[English] 日本語
Yorodumi
- PDB-3soe: Crystal Structure of the 3rd PDZ domain of the human Membrane-ass... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3soe
TitleCrystal Structure of the 3rd PDZ domain of the human Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3 (MAGI3)
ComponentsMembrane-associated guanylate kinase, WW and PDZ domain-containing protein 3
KeywordsSIGNALING PROTEIN / Structural Genomics Consortium / SGC / PDZ domain
Function / homology
Function and homology information


guanylate kinase activity / regulation of JNK cascade / bicellular tight junction / viral process / cell-cell junction / cell junction / molecular adaptor activity / intracellular signal transduction / apoptotic process / signal transduction ...guanylate kinase activity / regulation of JNK cascade / bicellular tight junction / viral process / cell-cell junction / cell junction / molecular adaptor activity / intracellular signal transduction / apoptotic process / signal transduction / ATP binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3 / 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. / WW domain / WW/rsp5/WWP domain signature. ...Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3 / 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. / WW domain / WW/rsp5/WWP domain signature. / PDZ domain / Pdz3 Domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsIvarsson, Y. / Filippakopoulos, P. / Picaud, S. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Knapp, S. ...Ivarsson, Y. / Filippakopoulos, P. / Picaud, S. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Knapp, S. / Zimmermann, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the 3rd PDZ domain of the human Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3 (MAGI3)
Authors: Ivarsson, Y. / Filippakopoulos, P. / Picaud, S. / Vollmar, M. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Knapp, S. / Zimmermann, P.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0992
Polymers12,0371
Non-polymers621
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.630, 59.280, 65.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3 / Membrane-associated guanylate kinase inverted 3 / MAGI-3


Mass: 12037.209 Da / Num. of mol.: 1 / Fragment: UNP residues 601-691
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA1634, MAGI3 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q5TCQ9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M Bis-tris pH 6.0 0.25M Li2SO4 35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionRedundancy: 4.7 % / Av σ(I) over netI: 7.4 / Number: 84916 / Rsym value: 0.046 / D res high: 1.595 Å / D res low: 21.29 Å / Num. obs: 18132 / % possible obs: 97.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.0421.2998.110.0350.0354.4
3.575.0410010.0310.0314.8
2.913.5710010.0350.0354.9
2.522.9199.710.0380.0384.9
2.262.5299.110.0510.0514.9
2.062.269910.0690.0694.9
1.912.0697.810.1040.1044.8
1.781.9197.310.1780.1784.8
1.681.7896.810.3050.3054.7
1.61.689510.5150.5153.8
ReflectionResolution: 1.6→22.52 Å / Num. all: 18521 / Num. obs: 18132 / % possible obs: 97.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.683.80.5151.5948824910.51595
1.68-1.784.70.3052.51143024190.30596.8
1.78-1.914.80.1784.11112623200.17897.3
1.91-2.064.80.1046.91046321640.10497.8
2.06-2.264.90.0699.7986120230.06999
2.26-2.524.90.05112.7906818440.05199.1
2.52-2.914.90.03816809916450.03899.7
2.91-3.574.90.03516.1701214320.035100
3.57-5.044.80.03112.8547411390.031100
5.04-21.294.40.03510.428956550.03598.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 58.52 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å21.29 Å
Translation2.5 Å21.29 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 3BPU, 2R4H, 2Q9V

3bpu

2r4h

2q9v


Resolution: 1.6→22.52 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2067 / WRfactor Rwork: 0.1832 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8922 / SU B: 2.503 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0829 / SU Rfree: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 924 5.1 %RANDOM
Rwork0.188 ---
all0.1894 18532 --
obs0.1894 18095 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.72 Å2 / Biso mean: 23.4798 Å2 / Biso min: 10.56 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--1.14 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms765 0 4 157 926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.015
X-RAY DIFFRACTIONr_bond_other_d0.001
X-RAY DIFFRACTIONr_angle_refined_deg1.403
X-RAY DIFFRACTIONr_angle_other_deg0.887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.595
X-RAY DIFFRACTIONr_chiral_restr0.092
X-RAY DIFFRACTIONr_gen_planes_refined0.006
X-RAY DIFFRACTIONr_gen_planes_other0.001
X-RAY DIFFRACTIONr_mcbond_it1.576
X-RAY DIFFRACTIONr_mcbond_other0.449
X-RAY DIFFRACTIONr_mcangle_it2.74
X-RAY DIFFRACTIONr_scbond_it4.211
X-RAY DIFFRACTIONr_scangle_it6.467
LS refinement shellResolution: 1.6→1.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.698 65 -
Rwork0.588 1157 -
all-1222 -
obs--91.26 %
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)
10.0522-0.02890.28780.55890.47932.40340.02710.0060.0244-0.0723-0.0546-0.09310.03240.03110.02750.06550.02010.01390.1012-0.01760.031710.41195.946815.1616
20.90160.09090.02140.96780.14180.42520.02790.0319-0.02420.0146-0.05950.0250.0514-0.00820.03160.0455-0.0016-0.01080.073-0.01460.02843.9094.732328.5638
31.3867-0.4923-1.12990.26880.83913.0986-0.08370.1188-0.18550.0325-0.06460.0810.1555-0.09310.14840.1015-0.006-0.01430.0675-0.05570.0589-0.31193.720520.1473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A589 - 608
2X-RAY DIFFRACTION2A609 - 676
3X-RAY DIFFRACTION3A677 - 701

+
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://pdbjlvh1.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