[English] 日本語
Yorodumi
- PDB-4wnf: Crystal structure of the oxidized TPR domain of LGN in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wnf
TitleCrystal structure of the oxidized TPR domain of LGN in complex with Frmpd4/Preso1 at 2.9 Angstrom resolution
Components
  • FERM and PDZ domain-containing protein 4
  • G-protein-signaling modulator 2
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / TETRATRICOPEPTIDE REPEAT / TPR / CELL POLARITY / CYTOPLASM AND CELL CORTEX / SIGNALING PROTEIN-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


lateral cell cortex / positive regulation of synapse structural plasticity / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / response to light intensity / GDP-dissociation inhibitor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / mitotic spindle pole / dynein complex binding ...lateral cell cortex / positive regulation of synapse structural plasticity / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / response to light intensity / GDP-dissociation inhibitor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / mitotic spindle pole / dynein complex binding / establishment of mitotic spindle orientation / lateral plasma membrane / G-protein alpha-subunit binding / positive regulation of protein localization to cell cortex / phosphatidylinositol-4,5-bisphosphate binding / regulation of mitotic spindle organization / mitotic spindle organization / cell cortex / G alpha (i) signalling events / dendritic spine / cytoskeleton / postsynaptic density / G protein-coupled receptor signaling pathway / protein domain specific binding / cell division / nucleotide binding / centrosome / protein-containing complex / identical protein binding / cytoplasm / cytosol
Similarity search - Function
FERM and PDZ domain-containing protein 1/3/4, FERM domain C-lobe / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / : / Tetratricopeptide repeat / FAK1/PYK2, FERM domain C-lobe ...FERM and PDZ domain-containing protein 1/3/4, FERM domain C-lobe / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / : / Tetratricopeptide repeat / FAK1/PYK2, FERM domain C-lobe / Tetratricopeptide repeat / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Tetratricopeptide repeat domain / Tetratricopeptide repeat / WW/rsp5/WWP domain profile. / FERM central domain / WW domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / PDZ domain / Tetratricopeptide repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
G-protein-signaling modulator 2 / FERM and PDZ domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTakayanagi, H. / Yuzawa, S. / Sumimoto, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structural basis for the recognition of the scaffold protein Frmpd4/Preso1 by the TPR domain of the adaptor protein LGN
Authors: Takayanagi, H. / Yuzawa, S. / Sumimoto, H.
History
DepositionOct 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: G-protein-signaling modulator 2
B: FERM and PDZ domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)50,7802
Polymers50,7802
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-11 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.599, 92.599, 175.238
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein G-protein-signaling modulator 2 / Mosaic protein LGN


Mass: 44948.281 Da / Num. of mol.: 1 / Fragment: N-terminal TPR domain, UNP residues 20-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPSM2, LGN / Plasmid: pRSFDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P81274
#2: Protein FERM and PDZ domain-containing protein 4 / PDZ domain-containing protein 10 / PSD-95-interacting regulator of spine morphogenesis / Preso


Mass: 5831.625 Da / Num. of mol.: 1 / Fragment: FRMPD4-L, UNP residues 978-1025
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FRMPD4, KIAA0316, PDZD10, PDZK10 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14CM0
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M BisTrispropane (pH 7.5), 0.2 M potassium thiocyanate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 10385 / % possible obs: 99.3 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.075 / Χ2: 0.998 / Net I/av σ(I): 18.174 / Net I/σ(I): 15 / Num. measured all: 74336
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.9-2.957.60.5022.7284961.081100
2.95-37.40.4455050.969100
3-3.067.40.4754990.976100
3.06-3.127.50.355110.994100
3.12-3.197.40.2965101.05100
3.19-3.277.50.2545000.91999.8
3.27-3.357.50.1935170.994100
3.35-3.447.20.2185110.996100
3.44-3.547.10.1645091.106100
3.54-3.656.90.1365120.97299.6
3.65-3.786.80.1654970.95599
3.78-3.946.50.1345100.96698.8
3.94-4.117.40.0685230.963100
4.11-4.337.20.0595241.03100
4.33-4.67.30.0495290.92599.6
4.6-4.967.20.0495200.949100
4.96-5.467.10.0465421.09599.8
5.46-6.247.10.0395390.957100
6.24-7.866.90.0275551.199.3
7.86-506.10.0225760.95391.6

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREP11.0.05phasing
Coot0.7-premodel building
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WNE

4wne


Resolution: 2.9→39.12 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2832 / WRfactor Rwork: 0.2379 / FOM work R set: 0.7607 / SU B: 17.097 / SU ML: 0.315 / SU R Cruickshank DPI: 0.8202 / SU Rfree: 0.382 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.82 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 513 5 %RANDOM
Rwork0.237 9777 --
obs0.2391 9777 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 202.88 Å2 / Biso mean: 88.325 Å2 / Biso min: 50.24 Å2
Baniso -1Baniso -2Baniso -3
1-3.13 Å23.13 Å20 Å2
2--3.13 Å20 Å2
3----10.16 Å2
Refinement stepCycle: final / Resolution: 2.9→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 0 0 2065
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192100
X-RAY DIFFRACTIONr_bond_other_d0.0010.021923
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.952834
X-RAY DIFFRACTIONr_angle_other_deg0.6853.0014406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5225270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50124.706102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.49615337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7791510
X-RAY DIFFRACTIONr_chiral_restr0.0580.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02493
LS refinement shellResolution: 2.903→2.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 47 -
Rwork0.316 692 -
all-739 -
obs--99.73 %

+
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