[English] 日本語
Yorodumi
- PDB-8r3f: C-terminal Rel-homology Domain of NFAT1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r3f
TitleC-terminal Rel-homology Domain of NFAT1
ComponentsNuclear factor of activated T-cells, cytoplasmic 2
KeywordsTRANSCRIPTION / NFAT1 / Transcription Factor / Fragment
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 / ribonucleoprotein complex / response to xenobiotic stimulus / 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 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 ...Nuclear factor of activated T cells (NFAT) / 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
Similarity search - Domain/homology
: / Nuclear factor of activated T-cells, cytoplasmic 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsZak, K.M. / Boettcher, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Arch Pharm / Year: 2024
Title: Ligandability assessment of the C-terminal Rel-homology domain of NFAT1.
Authors: Bottcher, J. / Fuchs, J.E. / Mayer, M. / Kahmann, J. / Zak, K.M. / Wunberg, T. / Woehrle, S. / Kessler, D.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Authors: Liebschner, D.
History
DepositionNov 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear factor of activated T-cells, cytoplasmic 2
B: Nuclear factor of activated T-cells, cytoplasmic 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8864
Polymers24,5522
Non-polymers3342
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-0 kcal/mol
Surface area11810 Å2
Unit cell
Length a, b, c (Å)48.775, 40.279, 57.419
Angle α, β, γ (deg.)90.000, 97.255, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 576 through 578 or resid 580...
d_2ens_1(chain "B" and (resid 576 through 578 or resid 580 through 653 or resid 655 through 677))

NCS domain segments:

Ens-ID: ens_1 / End auth comp-ID: PRO / End label comp-ID: PRO

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUAA576 - 5783 - 5
d_12VALVALAA580 - 6537 - 80
d_13LYSLYSAA655 - 67782 - 104
d_21GLUGLUBB576 - 5783 - 5
d_22VALVALBB580 - 6537 - 80
d_23LYSLYSBB655 - 67782 - 104

NCS oper: (Code: givenMatrix: (-0.574888471566, 0.386940764239, -0.720957758979), (-0.631580264377, -0.770029050331, 0.0903417472476), (-0.520201513752, 0.507279121014, 0.687064973982)Vector: 35. ...NCS oper: (Code: given
Matrix: (-0.574888471566, 0.386940764239, -0.720957758979), (-0.631580264377, -0.770029050331, 0.0903417472476), (-0.520201513752, 0.507279121014, 0.687064973982)
Vector: 35.2414630881, 15.5281686484, 8.09222003114)

-
Components

#1: Protein Nuclear factor of activated T-cells, cytoplasmic 2 / NF-ATc2 / NFATc2 / NFAT pre-existing subunit / NF-ATp / T-cell transcription factor NFAT1


Mass: 12275.864 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFATC2, NFAT1, NFATP / Production host: Escherichia coli (E. coli) / References: UniProt: Q13469
#2: Chemical ChemComp-XS8 / (4~{S})-6-fluoranyl-3,4-dihydro-2~{H}-chromen-4-amine


Mass: 167.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10FNO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: containing 25% PEG 3350, 200 mM Sodium Chloride and 100 mM BIS-TRIS buffer at a pH of 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.547→56.96 Å / Num. obs: 24212 / % possible obs: 74.4 % / Redundancy: 2 % / Biso Wilson estimate: 17.76 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.33
Reflection shellResolution: 1.547→1.62 Å / CC1/2: 0.52

-
Processing

Software
NameVersionClassification
PHENIXdev_4839refinement
PHENIXdev_4839refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P7H

1p7h


Resolution: 1.55→56.96 Å / SU ML: 0.1981 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.4617
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2363 1183 4.89 %
Rwork0.1942 23029 -
obs0.1963 24212 74.4 %
all-48015 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.4 Å2
Refinement stepCycle: LAST / Resolution: 1.55→56.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1682 0 24 268 1974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01271762
X-RAY DIFFRACTIONf_angle_d1.22742388
X-RAY DIFFRACTIONf_chiral_restr0.0759256
X-RAY DIFFRACTIONf_plane_restr0.0105311
X-RAY DIFFRACTIONf_dihedral_angle_d6.1013250
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.14481495239 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.620.3089140.289314X-RAY DIFFRACTION8.14
1.62-1.70.3142620.29041279X-RAY DIFFRACTION33.37
1.7-1.810.31911390.28782516X-RAY DIFFRACTION65.2
1.81-1.950.34321670.25833608X-RAY DIFFRACTION93.7
1.95-2.150.25742130.20993783X-RAY DIFFRACTION98.57
2.15-2.460.23681810.1883802X-RAY DIFFRACTION98.35
2.46-3.090.22392020.18483823X-RAY DIFFRACTION98.05
3.09-56.960.20542050.16833904X-RAY DIFFRACTION98.3
Refinement TLS params.Method: refined / Origin x: 14.0133951759 Å / Origin y: 7.29146038569 Å / Origin z: 13.5852543605 Å
111213212223313233
T0.121694625016 Å20.0169703077769 Å20.00267879759663 Å2-0.107370708487 Å2-0.000845034680906 Å2--0.0831573842863 Å2
L1.55954548873 °20.460464930381 °20.144407077586 °2-1.05420917525 °2-0.00586381720642 °2--0.274607620729 °2
S0.0160181758658 Å °-0.112075352526 Å °-0.00423377531153 Å °0.112729672309 Å °-0.0209710388501 Å °0.0094326031609 Å °0.0326344679542 Å °0.0239421065164 Å °0.00956202946223 Å °
Refinement TLS groupSelection details: all

+
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