[English] 日本語
Yorodumi
- PDB-8buw: Crystal structure of Trichoplax Scribble PDZ1 domain in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8buw
TitleCrystal structure of Trichoplax Scribble PDZ1 domain in complex with Trichoplax Vangl peptide
Components
  • Leucine-rich repeat-containing protein 1
  • Vang-like protein 1
KeywordsPROTEIN BINDING / PDZ domain / cell polarity / Scribble / Vangl / Trichopla
Function / homology
Function and homology information


receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / receptor clustering / adherens junction / cell-cell adhesion / basolateral plasma membrane / protein kinase binding
Similarity search - Function
: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat ...: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Leucine-rich repeat-containing protein 1
Similarity search - Component
Biological speciesTrichoplax sp. H2 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMaddumage, J.C. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1103871 Australia
CitationJournal: To Be Published
Title: Crystal structure of Trichoplax Scribble PDZ1 domain in complex with Trichoplax Vangl peptide
Authors: Maddumage, J.C. / Kvansakul, M. / Humbert, P.O.
History
DepositionDec 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine-rich repeat-containing protein 1
B: Leucine-rich repeat-containing protein 1
D: Vang-like protein 1
C: Vang-like protein 1


Theoretical massNumber of molelcules
Total (without water)21,7124
Polymers21,7124
Non-polymers00
Water00
1
A: Leucine-rich repeat-containing protein 1
D: Vang-like protein 1


Theoretical massNumber of molelcules
Total (without water)10,8562
Polymers10,8562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-4 kcal/mol
Surface area5380 Å2
MethodPISA
2
B: Leucine-rich repeat-containing protein 1
C: Vang-like protein 1


Theoretical massNumber of molelcules
Total (without water)10,8562
Polymers10,8562
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-4 kcal/mol
Surface area5270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.547, 30.298, 89.460
Angle α, β, γ (deg.)90.000, 90.920, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -1 through 10 or resid 12 through 79 or resid 82 through 90))
d_2ens_1(chain "B" and (resid -1 through 28 or (resid 29...
d_1ens_2chain "C"
d_2ens_2(chain "D" and (resid 66 through 71 or (resid 72...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYASPASPAA-1 - 104 - 15
d_12ens_1GLYGLYASNASNAA12 - 7917 - 84
d_13ens_1SERSERARGARGAA82 - 9087 - 95
d_21ens_1GLYGLYASNASNBB-1 - 794 - 84
d_22ens_1SERSERARGARGBB82 - 9087 - 95
d_11ens_2ASNASNVALVALDC66 - 731 - 8
d_21ens_2ASNASNVALVALCD193 - 2001 - 8

NCS ensembles :
ID
ens_1
ens_2

-
Components

#1: Protein Leucine-rich repeat-containing protein 1


Mass: 9999.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax sp. H2 (invertebrata) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): codon + / References: UniProt: A0A369S7Y8
#2: Protein/peptide Vang-like protein 1


Mass: 856.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Trichoplax sp. H2 (invertebrata)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris pH 8.5, 30% PEG 4000, 30% (v/v) ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.8→30.3 Å / Num. obs: 4011 / % possible obs: 96.4 % / Redundancy: 2.7 % / Biso Wilson estimate: 11.59 Å2 / CC1/2: 0.954 / Net I/σ(I): 4.3
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 587 / CC1/2: 0.835

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VWC

5vwc


Resolution: 2.85→29.82 Å / SU ML: 0.2848 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.896
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2626 200 5.27 %
Rwork0.2273 3597 -
obs0.2292 3797 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.64 Å2
Refinement stepCycle: LAST / Resolution: 2.85→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 0 0 1455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321467
X-RAY DIFFRACTIONf_angle_d0.61421967
X-RAY DIFFRACTIONf_chiral_restr0.0506232
X-RAY DIFFRACTIONf_plane_restr0.0032254
X-RAY DIFFRACTIONf_dihedral_angle_d13.6012537
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.03931156248
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.512996800343
LS refinement shellResolution: 2.85→29.82 Å
RfactorNum. reflection% reflection
Rfree0.2626 200 -
Rwork0.2273 3597 -
obs--94.85 %
Refinement TLS params.Method: refined / Origin x: -1.91077527322 Å / Origin y: -0.582042905752 Å / Origin z: -22.7954671098 Å
111213212223313233
T0.163772686233 Å20.0224620182733 Å2-0.0481417566589 Å2-0.0989517110912 Å20.00536403672506 Å2--0.0922918269124 Å2
L0.293518567241 °2-0.0935741976593 °20.0860567176268 °2-0.116459106194 °20.174711236381 °2--0.562279417082 °2
S0.0472418177264 Å °0.0486352055028 Å °0.053534288214 Å °-0.0438978665054 Å °0.0158710677829 Å °-0.0448799125361 Å °-0.0679340617934 Å °0.0172036714555 Å °0.118859824986 Å °
Refinement TLS groupSelection details: all

+
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