[English] 日本語
Yorodumi
- PDB-6mbz: Structure of Transcription Factor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mbz
TitleStructure of Transcription Factor
ComponentsSignal transducer and activator of transcription 5B
KeywordsTRANSCRIPTION ACTIVATOR / transcription factor
Function / homology
Function and homology information


development of secondary female sexual characteristics / development of secondary male sexual characteristics / natural killer cell proliferation / positive regulation of natural killer cell differentiation / mast cell migration / negative regulation of erythrocyte differentiation / taurine metabolic process / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 ...development of secondary female sexual characteristics / development of secondary male sexual characteristics / natural killer cell proliferation / positive regulation of natural killer cell differentiation / mast cell migration / negative regulation of erythrocyte differentiation / taurine metabolic process / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / myeloid cell apoptotic process / regulation of epithelial cell differentiation / luteinization / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / natural killer cell differentiation / nuclear glucocorticoid receptor binding / Interleukin-9 signaling / Interleukin-21 signaling / progesterone metabolic process / regulation of steroid metabolic process / positive regulation of natural killer cell mediated cytotoxicity / STAT5 Activation / Peyer's patch development / negative regulation of myeloid cell apoptotic process / Erythropoietin activates STAT5 / erythropoietin-mediated signaling pathway / lipid storage / positive regulation of multicellular organism growth / activated T cell proliferation / positive regulation of natural killer cell proliferation / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / Signaling by Leptin / Interleukin-2 signaling / Interleukin-20 family signaling / positive regulation of B cell differentiation / natural killer cell mediated cytotoxicity / STAT5 activation downstream of FLT3 ITD mutants / Prolactin receptor signaling / positive regulation of activated T cell proliferation / T cell homeostasis / Interleukin-3, Interleukin-5 and GM-CSF signaling / growth hormone receptor signaling pathway via JAK-STAT / regulation of multicellular organism growth / cell surface receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / Signaling by CSF3 (G-CSF) / cellular response to hormone stimulus / lactation / Signaling by FLT3 fusion proteins / Interleukin-7 signaling / positive regulation of interleukin-2 production / Downstream signal transduction / positive regulation of mitotic cell cycle / cellular response to epidermal growth factor stimulus / B cell differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / erythrocyte differentiation / positive regulation of erythrocyte differentiation / female pregnancy / defense response / Signaling by SCF-KIT / cytokine-mediated signaling pathway / Inactivation of CSF3 (G-CSF) signaling / cellular response to growth factor stimulus / response to peptide hormone / RNA polymerase II transcription regulator complex / positive regulation of inflammatory response / response to estradiol / mitotic cell cycle / regulation of cell population proliferation / T cell differentiation in thymus / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
STAT5b, SH2 domain / STAT5a/5b / : / STAT transcription factor, DNA-binding domain / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : ...STAT5b, SH2 domain / STAT5a/5b / : / STAT transcription factor, DNA-binding domain / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / : / STAT transcription factor, coiled-coil domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / Signal transducer and activator of transcription, linker domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / p53-like transcription factor, DNA-binding / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Signal transducer and activator of transcription 5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.21 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
CitationJournal: Nat Commun / Year: 2019
Title: Structural and functional consequences of the STAT5BN642Hdriver mutation.
Authors: de Araujo, E.D. / Erdogan, F. / Neubauer, H.A. / Meneksedag-Erol, D. / Manaswiyoungkul, P. / Eram, M.S. / Seo, H.S. / Qadree, A.K. / Israelian, J. / Orlova, A. / Suske, T. / Pham, H.T.T. / ...Authors: de Araujo, E.D. / Erdogan, F. / Neubauer, H.A. / Meneksedag-Erol, D. / Manaswiyoungkul, P. / Eram, M.S. / Seo, H.S. / Qadree, A.K. / Israelian, J. / Orlova, A. / Suske, T. / Pham, H.T.T. / Boersma, A. / Tangermann, S. / Kenner, L. / Rulicke, T. / Dong, A. / Ravichandran, M. / Brown, P.J. / Audette, G.F. / Rauscher, S. / Dhe-Paganon, S. / Moriggl, R. / Gunning, P.T.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Signal transducer and activator of transcription 5B
B: Signal transducer and activator of transcription 5B


Theoretical massNumber of molelcules
Total (without water)131,2872
Polymers131,2872
Non-polymers00
Water64936
1
A: Signal transducer and activator of transcription 5B


Theoretical massNumber of molelcules
Total (without water)65,6431
Polymers65,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal transducer and activator of transcription 5B


Theoretical massNumber of molelcules
Total (without water)65,6431
Polymers65,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.380, 141.400, 72.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-810-

HOH

-
Components

#1: Protein Signal transducer and activator of transcription 5B


Mass: 65643.422 Da / Num. of mol.: 2 / Mutation: N642H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT5B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51692
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.21→70.7 Å / Num. obs: 23029 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 95.95 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 13.79
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.21-3.296.81.1521100
14.36-70.75.50.032198.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y1U

1y1u


Resolution: 3.21→70.7 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2868 1143 4.96 %
Rwork0.2649 --
obs0.266 23022 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.21→70.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7897 0 0 36 7933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048072
X-RAY DIFFRACTIONf_angle_d0.79311019
X-RAY DIFFRACTIONf_dihedral_angle_d4.5724785
X-RAY DIFFRACTIONf_chiral_restr0.0461279
X-RAY DIFFRACTIONf_plane_restr0.0061431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.35610.42751620.38572654X-RAY DIFFRACTION100
3.3561-3.5330.36171520.34262674X-RAY DIFFRACTION100
3.533-3.75440.37171570.31712672X-RAY DIFFRACTION100
3.7544-4.04420.27911180.29292745X-RAY DIFFRACTION100
4.0442-4.45120.26021310.25632717X-RAY DIFFRACTION100
4.4512-5.09510.26961540.22372725X-RAY DIFFRACTION100
5.0951-6.41860.2481220.27852786X-RAY DIFFRACTION100
6.4186-70.71710.261470.22792906X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0024-3.91371.0784.3061-1.66310.7441-0.2536-0.6057-0.13590.09570.38780.25280.1236-0.1139-0.11040.93160.1235-0.0080.77820.11170.9052-11.901659.518666.7131
24.7539-1.01230.01693.5305-1.34346.5005-0.15490.17620.27360.32310.0693-0.1166-0.18740.25340.21440.76970.06090.07850.56580.07660.717417.652241.451968.3785
30.5936-0.754-0.38417.5649-0.34081.2538-0.0815-0.2528-0.14810.24490.36660.5401-0.0875-0.5319-0.2650.75590.0577-0.00990.81290.08990.719120.34959.607289.9028
46.07-2.41963.36930.5887-0.64491.56170.330.5632-0.5859-0.146-0.20730.09830.39580.2397-0.22220.98160.1851-0.04180.8151-0.15261.277617.426734.959115.5223
58.3799-3.42111.94422.1317-0.88070.98060.071-0.04-0.5268-0.14970.0022-0.07680.101-0.0756-0.10690.89710.035-0.06120.7914-0.030.8116-5.811252.6675111.3304
64.5332-2.00940.63744.29830.61543.8686-0.16370.1470.25620.4925-0.007-0.4163-0.12560.46770.26990.6527-0.03220.09630.64010.04690.6301-16.589167.7191109.9029
75.5056-1.31761.45652.2970.22651.68420.11760.1941-0.1585-0.1512-0.012-0.11260.1716-0.2871-0.09270.6817-0.0222-0.03661.05620.01880.5189-50.478762.953192.0551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 138 through 349 )
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 488 )
3X-RAY DIFFRACTION3chain 'A' and (resid 489 through 685 )
4X-RAY DIFFRACTION4chain 'B' and (resid 138 through 249 )
5X-RAY DIFFRACTION5chain 'B' and (resid 250 through 349 )
6X-RAY DIFFRACTION6chain 'B' and (resid 350 through 503 )
7X-RAY DIFFRACTION7chain 'B' and (resid 504 through 685 )

+
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