[English] 日本語
Yorodumi
- PDB-2d10: Crystal structure of the Radixin FERM domain complexed with the N... -

+
Open data


ID or keywords:

Loading...

-
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 / stereocilium base / regulation of actin filament bundle assembly / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / regulation of organelle assembly / regulation of ruffle assembly ...renal phosphate ion absorption / regulation of renal phosphate excretion / stereocilium base / regulation of actin filament bundle assembly / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / cerebrospinal fluid circulation / import across plasma membrane / positive regulation of early endosome to late endosome transport / negative regulation of sodium ion transport / microvillus assembly / gamma-aminobutyric acid import / negative regulation of adherens junction organization / maintenance of epithelial cell apical/basal polarity / bile acid secretion / regulation of protein kinase activity / regulation of Rap protein signal transduction / Recycling pathway of L1 / stereocilium tip / negative regulation of homotypic cell-cell adhesion / plasma membrane organization / phospholipase C-activating dopamine receptor signaling pathway / cilium organization / gland morphogenesis / channel activator activity / growth factor receptor binding / positive regulation of protein localization to early endosome / cell tip / regulation of postsynaptic neurotransmitter receptor diffusion trapping / protein kinase A signaling / intracellular phosphate ion homeostasis / fibroblast migration / establishment of Golgi localization / barbed-end actin filament capping / plasma membrane protein complex / stereocilium / establishment of epithelial cell apical/basal polarity / negative regulation of cell size / negative regulation of fibroblast migration / type 3 metabotropic glutamate receptor binding / apical protein localization / cellular response to thyroid hormone stimulus / auditory receptor cell stereocilium organization / chloride channel regulator activity / establishment of endothelial barrier / negative regulation of platelet-derived growth factor receptor signaling pathway / beta-2 adrenergic receptor binding / nuclear migration / cortical actin cytoskeleton / protein kinase A binding / regulation of cell size / microvillus membrane / renal absorption / microvillus / cleavage furrow / negative regulation of mitotic cell cycle / 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 / sperm midpiece / ruffle / T-tubule / endomembrane system / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell periphery / morphogenesis of an epithelium / protein localization to plasma membrane / PDZ domain binding / filopodium / adherens junction / brush border membrane / sensory perception of sound / establishment of protein localization / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / beta-catenin binding / Wnt signaling pathway / positive regulation of protein catabolic process / adenylate cyclase-activating dopamine receptor signaling pathway / apical part of cell / actin cytoskeleton / lamellipodium / myelin sheath / regulation of cell shape / actin binding / actin cytoskeleton organization / ATPase binding / midbody / protein-containing complex assembly / 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 / Ubiquitin-like domain superfamily / Roll / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more