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- PDB-4zia: Crystal Structure of STAT3 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4zia
TitleCrystal Structure of STAT3 N-terminal domain
ComponentsSignal transducer and activator of transcription 3
KeywordsTRANSCRIPTION / STAT N-terminal domain
Function / homology
Function and homology information


STAT3 nuclear events downstream of ALK signaling / Interleukin-10 signaling / MET activates STAT3 / Interleukin-37 signaling / Signaling by ALK / PTK6 Activates STAT3 / Interleukin-21 signaling / RNA sequestering activity / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling ...STAT3 nuclear events downstream of ALK signaling / Interleukin-10 signaling / MET activates STAT3 / Interleukin-37 signaling / Signaling by ALK / PTK6 Activates STAT3 / Interleukin-21 signaling / RNA sequestering activity / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling / Interleukin-15 signaling / Interleukin-23 signaling / Interleukin-20 family signaling / Interleukin-27 signaling / retinal rod cell differentiation / Interleukin-6 signaling / radial glial cell differentiation / Interleukin-35 Signalling / Downstream signal transduction / cell surface receptor signaling pathway via STAT / negative regulation of primary miRNA processing / Interleukin-7 signaling / Signaling by SCF-KIT / leptin-mediated signaling pathway / negative regulation of neuron migration / PKR-mediated signaling / T-helper 17 type immune response / negative regulation of hydrogen peroxide biosynthetic process / negative regulation of inflammatory response to wounding / primary miRNA binding / response to leptin / regulation of feeding behavior / sexual reproduction / interleukin-11-mediated signaling pathway / CCR5 chemokine receptor binding / T-helper 17 cell lineage commitment / cellular response to interleukin-17 / interleukin-9-mediated signaling pathway / regulation of cellular response to hypoxia / nuclear glucocorticoid receptor binding / interleukin-2-mediated signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / intracellular receptor signaling pathway / acetylation-dependent protein binding / negative regulation of stem cell differentiation / interleukin-15-mediated signaling pathway / cellular response to leptin stimulus / positive regulation of cytokine production involved in inflammatory response / astrocyte differentiation / postsynapse to nucleus signaling pathway / negative regulation of glycolytic process / regulation of mitochondrial membrane permeability / positive regulation of vascular endothelial cell proliferation / growth hormone receptor signaling pathway / temperature homeostasis / eating behavior / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / positive regulation of ATP biosynthetic process / cellular response to cytokine stimulus / somatic stem cell population maintenance / cell surface receptor signaling pathway via JAK-STAT / positive regulation of interleukin-10 production / regulation of multicellular organism growth / cellular response to organic cyclic compound / positive regulation of vascular endothelial growth factor production / growth hormone receptor signaling pathway via JAK-STAT / signaling adaptor activity / energy homeostasis / cellular response to hormone stimulus / negative regulation of autophagy / transforming growth factor beta receptor signaling pathway / positive regulation of erythrocyte differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of interleukin-1 beta production / response to cytokine / response to ischemia / positive regulation of interleukin-8 production / acute-phase response / modulation of chemical synaptic transmission / mRNA transcription by RNA polymerase II / Schaffer collateral - CA1 synapse / defense response / chromatin DNA binding / response to peptide hormone / negative regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of miRNA transcription / cytokine-mediated signaling pathway / protein import into nucleus / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / nuclear receptor activity / positive regulation of tumor necrosis factor production / glucose homeostasis / response to estradiol / gene expression / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / protein phosphatase binding
Similarity search - Function
Transcription Factor, Stat-4 / STAT transcription factor, N-terminal domain / STAT3, SH2 domain / : / Signal transducer and activator of transcription, linker 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 protein, all-alpha domain ...Transcription Factor, Stat-4 / STAT transcription factor, N-terminal domain / STAT3, SH2 domain / : / Signal transducer and activator of transcription, linker 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 protein, all-alpha domain / STAT protein, DNA binding domain / STAT protein, protein interaction 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 / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / NICKEL (II) ION / Signal transducer and activator of transcription 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHu, T. / Chopra, R.
CitationJournal: Mol.Cell.Biol. / Year: 2015
Title: Impact of the N-Terminal Domain of STAT3 in STAT3-Dependent Transcriptional Activity.
Authors: Hu, T. / Yeh, J.E. / Pinello, L. / Jacob, J. / Chakravarthy, S. / Yuan, G.C. / Chopra, R. / Frank, D.A.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal transducer and activator of transcription 3
B: Signal transducer and activator of transcription 3
C: Signal transducer and activator of transcription 3
D: Signal transducer and activator of transcription 3
E: Signal transducer and activator of transcription 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2048
Polymers76,0755
Non-polymers1293
Water1,13563
1
A: Signal transducer and activator of transcription 3
B: Signal transducer and activator of transcription 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4893
Polymers30,4302
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-9 kcal/mol
Surface area13240 Å2
MethodPISA
2
C: Signal transducer and activator of transcription 3
D: Signal transducer and activator of transcription 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4763
Polymers30,4302
Non-polymers461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-6 kcal/mol
Surface area12680 Å2
MethodPISA
3
E: Signal transducer and activator of transcription 3
hetero molecules

E: Signal transducer and activator of transcription 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4794
Polymers30,4302
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_646y+1,x-1,-z+7/41
Buried area2050 Å2
ΔGint-6 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.012, 109.012, 154.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-201-

NI

21E-201-

MG

31B-310-

HOH

41C-204-

HOH

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Components

#1: Protein
Signal transducer and activator of transcription 3 / Acute-phase response factor


Mass: 15215.049 Da / Num. of mol.: 5 / Fragment: N-terminal domain (UNP residues 3-127)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stat3, Aprf / Plasmid: pNAT40 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42227
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% v/v PEG 3350, 0.2M magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 26131 / % possible obs: 99.6 % / Redundancy: 8 % / Rsym value: 0.075 / Net I/σ(I): 19.4
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 5.5 / % possible all: 100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 1BGF

1bgf


Resolution: 2.7→20 Å / FOM work R set: 0.8022 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2701 1329 5.1 %
Rwork0.2362 24802 -
obs-26131 100 %
Solvent computationBsol: 46.352 Å2
Displacement parametersBiso max: 113.94 Å2 / Biso mean: 59.0826 Å2 / Biso min: 15.21 Å2
Baniso -1Baniso -2Baniso -3
1--5.27 Å20 Å20 Å2
2---5.27 Å20 Å2
3---10.54 Å2
Refinement stepCycle: final / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5081 0 5 63 5149
Biso mean--48.74 41.99 -
Num. residues----601
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.081
X-RAY DIFFRACTIONc_mcbond_it1.4081.5
X-RAY DIFFRACTIONc_scbond_it2.0752
X-RAY DIFFRACTIONc_mcangle_it2.4342
X-RAY DIFFRACTIONc_scangle_it3.3272.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-2.740.3816560.3598913969
2.74-2.770.3716540.3376933987
2.77-2.810.4425550.3317932987
2.81-2.850.467490.3175931980
2.85-2.90.3263400.3028946986
2.9-2.950.3513590.30159461005
2.95-30.3061460.3039929975
3-3.050.2896430.2818939982
3.05-3.110.399520.2812940992
3.11-3.170.3213450.3034944989
3.17-3.240.3358390.2643944983
3.24-3.320.2441650.23989571022
3.32-3.40.2596620.2493913975
3.4-3.490.2808520.259501002
3.49-3.590.2607520.22769541006
3.59-3.710.2642520.22219551007
3.71-3.840.2618500.2032932982
3.84-3.990.2383650.21549441009
3.99-4.170.2176520.20349591011
4.17-4.390.2075510.19259681019
4.39-4.660.2408450.19389611006
4.66-5.020.2458610.20579611022
5.02-5.510.2719450.24829811026
5.51-6.290.2866390.279510001039
6.29-7.840.325520.232710181070
7.84-200.2018480.186810521100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5fmt.paramfmt.top

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