[English] 日本語
Yorodumi
- PDB-2byg: 2nd PDZ Domain of Discs Large Homologue 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2byg
Title2nd PDZ Domain of Discs Large Homologue 2
ComponentsCHANNEL ASSOCIATED PROTEIN OF SYNAPSE-110
KeywordsSIGNAL TRANSDUCTION / DLG2 / PDZ / PDZ DOMAIN / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / PHOSPHORYLATION / SH3 DOMAIN
Function / homology
Function and homology information


retrograde axonal protein transport / GMP kinase activity / anterograde axonal protein transport / receptor localization to synapse / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / juxtaparanode region of axon / cellular response to potassium ion / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins ...retrograde axonal protein transport / GMP kinase activity / anterograde axonal protein transport / receptor localization to synapse / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / juxtaparanode region of axon / cellular response to potassium ion / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Long-term potentiation / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / axon cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / adherens junction / neuromuscular junction / cell-cell adhesion / postsynaptic density membrane / kinase binding / nervous system development / RAF/MAP kinase cascade / perikaryon / basolateral plasma membrane / chemical synaptic transmission / neuron projection / postsynaptic density / protein kinase binding / membrane / plasma membrane / cytosol
Similarity search - Function
Disks Large homologue 2, SH3 domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. ...Disks Large homologue 2, SH3 domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / 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 / Pdz3 Domain / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Disks large homolog 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsElkins, J.M. / Schoch, G.A. / Smee, C.E.A. / Berridge, G. / Salah, E. / Sundstrom, M. / Edwards, A. / Arrowsmith, C. / Weigelt, J. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Sci. / Year: 2007
Title: Structure of Pick1 and Other Pdz Domains Obtained with the Help of Self-Binding C-Terminal Extensions.
Authors: Elkins, J.M. / Papagrigoriou, E. / Berridge, G. / Yang, X. / Phillips, C. / Gileadi, C. / Savitsky, C. / Doyle, D.A.
History
DepositionAug 1, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHANNEL ASSOCIATED PROTEIN OF SYNAPSE-110


Theoretical massNumber of molelcules
Total (without water)12,7881
Polymers12,7881
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.774, 69.081, 73.967
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2064-

HOH

21A-2082-

HOH

-
Components

#1: Protein CHANNEL ASSOCIATED PROTEIN OF SYNAPSE-110 / CHAPSYN-110 / DISCS LARGE HOMOLOG 2


Mass: 12787.502 Da / Num. of mol.: 1 / Fragment: 2ND PDZ DOMAIN, RESIDUES 190-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15700
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINTERACTS WITH THE CYTOPLASMIC TAIL OF NMDA RECEPTOR SUBUNITS AND THE POTASSIUM CHANNELS
Sequence detailsMUTATION RESIDUE ASN278 TO LYS A278 IS A CLONING ARTEFACT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.6 % / Description: NONE
Crystal growpH: 8 / Details: 25% PEG 3350, 0.2M NACL, 0.1M BIS-TRIS PH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU-MSC / Detector: IMAGE PLATE / Date: Jun 23, 2005 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→34.54 Å / Num. obs: 9967 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.9
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 91.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PDR

1pdr


Resolution: 1.85→50.51 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.246 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 754 7.6 %RANDOM
Rwork0.196 ---
obs0.2 9195 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å20 Å2
2--0.11 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms738 0 0 100 838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022748
X-RAY DIFFRACTIONr_bond_other_d0.0010.02699
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9761011
X-RAY DIFFRACTIONr_angle_other_deg0.70431632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.644597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33825.86229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17615134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.929152
X-RAY DIFFRACTIONr_chiral_restr0.0710.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02132
X-RAY DIFFRACTIONr_nbd_refined0.1910.2123
X-RAY DIFFRACTIONr_nbd_other0.1640.2660
X-RAY DIFFRACTIONr_nbtor_refined0.170.2348
X-RAY DIFFRACTIONr_nbtor_other0.0780.2475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1050.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1430.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5523513
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.425776
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.8067282
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.56711235
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.575 46
Rwork0.422 574
Refinement TLS params.Method: refined / Origin x: 6.959 Å / Origin y: 19.604 Å / Origin z: 10.377 Å
111213212223313233
T-0.1313 Å20.0061 Å2-0.0149 Å2--0.1881 Å20.013 Å2---0.1163 Å2
L2.7266 °20.1321 °21.6386 °2-2.4008 °20.4836 °2--2.0828 °2
S0.0625 Å °-0.1114 Å °-0.0835 Å °0.0627 Å °-0.0336 Å °-0.0643 Å °0.1205 Å °-0.0259 Å °-0.0289 Å °

+
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