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- PDB-4rp3: Crystal Structure of the L27 Domain of Discs Large 1 (target ID N... -

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Entry
Database: PDB / ID: 4rp3
TitleCrystal Structure of the L27 Domain of Discs Large 1 (target ID NYSGRC-010766) from Drosophila melanogaster bound to a potassium ion (space group P212121)
ComponentsDisks large 1 tumor suppressor protein
KeywordsANTITUMOR PROTEIN / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / Scaffolding
Function / homology
Function and homology information


smooth septate junction / positive phototaxis / RHO GTPases activate CIT / Neurexins and neuroligins / establishment or maintenance of polarity of larval imaginal disc epithelium / cell fate commitment involved in pattern specification / type I terminal bouton / septate junction / septate junction assembly / negative regulation of imaginal disc growth ...smooth septate junction / positive phototaxis / RHO GTPases activate CIT / Neurexins and neuroligins / establishment or maintenance of polarity of larval imaginal disc epithelium / cell fate commitment involved in pattern specification / type I terminal bouton / septate junction / septate junction assembly / negative regulation of imaginal disc growth / Activation of Ca-permeable Kainate Receptor / morphogenesis of follicular epithelium / type Ib terminal bouton / subsynaptic reticulum / Synaptic adhesion-like molecules / establishment or maintenance of polarity of follicular epithelium / morphogenesis of larval imaginal disc epithelium / Unblocking of NMDA receptors, glutamate binding and activation / gravitaxis / tricellular tight junction / establishment of spindle orientation / anterior/posterior axis specification, follicular epithelium / negative regulation of peptidoglycan recognition protein signaling pathway / pole plasm protein localization / basal protein localization / asymmetric protein localization involved in cell fate determination / dorsal closure / follicle cell of egg chamber development / regulation of epidermal growth factor receptor signaling pathway / positive regulation of synaptic assembly at neuromuscular junction / male courtship behavior / guanylate kinase activity / receptor localization to synapse / morphogenesis of a polarized epithelium / behavioral response to ethanol / apical cortex / apicolateral plasma membrane / leading edge membrane / establishment or maintenance of epithelial cell apical/basal polarity / synaptic assembly at neuromuscular junction / mating behavior / cell fate specification / receptor clustering / locomotor rhythm / establishment of mitotic spindle orientation / lateral plasma membrane / postsynaptic density membrane / neuromuscular junction / protein localization / terminal bouton / cell-cell adhesion / kinase binding / nervous system development / cell cortex / chemical synaptic transmission / postsynaptic membrane / basolateral plasma membrane / cytoskeleton / neuron projection / synapse / perinuclear region of cytoplasm / signal transduction / plasma membrane
Similarity search - Function
L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. ...L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
FORMIC ACID / : / Disks large 1 tumor suppressor protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.36 Å
AuthorsGhosh, A. / Ramagopal, U. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Biochemistry / Year: 2018
Title: Structures of the L27 Domain of Disc Large Homologue 1 Protein Illustrate a Self-Assembly Module.
Authors: Ghosh, A. / Ramagopal, U.A. / Bonanno, J.B. / Brenowitz, M. / Almo, S.C.
History
DepositionOct 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 21, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disks large 1 tumor suppressor protein
B: Disks large 1 tumor suppressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0316
Polymers22,8642
Non-polymers1674
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-47 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.979, 57.571, 64.529
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 Disks large 1 tumor suppressor protein


Mass: 11432.120 Da / Num. of mol.: 2 / Fragment: L27 domain residues 1-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG1725, Discs Large 1 Isoform B, dlg1, l(1)dlg1 / Plasmid: pSGC-His / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) pRIL / References: UniProt: P31007
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / 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: 1.95 Å3/Da / Density % sol: 36.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium Format, 20 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2013
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Number: 280814 / Rmerge(I) obs: 0.059 / Χ2: 1.11 / D res high: 1.36 Å / D res low: 30 Å / Num. obs: 39086 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
3.693010.0381.026.9
2.933.6910.050.9799.5
2.562.9310.0530.9749.8
2.332.5610.0621.0269.9
2.162.3310.071.110
2.032.1610.081.13810
1.932.0310.091.08810
1.851.9310.1191.10810
1.771.8510.1541.11110
1.711.7710.1361.0745.6
1.661.7110.1511.0865.2
1.611.6610.1931.1375.2
1.571.6110.2451.1725.1
1.531.5710.2741.1795.2
1.51.5310.2541.1945.2
1.471.510.2741.2365.2
1.441.4710.481.2395.1
1.411.4410.721.2545.2
1.381.4110.8241.2845.1
1.361.3810.9191.2875.1
ReflectionResolution: 1.36→30 Å / Num. all: 39126 / Num. obs: 39086 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.059 / Χ2: 1.11 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.36-1.385.10.91919181.287199.9
1.38-1.415.10.82419431.284199.9
1.41-1.445.20.7219321.2541100
1.44-1.475.10.4819071.2391100
1.47-1.55.20.27419471.236199.9
1.5-1.535.20.25418941.1941100
1.53-1.575.20.27419561.1791100
1.57-1.615.10.24519231.1721100
1.61-1.665.20.19319421.137199.9
1.66-1.715.20.15119441.0861100
1.71-1.775.60.13619341.0741100
1.77-1.85100.15419441.111199.9
1.85-1.93100.11919511.108199.9
1.93-2.03100.0919481.0881100
2.03-2.16100.0819621.1381100
2.16-2.33100.0719581.11100
2.33-2.569.90.06219761.0261100
2.56-2.939.80.05320040.9741100
2.93-3.699.50.0520150.9791100
3.69-306.90.03820881.02197.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
CBASSdata collection
HKL-3000data reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.36→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.603 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 1959 5 %RANDOM
Rwork0.1472 ---
obs0.1501 37070 99.54 %-
all-37358 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 183.07 Å2 / Biso mean: 27.565 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2--1.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.36→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 8 163 1672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191570
X-RAY DIFFRACTIONr_bond_other_d0.0010.021585
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.9742118
X-RAY DIFFRACTIONr_angle_other_deg1.16333645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2315193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39324.3982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45515319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0851514
X-RAY DIFFRACTIONr_chiral_restr0.130.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021753
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02361
X-RAY DIFFRACTIONr_mcbond_it8.6922.177739
X-RAY DIFFRACTIONr_mcbond_other8.6882.178740
X-RAY DIFFRACTIONr_mcangle_it10.4473.267925
X-RAY DIFFRACTIONr_rigid_bond_restr6.61633155
X-RAY DIFFRACTIONr_sphericity_free29.692550
X-RAY DIFFRACTIONr_sphericity_bonded21.44553250
LS refinement shellResolution: 1.36→1.394 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 156 -
Rwork0.242 2593 -
all-2749 -
obs--95.92 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
12.522729.915814.5396
2-2.691130.052915.3694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 10
2X-RAY DIFFRACTION1A11 - 56
3X-RAY DIFFRACTION1A57 - 75
4X-RAY DIFFRACTION1A76 - 95
5X-RAY DIFFRACTION2B6 - 9
6X-RAY DIFFRACTION2B10 - 41
7X-RAY DIFFRACTION2B42 - 81
8X-RAY DIFFRACTION2B82 - 95

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