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- PDB-4yl8: Crystal structure of the Crumbs/Moesin complex -

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Basic information

Entry
Database: PDB / ID: 4yl8
TitleCrystal structure of the Crumbs/Moesin complex
Components
  • Moesin
  • Protein crumbs
KeywordsPROTEIN BINDING / protein complex / FERM domain
Function / homology
Function and homology information


liquid clearance, open tracheal system / maintenance of apical/basal cell polarity / dorsal closure, amnioserosa morphology change / cell morphogenesis involved in Malpighian tubule morphogenesis / rhabdomere morphogenesis / nuclear chromosome segregation / assembly of apicomedial cortex actomyosin / Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling ...liquid clearance, open tracheal system / maintenance of apical/basal cell polarity / dorsal closure, amnioserosa morphology change / cell morphogenesis involved in Malpighian tubule morphogenesis / rhabdomere morphogenesis / nuclear chromosome segregation / assembly of apicomedial cortex actomyosin / Pre-NOTCH Processing in Golgi / NOTCH4 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / tube morphogenesis / compound eye photoreceptor development / rhabdomere membrane / amnioserosa maintenance / Malpighian tubule morphogenesis / establishment or maintenance of polarity of follicular epithelium / regulation of imaginal disc growth / zonula adherens maintenance / zonula adherens assembly / wing disc dorsal/ventral pattern formation / subapical complex / establishment or maintenance of polarity of embryonic epithelium / open tracheal system development / regulation of lymphocyte migration / dorsal closure / T cell aggregation / compound eye morphogenesis / rhabdomere development / establishment or maintenance of apical/basal cell polarity / rhabdomere / trachea development / apical constriction / positive regulation of early endosome to late endosome transport / membrane to membrane docking / photoreceptor connecting cilium / Recycling pathway of L1 / uropod / positive regulation of hippo signaling / immunological synapse formation / positive regulation of protein localization to early endosome / gland morphogenesis / negative regulation of organ growth / apicolateral plasma membrane / cellular response to testosterone stimulus / establishment of epithelial cell apical/basal polarity / membrane organization / apical protein localization / photoreceptor cell maintenance / adherens junction organization / establishment of endothelial barrier / positive regulation of podosome assembly / Notch binding / centrosome localization / spectrin binding / microvillus membrane / regulation of intracellular protein transport / regulation of cell size / establishment or maintenance of cell polarity / pseudopodium / microvillus / negative regulation of Notch signaling pathway / salivary gland morphogenesis / T cell migration / T cell proliferation / cell adhesion molecule binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein kinase C binding / filopodium / spindle / positive regulation of protein catabolic process / apical part of cell / myelin sheath / regulation of cell shape / double-stranded RNA binding / regulation of protein localization / actin binding / basolateral plasma membrane / cytoskeleton / protein stabilization / apical plasma membrane / signaling receptor binding / cell division / focal adhesion / calcium ion binding / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / cell surface / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Laminin G domain / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like ...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 / Laminin G domain / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Laminin G domain / EGF-like, conserved site / Human growth factor-like EGF / Acyl-CoA Binding Protein / Laminin G domain profile. / 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 / Laminin G domain / Laminin G domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / : / Calcium-binding EGF domain / 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 / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Protein crumbs / Moesin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWei, Z. / Li, Y. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Research Grant Council663811, 663812, 664113, AoE/M09/12, and T13-607/12R Hong Kong
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for the Phosphorylation-regulated Interaction between the Cytoplasmic Tail of Cell Polarity Protein Crumbs and the Actin-binding Protein Moesin
Authors: Wei, Z. / Li, Y. / Ye, F. / Zhang, M.
History
DepositionMar 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Moesin
B: Protein crumbs
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,35425
Polymers40,4702
Non-polymers2,88423
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-23 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.115, 65.121, 83.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Moesin / Membrane-organizing extension spike protein


Mass: 35557.957 Da / Num. of mol.: 1 / Fragment: FERM domain, UNP residues 1-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Msn / Plasmid: pET32m / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26041
#2: Protein/peptide Protein crumbs / 95F


Mass: 4912.500 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 2110-2146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: crb / Plasmid: pET32m / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P10040
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M ammonium iodine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 55529 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 17.25 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.424 / Net I/av σ(I): 33.49 / Net I/σ(I): 13.2 / Num. measured all: 398670
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.537.30.65827241.062100
1.53-1.557.50.57627641.073100
1.55-1.587.50.46827351.103100
1.58-1.627.50.41727501.133100
1.62-1.657.50.35527371.148100
1.65-1.697.50.29127401.229100
1.69-1.737.50.23527651.297100
1.73-1.787.40.19327461.339100
1.78-1.837.50.16327491.392100
1.83-1.897.40.13227711.496100
1.89-1.967.40.11227691.522100
1.96-2.047.30.09427771.599100
2.04-2.137.30.08227591.548100
2.13-2.247.20.07327721.637100
2.24-2.387.10.06727841.466100
2.38-2.566.90.06627891.599100
2.56-2.826.70.06128101.66899.9
2.82-3.236.60.05528281.66899.9
3.23-4.076.60.04228581.78599.7
4.07-506.30.03929021.90596.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX(phenix.refine: 1.7.1_743)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EF1

1ef1


Resolution: 1.5→39.8 Å / FOM work R set: 0.8749 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1907 1994 3.6 %
Rwork0.1587 53440 -
obs0.1599 55434 99.52 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.232 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 77.69 Å2 / Biso mean: 24.57 Å2 / Biso min: 11.38 Å2
Baniso -1Baniso -2Baniso -3
1--3.074 Å2-0 Å20 Å2
2---4.696 Å20 Å2
3---7.77 Å2
Refinement stepCycle: final / Resolution: 1.5→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 30 269 2989
Biso mean--34.44 34.13 -
Num. residues----327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062862
X-RAY DIFFRACTIONf_angle_d1.0473886
X-RAY DIFFRACTIONf_chiral_restr0.07418
X-RAY DIFFRACTIONf_plane_restr0.005501
X-RAY DIFFRACTIONf_dihedral_angle_d12.4661116
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.499-1.53650.2661370.21363645378297
1.5365-1.5780.21681450.18338023947100
1.578-1.62450.23641430.171637673910100
1.6245-1.67690.20471380.154237833921100
1.6769-1.73680.18391460.137437953941100
1.7368-1.80640.21341410.136537993940100
1.8064-1.88860.16861420.133437973939100
1.8886-1.98820.19531440.13238153959100
1.9882-2.11270.16911380.135838193957100
2.1127-2.27580.19961440.145138223966100
2.2758-2.50480.19831430.149238523995100
2.5048-2.86720.17741420.166238724014100
2.8672-3.6120.19921420.158939104052100
3.612-39.81430.18021490.17783962411197

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