[English] 日本語
Yorodumi
- PDB-6fcp: Crystal structure of 14-3-3 sigma in complex with Shroom3 P1244L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fcp
TitleCrystal structure of 14-3-3 sigma in complex with Shroom3 P1244L
Components
  • 14-3-3 protein sigma
  • Protein Shroom3
KeywordsPEPTIDE BINDING PROTEIN / Complex
Function / homology
Function and homology information


cellular pigment accumulation / pattern specification process / apical protein localization / apical junction complex / cortical actin cytoskeleton / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization ...cellular pigment accumulation / pattern specification process / apical protein localization / apical junction complex / cortical actin cytoskeleton / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / epithelial cell development / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein kinase A signaling / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament organization / TP53 Regulates Metabolic Genes / adherens junction / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cell morphogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / actin filament binding / regulation of cell shape / positive regulation of cell growth / microtubule / cytoskeleton / regulation of cell cycle / cadherin binding / apical plasma membrane / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Shroom3 / Apx/Shrm Domain 1 / Apx/Shroom domain ASD1 / ASD1 domain profile. / Apx/Shrm Domain 2 / Shroom family / Apx/Shroom domain ASD2 / ASD2 domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 ...Shroom3 / Apx/Shrm Domain 1 / Apx/Shroom domain ASD1 / ASD1 domain profile. / Apx/Shrm Domain 2 / Shroom family / Apx/Shroom domain ASD2 / ASD2 domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma / Protein Shroom3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLeysen, S. / Meijer, F.A. / Milroy, L.G. / Ottmann, C.
CitationJournal: J. Am. Soc. Nephrol. / Year: 2018
Title: Characterization of Coding/Noncoding Variants forSHROOM3in Patients with CKD.
Authors: Prokop, J.W. / Yeo, N.C. / Ottmann, C. / Chhetri, S.B. / Florus, K.L. / Ross, E.J. / Sosonkina, N. / Link, B.A. / Freedman, B.I. / Coppola, C.J. / McDermott-Roe, C. / Leysen, S. / Milroy, L. ...Authors: Prokop, J.W. / Yeo, N.C. / Ottmann, C. / Chhetri, S.B. / Florus, K.L. / Ross, E.J. / Sosonkina, N. / Link, B.A. / Freedman, B.I. / Coppola, C.J. / McDermott-Roe, C. / Leysen, S. / Milroy, L.G. / Meijer, F.A. / Geurts, A.M. / Rauscher, F.J. / Ramaker, R. / Flister, M.J. / Jacob, H.J. / Mendenhall, E.M. / Lazar, J.
History
DepositionDec 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Protein Shroom3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2546
Polymers28,1352
Non-polymers1204
Water7,206400
1
A: 14-3-3 protein sigma
P: Protein Shroom3
hetero molecules

A: 14-3-3 protein sigma
P: Protein Shroom3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,50812
Polymers56,2694
Non-polymers2398
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4950 Å2
ΔGint-81 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.533, 112.185, 62.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

MG

21A-441-

HOH

-
Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26542.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / Strain (production host): Nico21(DE3) / References: UniProt: P31947
#2: Protein/peptide Protein Shroom3 / Shroom-related protein / hShrmL


Mass: 1591.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8TF72
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M HEPES pH7.3 0.19M CaCl2 26% v/v PEG400 5% v/v glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→45.55 Å / Num. obs: 51510 / % possible obs: 99.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 12.6 Å2 / Rrim(I) all: 0.074 / Net I/σ(I): 21.1
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2541 / Rrim(I) all: 0.712

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW1

3lw1


Resolution: 1.45→45.548 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.1
RfactorNum. reflection% reflection
Rfree0.1584 2554 4.96 %
Rwork0.1306 --
obs0.132 51484 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→45.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 4 400 2296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082074
X-RAY DIFFRACTIONf_angle_d0.8852822
X-RAY DIFFRACTIONf_dihedral_angle_d17.612839
X-RAY DIFFRACTIONf_chiral_restr0.06315
X-RAY DIFFRACTIONf_plane_restr0.006368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.47790.21891450.15562600X-RAY DIFFRACTION97
1.4779-1.50810.17151490.13042651X-RAY DIFFRACTION98
1.5081-1.54090.17261250.12172664X-RAY DIFFRACTION98
1.5409-1.57670.14621400.11112672X-RAY DIFFRACTION99
1.5767-1.61610.13511330.1062713X-RAY DIFFRACTION99
1.6161-1.65980.14241470.10662680X-RAY DIFFRACTION100
1.6598-1.70870.14571360.10682700X-RAY DIFFRACTION100
1.7087-1.76380.1491430.11652706X-RAY DIFFRACTION100
1.7638-1.82690.17431610.11722705X-RAY DIFFRACTION100
1.8269-1.90.16671390.12662714X-RAY DIFFRACTION100
1.9-1.98650.14751320.12192733X-RAY DIFFRACTION100
1.9865-2.09120.16971400.12122724X-RAY DIFFRACTION100
2.0912-2.22220.14751500.11912723X-RAY DIFFRACTION100
2.2222-2.39380.14571340.11642749X-RAY DIFFRACTION100
2.3938-2.63470.13631480.12342735X-RAY DIFFRACTION100
2.6347-3.01590.16881500.1352764X-RAY DIFFRACTION100
3.0159-3.79940.15151480.13152774X-RAY DIFFRACTION100
3.7994-45.570.17741340.16452923X-RAY DIFFRACTION100

+
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