[English] 日本語
Yorodumi
- PDB-2bq0: 14-3-3 Protein Beta (Human) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bq0
Title14-3-3 Protein Beta (Human)
Components14-3-3 BETA/ALPHA
KeywordsCELL REGULATOR PROTEIN / 14-3-3 / YWHAB / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / ALTERNATIVE INITIATION / MULTIGENE FAMILY / PHOSPHORYLATION
Function / homology
Function and homology information


: / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane ...: / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / negative regulation of G protein-coupled receptor signaling pathway / Frs2-mediated activation / protein phosphatase inhibitor activity / protein kinase inhibitor activity / mTORC1-mediated signalling / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / histone deacetylase binding / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / protein localization / melanosome / cadherin binding / protein domain specific binding / focal adhesion / perinuclear region of cytoplasm / enzyme binding / signal transduction / extracellular exosome / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 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 ...14-3-3 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYang, X. / Elkins, J.M. / Fedorov, O. / Longman, E.J. / Sobott, L. / Ball, L.J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Doyle, D.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structural Basis for Protein-Protein Interactions in the 14-3-3 Protein Family.
Authors: Yang, X. / Lee, W.H. / Sobott, F. / Papagrigoriou, E. / Robinson, C.V. / Grossmann, J.G. / Sundstrom, M. / Doyle, D.A. / Elkins, J.M.
History
DepositionApr 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2005Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 BETA/ALPHA
B: 14-3-3 BETA/ALPHA


Theoretical massNumber of molelcules
Total (without water)56,4732
Polymers56,4732
Non-polymers00
Water1,15364
1
A: 14-3-3 BETA/ALPHA

B: 14-3-3 BETA/ALPHA


Theoretical massNumber of molelcules
Total (without water)56,4732
Polymers56,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
MethodPQS
2
B: 14-3-3 BETA/ALPHA

A: 14-3-3 BETA/ALPHA


Theoretical massNumber of molelcules
Total (without water)56,4732
Polymers56,4732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1,y-1/2,-z-11
MethodPQS
Unit cell
Length a, b, c (Å)51.605, 123.790, 54.755
Angle α, β, γ (deg.)90.00, 114.98, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 68
2115B1 - 68
1215A80 - 135
2215B80 - 135
1315A140 - 163
2315B140 - 163
1125A164 - 245
2125B164 - 245

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.58479, -0.16656, 0.7939), (0.16258, -0.9829, -0.08646), (0.79473, 0.07852, 0.60187)
Vector: -16.90796, -85.31619, -21.58131)

-
Components

#1: Protein 14-3-3 BETA/ALPHA / PROTEIN KINASE C INHIBITOR PROTEIN-1 / KCIP-1 / PROTEIN 1054


Mass: 28236.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: THE MAMMALIAN GENE COLLECTION, I.M.A.G.E. CONSORTIUM CLONEID 3051079
Plasmid: PTVHR21-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31946
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 240-245 ARE CLONING ARTEFACT FOR CHAINS A AND B. THE UNIPROT CROSS-REFERENCE GIVEN IN THE ...RESIDUES 240-245 ARE CLONING ARTEFACT FOR CHAINS A AND B. THE UNIPROT CROSS-REFERENCE GIVEN IN THE DBREF RECORDS BELOW CORRESPONDS TO GENBANK ENTRY BC001359.2 (HOMO SAPIENS TYROSINE 3-MONOOXYGENASE ACTIVATION PROTEIN BETA POLYPEPTIDE TRANSCRIPT VARIANT 2)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.6 %
Crystal growpH: 8
Details: 0.05M MGCL2,0.1M HEPES PH7.5, 30% PEG MME 550, pH 8.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 8, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→38.72 Å / Num. obs: 21068 / % possible obs: 97.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJA

1qja


Resolution: 2.5→61.9 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.864 / SU B: 9.583 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.468 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1074 5.1 %RANDOM
Rwork0.214 ---
obs0.217 19984 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-1.1 Å2
2---1.31 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.5→61.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 0 64 3721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223711
X-RAY DIFFRACTIONr_bond_other_d0.0010.023323
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9675007
X-RAY DIFFRACTIONr_angle_other_deg0.77637770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5625.604182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71615693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0651519
X-RAY DIFFRACTIONr_chiral_restr0.0680.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02701
X-RAY DIFFRACTIONr_nbd_refined0.2260.2926
X-RAY DIFFRACTIONr_nbd_other0.1650.23227
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21841
X-RAY DIFFRACTIONr_nbtor_other0.0860.22195
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2129
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0970.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5791.52503
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89623688
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.33831551
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1274.51319
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1857medium positional0.420.5
2410medium positional0.660.5
11352loose positional0.655
2645loose positional1.075
1857medium thermal1.212
2410medium thermal1.042
11352loose thermal1.9410
2645loose thermal1.5810
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.319 70
Rwork0.244 1462

+
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