[English] 日本語
Yorodumi
- PDB-1pzu: An asymmetric NFAT1-RHR homodimer on a pseudo-palindromic, Kappa-... -

+
Open data


ID or keywords:

Loading...

-
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


lncRNA transcription / 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 ...lncRNA transcription / 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 / FCERI mediated Ca+2 mobilization / cellular response to calcium ion / 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 / molecular adaptor activity / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / ribonucleoprotein complex / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
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 / Immunoglobulin-like fold / Immunoglobulins / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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