[English] 日本語
Yorodumi
- PDB-4wyu: Crystal Structure of Scribble PDZ34 tandem in complex with its ta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wyu
TitleCrystal Structure of Scribble PDZ34 tandem in complex with its target peptide
Components
  • Protein scribble homolog
  • peptide SER-TRP-PHE-GLN-THR-ASP-LEU
KeywordsSTRUCTURAL PROTEIN/PEPTIDE / PDZ tandem / PBM / STRUCTURAL PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


neurotransmitter receptor transport postsynaptic membrane to endosome / extrinsic component of postsynaptic density membrane / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation ...neurotransmitter receptor transport postsynaptic membrane to endosome / extrinsic component of postsynaptic density membrane / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to adherens junction / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / positive chemotaxis / receptor clustering / RHOJ GTPase cycle / RHOQ GTPase cycle / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / synaptic vesicle endocytosis / immunological synapse / negative regulation of mitotic cell cycle / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / cell-cell junction / cell migration / positive regulation of type II interferon production / presynapse / lamellipodium / cell junction / basolateral plasma membrane / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / glutamatergic synapse / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
Leucine-rich repeats, bacterial type / Leucine Rich Repeat / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / PDZ domain ...Leucine-rich repeats, bacterial type / Leucine Rich Repeat / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Protein scribble homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsRen, J.Q. / Pei, H.H. / Feng, W.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Biochem.J. / Year: 2015
Title: Interdomain interface-mediated target recognition by the Scribble PDZ34 supramodule.
Authors: Ren, J. / Feng, L. / Bai, Y. / Pei, H. / Yuan, Z. / Feng, W.
History
DepositionNov 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein scribble homolog
D: peptide SER-TRP-PHE-GLN-THR-ASP-LEU
B: Protein scribble homolog
C: peptide SER-TRP-PHE-GLN-THR-ASP-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,02511
Polymers46,1364
Non-polymers8887
Water1,946108
1
A: Protein scribble homolog
D: peptide SER-TRP-PHE-GLN-THR-ASP-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4495
Polymers23,0682
Non-polymers3813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-4 kcal/mol
Surface area10970 Å2
MethodPISA
2
B: Protein scribble homolog
C: peptide SER-TRP-PHE-GLN-THR-ASP-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5766
Polymers23,0682
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-6 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.270, 78.430, 94.080
Angle α, β, γ (deg.)90.000, 99.510, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein scribble homolog / hScrib / Protein LAP4


Mass: 22172.270 Da / Num. of mol.: 2 / Fragment: PDZ3/PDZ4 tandem (UNP RESIDUES 992-1203)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14160
#2: Protein/peptide peptide SER-TRP-PHE-GLN-THR-ASP-LEU / Synthetic PDZ binding motif


Mass: 895.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence is non-natural. / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% (w/v) PEG 3350, 0.2M KI, 0.1M HEPES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 18220 / Num. obs: 18220 / % possible obs: 98.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 38.23 Å2 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.133 / Rrim(I) all: 0.27 / Net I/σ(I): 8.8 / Num. measured all: 51169
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.644.80.5053.4782118440.3430.6183.499.5
3-3.194.20.4181.4737117620.2340.4183.999.7
3.19-3.414.20.2782695516510.1550.2784.899.5
3.41-3.684.20.2542.2634915230.1420.2545.699.4
3.68-4.034.10.2192.6570813970.1230.2196.199.3
4.03-4.5140.1782.9515112790.10.1787.299.6
4.51-5.23.80.1892.9435211370.1080.1897.499.5
5.2-6.373.70.1782.835269480.1060.1787.798.5
6.37-9.013.80.151328607430.090.1518.899.1
9.01-46.50230.1882.610763580.1180.1888.384.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
iMOSFLMdata processing
PHASERphasing
PDB_EXTRACT3.15data extraction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WYT

4wyt


Resolution: 2.5→36.758 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 903 4.97 %
Rwork0.1889 17273 -
obs0.1908 18176 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.97 Å2 / Biso mean: 46.9846 Å2 / Biso min: 17.07 Å2
Refinement stepCycle: final / Resolution: 2.5→36.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 7 108 3196
Biso mean--83.25 44.57 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043150
X-RAY DIFFRACTIONf_angle_d0.8134271
X-RAY DIFFRACTIONf_chiral_restr0.032485
X-RAY DIFFRACTIONf_plane_restr0.004577
X-RAY DIFFRACTIONf_dihedral_angle_d12.8361195
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.65660.29391520.25332891304399
2.6566-2.86170.30921490.24172902305199
2.8617-3.14950.22021520.20982902305499
3.1495-3.60490.21711550.1822872302798
3.6049-4.54050.19971480.15212867301597
4.5405-36.76170.21971470.1862839298695
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)
11.389-1.4379-1.11551.93670.29752.4974-0.1245-0.0212-0.04340.0481-0.00380.13370.02680.1640.12380.2847-0.0474-0.04170.22460.00440.2423-0.6062.7285204.4875
25.8684-0.7507-0.09790.146-0.32232.37660.20990.3038-0.1939-0.7435-0.1054-0.1040.5666-0.2573-0.06220.4037-0.00110.01320.42240.04390.292-3.20883.676187.9459
31.9939-0.2452-0.79512.5331-0.37823.3795-0.1028-0.11380.15730.01620.0698-0.1528-0.180.06960.03430.2034-0.0279-0.00940.1790.00580.2142-0.59636.1701201.364
43.6633-0.7049-0.14773.4115-1.00993.63480.0309-0.0243-0.1068-0.049-0.06920.02730.1822-0.02450.0350.2306-0.01260.02390.21180.03020.233313.808410.8605179.1587
53.42940.19660.39633.18171.16537.07660.44810.09031.47250.192-0.368-0.2684-1.22520.11120.27030.7304-0.09130.08770.48580.15580.62371.157216.6186192.8316
61.4624-0.9832-0.75314.73792.10432.8138-0.1467-0.0376-0.35550.0238-0.14880.7363-0.3661-0.24630.25140.33390.0266-0.00920.227-0.02190.2477-4.0065-6.4264211.006
72.8964-0.1760.10431.9895-0.21943.6809-0.1129-0.4425-0.13960.24480.06730.27430.0886-0.054-0.00740.32110.02660.020.25960.05130.3076-5.9012-17.7931221.3216
81.9805-0.3354-0.34552.4967-0.11033.5778-0.0824-0.0612-0.21880.1515-0.01290.0536-0.12570.21340.08360.1892-0.0033-0.01480.2560.04840.2434-3.2784-16.3388214.8321
91.81840.951-1.69841.3151-0.57443.2564-0.36280.0462-0.41660.3609-0.3393-1.01970.13521.2070.35880.56470.0764-0.04710.85910.17910.606613.5177-23.321242.1503
103.9332-1.0031.5731.9869-0.85663.5797-0.0071-0.25640.63960.17820.16540.3027-0.6508-1.0175-0.1230.61190.18420.07160.59620.1170.3791-7.777-17.3261240.9702
112.4222-0.8395-0.582.9689-1.07362.41320.06510.24780.08630.1596-0.2621-0.3802-0.24880.24960.170.4386-0.0085-0.0470.3680.06350.27664.2239-21.6095240.9109
122.7641.82590.01311.7402-1.39293.6613-0.07520.2009-0.00241.1066-0.41-0.268-0.48010.71130.25590.6455-0.0202-0.0380.6914-0.0030.26666.7167-19.4399237.8805
134.09620.30771.5847.00510.126.5426-0.1729-0.6532-0.46040.6205-0.1184-0.3150.6765-0.61190.11540.75910.020.03340.49380.16730.5909-4.7307-26.6214223.3601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-ID
1X-RAY DIFFRACTION1chain A and (resid 3 through 30 )A
2X-RAY DIFFRACTION2chain A and (resid 31 through 45 )A
3X-RAY DIFFRACTION3chain A and (resid 46 through 108 )A
4X-RAY DIFFRACTION4chain A and (resid 109 through 203 )A
5X-RAY DIFFRACTION5chain D and (resid -6 through 0 )D
6X-RAY DIFFRACTION6chain B and (resid 3 through 18 )B
7X-RAY DIFFRACTION7chain B and (resid 19 through 45 )B
8X-RAY DIFFRACTION8chain B and (resid 46 through 108 )B
9X-RAY DIFFRACTION9chain B and (resid 109 through 122 )B
10X-RAY DIFFRACTION10chain B and (resid 123 through 143 )B
11X-RAY DIFFRACTION11chain B and (resid 144 through 188 )B
12X-RAY DIFFRACTION12chain B and (resid 189 through 203 )B
13X-RAY DIFFRACTION13chain C and (resid -6 through 0 )C

+
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