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- PDB-1pzu: An asymmetric NFAT1-RHR homodimer on a pseudo-palindromic, Kappa-... -

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Basic information

Entry
Database: PDB / ID: 1pzu
TitleAn asymmetric NFAT1-RHR homodimer on a pseudo-palindromic, Kappa-B site
Components
  • 5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'
  • 5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3'
  • Nuclear factor of activated T-cells, cytoplasmic 2
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / NFAT1-RHR homodimer / PROTEIN-DNA COMPLEX / human IL8 promoter / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / myotube cell development / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / calcineurin-NFAT signaling cascade / cartilage development / positive regulation of myoblast fusion / CLEC7A (Dectin-1) induces NFAT activation / Calcineurin activates NFAT / phosphatase binding ...transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / myotube cell development / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / calcineurin-NFAT signaling cascade / cartilage development / positive regulation of myoblast fusion / CLEC7A (Dectin-1) induces NFAT activation / Calcineurin activates NFAT / phosphatase binding / positive regulation of B cell proliferation / 14-3-3 protein binding / cellular response to calcium ion / FCERI mediated Ca+2 mobilization / B cell receptor signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / cell migration / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / transcription by RNA polymerase II / molecular adaptor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / ribonucleoprotein complex / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / chromatin binding / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear factor of activated T cells (NFAT) / Rel homology domain (RHD), DNA-binding domain / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain ...Nuclear factor of activated T cells (NFAT) / Rel homology domain (RHD), DNA-binding domain / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor of activated T-cells, cytoplasmic 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsJin, L. / Sliz, P. / Chen, L. / Macian, F. / Rao, A. / Hogan, P.G. / Harrison, S.C.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: An asymmetric NFAT1 dimer on a pseudo-palindromic KB-like DNA site
Authors: Jin, L. / Sliz, P. / Chen, L. / Macian, F. / Rao, A. / Hogan, P.G. / Harrison, S.C.
#1: Journal: Nature / Year: 1998
Title: STRUCTURE OF THE DNA-BINDING DOMAINS FROM NFAT, FOS AND JUN BOUND SPECIFICALLY TO DNA
Authors: Chen, L. / Glover, J.N.M. / Hogan, P.G. / Rao, A. / Harrison, S.C.
History
DepositionJul 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: 5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3'
Y: 5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'
V: 5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3'
Z: 5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'
T: 5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3'
W: 5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'
B: Nuclear factor of activated T-cells, cytoplasmic 2
D: Nuclear factor of activated T-cells, cytoplasmic 2
H: Nuclear factor of activated T-cells, cytoplasmic 2
I: Nuclear factor of activated T-cells, cytoplasmic 2
L: Nuclear factor of activated T-cells, cytoplasmic 2
M: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)231,30112
Polymers231,30112
Non-polymers00
Water00
1
T: 5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3'
W: 5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'
B: Nuclear factor of activated T-cells, cytoplasmic 2
D: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)77,1004
Polymers77,1004
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
V: 5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3'
Z: 5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'
H: Nuclear factor of activated T-cells, cytoplasmic 2
I: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)77,1004
Polymers77,1004
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
X: 5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3'
Y: 5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'
L: Nuclear factor of activated T-cells, cytoplasmic 2
M: Nuclear factor of activated T-cells, cytoplasmic 2


Theoretical massNumber of molelcules
Total (without water)77,1004
Polymers77,1004
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.700, 122.900, 241.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a NFAT1-RHR homodimer on DNA. There are three such dimers in the asymmetric unit, related by a local 3 screw axis. DNA stacks continuously in the crystal.

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Components

#1: DNA chain 5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3'


Mass: 4294.814 Da / Num. of mol.: 3 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'


Mass: 4263.804 Da / Num. of mol.: 3 / Source method: obtained synthetically
#3: Protein
Nuclear factor of activated T-cells, cytoplasmic 2 / T cell transcription factor NFAT1 / NFAT pre-existing subunit / NF-ATp / RHR


Mass: 34270.898 Da / Num. of mol.: 6 / Fragment: NFAT1 DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFAT1 / Plasmid: PLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q13469

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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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 292 K / Method: microbatch / pH: 8
Details: HEPES, NaCl, glycerol, NH4OAc, MgCl2, spermine, PEG4000, Tris-HCl, pH 8.0, microbatch, temperature 292.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2NaCl11
3glycerol11
4NH4OAc11
5MgCl211
6spermine11
7PEG400011
8Tris-HCl11
9H2O11
10PEG400012
11spermine12
12NH4OAc12
13MgCl212
14glycerol12
15H2O12
Crystal grow
*PLUS
pH: 6.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1100 mM1reservoirNaCl
210 mM1reservoirMgCl2
32.5 mMspermine1reservoir
46 %(v/v)glycerol1reservoir
56 %(w/v)PEG40001reservoir
650 mMBis-Tris propane1reservoirpH6.3
71
81
91
101
111
121
131
141
151

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.948 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 21, 2001
RadiationMonochromator: Bent triangular asymmetric cut Si(111) monochromater (provides horizontal focussing) Rh-coated Si mirror for vertical focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 3.1→49.11 Å / Num. all: 44978 / Num. obs: 37121 / % possible obs: 82.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.1→3.29 Å / % possible all: 82.5
Reflection
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 30 Å / Num. obs: 37145 / % possible obs: 82.4 % / Num. measured all: 124267 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
Lowest resolution: 3.2 Å / % possible obs: 77 % / Num. unique obs: 4269 / Num. measured obs: 9841 / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→29.78 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 3392718.05 / Data cutoff high rms absF: 3392718.05 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.319 1857 5 %RANDOM
Rwork0.296 ---
all0.303 44978 --
obs0.303 37086 82.4 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 42.728 Å2 / ksol: 0.266903 e/Å3
Displacement parametersBiso mean: 68.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å20 Å2
2---3.96 Å20 Å2
3---1.4 Å2
Refine Biso Class: polymer / Treatment: isotropic
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13248 1704 0 0 14952
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it3.342
X-RAY DIFFRACTIONc_scangle_it4.192.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 271 4.8 %
Rwork0.348 5423 -
obs--77.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna.paramdna-rna.top
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11

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