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- PDB-4rp5: Crystal Structure of the L27 domain of Discs Large 1 (target ID N... -

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Basic information

Entry
Database: PDB / ID: 4rp5
TitleCrystal Structure of the L27 domain of Discs Large 1 (target ID NYSGRC-010766) from Drosophila melanogaster (space group P21)
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 / negative regulation of imaginal disc growth / cell fate commitment involved in pattern specification / septate junction / septate junction assembly / type I terminal bouton ...smooth septate junction / positive phototaxis / RHO GTPases activate CIT / Neurexins and neuroligins / establishment or maintenance of polarity of larval imaginal disc epithelium / negative regulation of imaginal disc growth / cell fate commitment involved in pattern specification / septate junction / septate junction assembly / type I terminal bouton / 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 / anterior/posterior axis specification, follicular epithelium / pole plasm protein localization / establishment of spindle orientation / negative regulation of peptidoglycan recognition protein signaling pathway / basal protein localization / asymmetric protein localization involved in cell fate determination / dorsal closure / follicle cell of egg chamber development / positive regulation of synaptic assembly at neuromuscular junction / regulation of epidermal growth factor receptor signaling pathway / male courtship behavior / GMP kinase activity / epithelial structure maintenance / receptor localization to synapse / apical cortex / behavioral response to ethanol / morphogenesis of a polarized epithelium / leading edge membrane / protein localization to synapse / apicolateral plasma membrane / establishment or maintenance of epithelial cell apical/basal polarity / synaptic assembly at neuromuscular junction / cell fate specification / mating behavior / receptor clustering / locomotor rhythm / establishment of mitotic spindle orientation / lateral plasma membrane / regulation of postsynaptic membrane neurotransmitter receptor levels / postsynaptic density membrane / terminal bouton / neuromuscular junction / cell-cell adhesion / nervous system development / cell cortex / basolateral plasma membrane / chemical synaptic transmission / postsynaptic membrane / cytoskeleton / neuron projection / synapse / protein kinase binding / 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. ...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
Disks large 1 tumor suppressor protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGhosh, A. / 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 1.1Feb 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 1.2Mar 21, 2018Group: Data collection / Source and taxonomy
Category: diffrn_radiation_wavelength / diffrn_source / entity_src_gen
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)22,9933
Polymers22,9582
Non-polymers351
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-37 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.546, 47.818, 64.424
Angle α, β, γ (deg.)90.000, 95.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Disks large 1 tumor suppressor protein


Mass: 11479.016 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, 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2 M Sodium Format, 20 % PEG 3350, 3 % 1,5-Diaminopentane dihydrochloride, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2013
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 21489 / Num. obs: 20902 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.047 / Χ2: 1.127 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.683.90.54410391.095199.8
1.68-1.7140.42510251.1131100
1.71-1.744.10.36210561.1681100
1.74-1.784.10.33310511.1371100
1.78-1.824.10.27110341.1861100
1.82-1.864.10.21510291.1891100
1.86-1.94.10.19210541.225199.9
1.9-1.964.10.14110231.197199.9
1.96-2.014.10.11510561.186199.9
2.01-2.084.10.09510421.2121100
2.08-2.154.20.07210281.1421100
2.15-2.244.10.06210531.0971100
2.24-2.344.10.05110421.0521100
2.34-2.464.10.04810361.0551100
2.46-2.624.10.04310701.031100
2.62-2.824.10.04410451.0861100
2.82-3.14.10.04610471.1351100
3.1-3.554.10.03910580.951199.7
3.55-4.473.90.02610451.141199
4.47-3040.03110691.151196.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
CBASSdata collection
HKL-3000data reduction
PHASERphasing
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RP3

4rp3


Resolution: 1.65→27.016 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 1071 5.13 %RANDOM
Rwork0.1819 ---
all0.1982 21939 --
obs0.1835 20868 99.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.5 Å2 / Biso mean: 38.1187 Å2 / Biso min: 14.89 Å2
Refinement stepCycle: LAST / Resolution: 1.65→27.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 1 129 1653
LS refinement shellResolution: 1.65→1.7212 Å
RfactorNum. reflection% reflection
Rfree0.2704 112 -
Rwork0.2413 --
obs--95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9626-2.33522.58443.9807-1.52468.2222-0.03990.27560.39570.14680.1252-1.9655-0.30851.69860.13670.4702-0.03240.06920.5606-0.09020.656227.5063-11.55225.7117
25.45870.6193-1.09618.6946-8.98889.4620.03070.06580.0318-0.0881-0.4606-0.69730.01820.84860.46010.314-0.01790.03930.2171-0.03970.283723.2164-0.34171.6932
31.145-0.07370.48573.1133-2.03671.24690.0209-0.22240.02650.6442-0.0163-0.0104-0.7011-0.0425-0.06410.2844-0.00920.00530.1168-0.01520.161512.63375.895415.9406
45.05361.08674.08074.93651.01033.3561-0.3395-0.4713-0.42660.10910.11491.223-1.098-0.8440.07330.4170.1066-0.02340.48620.03070.29393.5865-4.636730.4351
58.3111-2.76441.76754.4099-6.17849.64150.1909-0.14770.98570.67480.1082-0.2264-1.29320.05-0.33570.3788-0.03580.08140.3556-0.02390.3132-6.08414.400514.1021
60.720.1811-1.14411.6273-1.56364.8780.048-0.1574-0.03060.2794-0.1509-0.1452-0.40070.43350.09510.2364-0.0226-0.00640.14930.01370.198815.3807-4.796321.2717
75.4538-0.7923-4.14060.25231.07934.9104-0.0415-0.3006-0.07450.0070.02030.02250.33470.0875-0.13120.3042-0.02330.02790.15550.01360.24933.05650.90084.7654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 7 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 24 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 66 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 86 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 94 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 66 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 67 through 94 )B0

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