[English] 日本語
Yorodumi
- PDB-6fjc: Human KIBRA C2 domain mutant C771A in complex with phosphatidylin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fjc
TitleHuman KIBRA C2 domain mutant C771A in complex with phosphatidylinositol 3,4,5-trisphosphate
ComponentsProtein KIBRA
KeywordsLIPID BINDING PROTEIN / C2 domain / Kibra / phosphoinositide-binding / membrane interaction
Function / homology
Function and homology information


regulation of intracellular transport / regulation of hippo signaling / negative regulation of organ growth / Signaling by Hippo / NOTCH3 Intracellular Domain Regulates Transcription / establishment of cell polarity / negative regulation of hippo signaling / kinase binding / ruffle membrane / cell migration ...regulation of intracellular transport / regulation of hippo signaling / negative regulation of organ growth / Signaling by Hippo / NOTCH3 Intracellular Domain Regulates Transcription / establishment of cell polarity / negative regulation of hippo signaling / kinase binding / ruffle membrane / cell migration / positive regulation of MAPK cascade / transcription coactivator activity / molecular adaptor activity / negative regulation of cell population proliferation / regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
WWC, C2 domain / C2 domain / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues ...WWC, C2 domain / C2 domain / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-4PT / Protein KIBRA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsCrennell, S.J. / Posner, M.G. / Bagby, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
BBSRC (Biotechnology and Biological Sciences Research Council)BB/J008176/1 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Distinctive phosphoinositide- and Ca2+-binding properties of normal and cognitive performance-linked variant forms of KIBRA C2 domain.
Authors: Posner, M.G. / Upadhyay, A. / Ishima, R. / Kalli, A.C. / Harris, G. / Kremerskothen, J. / Sansom, M.S.P. / Crennell, S.J. / Bagby, S.
History
DepositionJan 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 2.0Jun 27, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy
Category: atom_site / citation / entity_src_gen
Item: _atom_site.occupancy / _citation.journal_volume ..._atom_site.occupancy / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein KIBRA
B: Protein KIBRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,92619
Polymers31,7322
Non-polymers2,19417
Water1,69394
1
A: Protein KIBRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,31910
Polymers15,8661
Non-polymers1,4539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein KIBRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6079
Polymers15,8661
Non-polymers7418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.404, 83.404, 208.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-938-

HOH

21B-925-

HOH

-
Components

#1: Protein Protein KIBRA / HBeAg-binding protein 3 / Kidney and brain protein / KIBRA / WW domain-containing protein 1


Mass: 15866.046 Da / Num. of mol.: 2 / Mutation: C771A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWC1, KIAA0869 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IX03
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-4PT / (2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXY BUTOXY)PROPYL BUTYRATE / DIC4-PHOSPHATIDYLINOSITOL(3,4,5)TRISPHOSPHATE


Mass: 716.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O22P4
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris pH 8.0, 1.5M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.598→72.23 Å / Num. obs: 13926 / % possible obs: 100 % / Redundancy: 12.09 % / Rmerge(I) obs: 0.167 / Rrim(I) all: 0.174 / Χ2: 0.95 / Net I/σ(I): 9.7
Reflection shellResolution: 2.598→2.69 Å / Redundancy: 8.34 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.3 / Rrim(I) all: 0.662 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
d*TREKdata reduction
d*TREKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z0U

2z0u


Resolution: 2.598→72.23 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.77
RfactorNum. reflection% reflection
Rfree0.2639 722 5.19 %
Rwork0.1915 --
obs0.1952 13914 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.598→72.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 138 94 2276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082220
X-RAY DIFFRACTIONf_angle_d1.1332997
X-RAY DIFFRACTIONf_dihedral_angle_d17.7641334
X-RAY DIFFRACTIONf_chiral_restr0.055347
X-RAY DIFFRACTIONf_plane_restr0.004365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5981-2.79870.33341340.23822533X-RAY DIFFRACTION99
2.7987-3.08040.33381460.22942584X-RAY DIFFRACTION100
3.0804-3.52610.29541580.19422584X-RAY DIFFRACTION100
3.5261-4.44240.20571290.1572656X-RAY DIFFRACTION100
4.4424-72.25790.24691550.19332835X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -20.3636 Å / Origin y: -20.9003 Å / Origin z: -6.9228 Å
111213212223313233
T0.1064 Å20.0131 Å2-0.018 Å2-0.0996 Å20.0072 Å2--0.1324 Å2
L0.3088 °2-0.0734 °20.1433 °2-0.4039 °2-0.2073 °2--1.1585 °2
S0.0029 Å °0.0424 Å °-0.0077 Å °0.0018 Å °-0.0184 Å °0.0098 Å °0.0483 Å °0.0626 Å °-0 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