[English] 日本語
Yorodumi
- PDB-4rp5: Crystal Structure of the L27 domain of Discs Large 1 (target ID N... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 129 / 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: 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

-
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

-
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

+
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