHE-RF2
F: Na(+)/H(+) exchange regulatory cofactor NHE-RF2
G: Na(+)/H(+) exchange regulatory cofactor NHE-RF2
H: Na(+)/H(+) exchange regulatory cofactor NHE-RF2


Theoretical massNumber of molelcules
Total (without water)161,7678
Polymers161,7678
Non-polymers00
Water2,936163
1
A: Radixin
E: Na(+)/H(+) exchange regulatory cofactor NHE-RF2


Theoretical massNumber of molelcules
Total (without water)40,4422
Polymers40,4422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-13 kcal/mol
Surface area16720 Å2
MethodPISA
2
B: Radixin
F: Na(+)/H(+) exchange regulatory cofactor NHE-RF2


Theoretical massNumber of molelcules
Total (without water)40,4422
Polymers40,4422
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-13 kcal/mol
Surface area16640 Å2
MethodPISA
3
C: Radixin
G: Na(+)/H(+) exchange regulatory cofactor NHE-RF2


Theoretical massNumber of molelcules
Total (without water)40,4422
Polymers40,4422
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-12 kcal/mol
Surface area16850 Å2
MethodPISA
4
D: Radixin
H: Na(+)/H(+) exchange regulatory cofactor NHE-RF2


Theoretical massNumber of molelcules
Total (without water)40,4422
Polymers40,4422
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-12 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.626, 144.375, 177.944
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 1-310)
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
Na(+)/H(+) exchange regulatory cofactor NHE-RF2 / NHERF-2 / Tyrosine kinase activator protein 1 / TKA-1 / SRY interacting protein 1 / SIP- 1 / Solute ...NHERF-2 / Tyrosine kinase activator protein 1 / TKA-1 / SRY interacting protein 1 / SIP- 1 / Solute carrier family 9 isoform A3 regulatory factor 2 / NHE3 kinase A regulatory protein E3KARP / Sodium-hydrogen exchanger regulatory factor 2


Mass: 3517.120 Da / Num. of mol.: 4 / Fragment: residues 310-337 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: Q15599
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.6 Å3/Da / Density % sol: 53 %
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: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 118872 / Num. obs: 41789 / % possible obs: 95 %
Reflection shellResolution: 2.8→2.9 Å / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→29.7 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.862 / SU B: 15.9 / SU ML: 0.311 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27815 1082 2.6 %RANDOM
Rwork0.22193 ---
obs0.22343 40780 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: 36.403 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å20 Å20 Å2
2--1.33 Å20 Å2
3----4.26 Å2
Refinement stepCycle: LAST / Resolution: 2.81→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10438 0 0 163 10601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210694
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.95414430
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15651238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36124.184564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.007151984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.781576
X-RAY DIFFRACTIONr_chiral_restr0.0720.21510
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028180
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.24626
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.27300
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2354
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5881.56425
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74210093
X-RAY DIFFRACTIONr_scbond_it1.04134895
X-RAY DIFFRACTIONr_scangle_it1.644.54337
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.806→2.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 66 -
Rwork0.309 2812 -
obs--100 %

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