[English] 日本語
Yorodumi
- PDB-3o46: Crystal structure of the PDZ domain of MPP7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o46
TitleCrystal structure of the PDZ domain of MPP7
ComponentsMAGUK p55 subfamily member 7
KeywordsPROTEIN BINDING / pdz domain / structural genomics consortium / SGC
Function / homology
Function and homology information


MPP7-DLG1-LIN7 complex / protein localization to adherens junction / bicellular tight junction assembly / establishment of cell polarity / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOG GTPase cycle / lateral plasma membrane / bicellular tight junction / RAC2 GTPase cycle ...MPP7-DLG1-LIN7 complex / protein localization to adherens junction / bicellular tight junction assembly / establishment of cell polarity / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOG GTPase cycle / lateral plasma membrane / bicellular tight junction / RAC2 GTPase cycle / RAC3 GTPase cycle / signaling adaptor activity / RAC1 GTPase cycle / adherens junction / positive regulation of protein-containing complex assembly / cell-cell junction / cell junction / cell cortex / molecular adaptor activity / cadherin binding / protein domain specific binding / nucleoplasm / plasma membrane
Similarity search - Function
MPP7, SH3 domain / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. ...MPP7, SH3 domain / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / 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
MAGUK p55 subfamily member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsNedyalkova, L. / Tong, Y. / Tempel, W. / Zhong, N. / Guan, X. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Nedyalkova, L. / Tong, Y. / Tempel, W. / Zhong, N. / Guan, X. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of the PDZ domain of MPP7
Authors: Nedyalkova, L. / Tong, Y. / Tempel, W. / Zhong, N. / Guan, X. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MAGUK p55 subfamily member 7


Theoretical massNumber of molelcules
Total (without water)10,10214
Polymers10,1021
Non-polymers013
Water1,24369
1
A: MAGUK p55 subfamily member 7

A: MAGUK p55 subfamily member 7

A: MAGUK p55 subfamily member 7


Theoretical massNumber of molelcules
Total (without water)30,30742
Polymers30,3073
Non-polymers039
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area4210 Å2
ΔGint-16 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.616, 66.616, 46.475
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-33-

HOH

21A-49-

HOH

-
Components

#1: Protein MAGUK p55 subfamily member 7


Mass: 10102.445 Da / Num. of mol.: 1 / Fragment: PDZ Domain (UNP residues 135-225)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPP7 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q5T2T1
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
21001
11001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97904
ROTATING ANODERIGAKU FR-E DW21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 17, 2010
RIGAKU RAXIS2IMAGE PLATEJun 13, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2SINGLE WAVELENGTHMx-ray1
1SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979041
21.54181
ReflectionResolution: 1.3→40 Å / Num. obs: 28982 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.041 / Χ2: 1.566 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.3-1.325.50.75128471.66100
1.32-1.355.50.66328151.59999.8
1.35-1.375.50.52228821.6199.9
1.37-1.45.50.42128441.514100
1.4-1.435.50.36928211.49199.9
1.43-1.465.60.3228501.45399.9
1.46-1.55.60.23128991.4199.9
1.5-1.545.60.18928121.43100
1.54-1.595.60.15928521.419100
1.59-1.645.60.12828011.389100
1.64-1.75.60.10129041.441100
1.7-1.765.60.08428371.409100
1.76-1.845.70.06828771.459100
1.84-1.945.70.05428351.587100
1.94-2.065.70.05328092.031100
2.06-2.225.60.04928852.329100
2.22-2.455.60.0428491.918100
2.45-2.85.50.0328651.429100
2.8-3.535.80.02728371.419100
3.53-405.50.02528001.30897.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→33.308 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.192 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 1.195 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY . The structure was originally solved using data measured with the same crystal on a copper rotating anode. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY . The structure was originally solved using data measured with the same crystal on a copper rotating anode. The model was refined against higher resolution synchrotron data. Scaled synchrotron intensities have been deposited along with the structure factors.
RfactorNum. reflection% reflectionSelection details
Rfree0.1908 1449 5.009 %RANDOM
Rwork0.1839 ---
obs0.184 28929 99.807 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 44.67 Å2 / Biso mean: 12.991 Å2 / Biso min: 9.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.584 Å20.292 Å20 Å2
2--0.584 Å20 Å2
3----0.876 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms617 0 13 69 699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022700
X-RAY DIFFRACTIONr_bond_other_d0.0020.02493
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.987963
X-RAY DIFFRACTIONr_angle_other_deg0.92131231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7335105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1652526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.915140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.682155
X-RAY DIFFRACTIONr_chiral_restr0.110.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02121
X-RAY DIFFRACTIONr_mcbond_it1.9021.5453
X-RAY DIFFRACTIONr_mcbond_other0.5651.5185
X-RAY DIFFRACTIONr_mcangle_it2.9732749
X-RAY DIFFRACTIONr_scbond_it3.9893247
X-RAY DIFFRACTIONr_scangle_it6.0284.5203
X-RAY DIFFRACTIONr_rigid_bond_restr1.41331193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.3340.2381140.2172020213799.86
1.334-1.370.2211030.19619722075100
1.37-1.410.1641310.1691877201299.801
1.41-1.4530.21960.1661866196499.898
1.453-1.5010.1651130.1451785190099.895
1.501-1.5530.185840.1521745183299.836
1.553-1.6120.207840.1551689177499.944
1.612-1.6770.151760.1531647172599.884
1.677-1.7520.188750.1581565164199.939
1.752-1.8370.168730.1591496157199.873
1.837-1.9360.206740.1571421149799.866
1.936-2.0530.187600.1551337139999.857
2.053-2.1940.156840.1551257134299.925
2.194-2.3690.122470.1511991246100
2.369-2.5940.203550.1871093115199.739
2.594-2.8980.187370.21007104599.904
2.898-3.3420.192530.215856909100
3.342-4.0830.199340.195752786100
4.083-5.7310.206350.19658161999.515
5.731-33.3080.31210.32431536093.333

+
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