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- PDB-1a02: STRUCTURE OF THE DNA BINDING DOMAINS OF NFAT, FOS AND JUN BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1a02
TitleSTRUCTURE OF THE DNA BINDING DOMAINS OF NFAT, FOS AND JUN BOUND TO DNA
Components
  • (AP-1 FRAGMENT ...) x 2
  • DNA (5'-D(*DAP*DAP*DCP*DTP*DAP*DTP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DCP*DC)-3')
  • DNA (5'-D(*DTP*DTP*DGP*DGP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DTP*DCP*DAP*DTP*DAP*DG)-3')
  • NUCLEAR FACTOR OF ACTIVATED T CELLS
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / NFAT / NF-AT / AP-1 / FOS-JUN / QUATERNARY PROTEIN-DNA COMPLEX / TRANSCRIPTION SYNERGY / COMBINATORIAL GENE REGULATION / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


: / cAMP response element binding / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / release from viral latency / cellular response to prolactin / mononuclear cell differentiation / myotube cell development ...: / cAMP response element binding / transcription factor AP-1 complex / negative regulation of vascular associated smooth muscle cell differentiation / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / release from viral latency / cellular response to prolactin / mononuclear cell differentiation / myotube cell development / response to gravity / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / calcineurin-NFAT signaling cascade / skeletal muscle cell proliferation / WNT5:FZD7-mediated leishmania damping / cellular response to zinc ion starvation / cellular response to phorbol 13-acetate 12-myristate / conditioned taste aversion / NGF-stimulated transcription / positive regulation of osteoclast differentiation / SMAD protein signal transduction / positive regulation by host of viral transcription / cartilage development / cellular response to parathyroid hormone stimulus / myoblast proliferation / : / CLEC7A (Dectin-1) induces NFAT activation / response to corticosterone / nuclear chromosome / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / positive regulation of myoblast fusion / negative regulation of DNA binding / Activation of the AP-1 family of transcription factors / ubiquitin-like protein ligase binding / skeletal muscle cell differentiation / R-SMAD binding / response to light stimulus / Calcineurin activates NFAT / general transcription initiation factor binding / response to immobilization stress / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / negative regulation by host of viral transcription / RNA polymerase II core promoter sequence-specific DNA binding / phosphatase binding / positive regulation of B cell proliferation / response to cAMP / cellular response to epidermal growth factor stimulus / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to cadmium ion / response to muscle stretch / cellular response to calcium ion / NPAS4 regulates expression of target genes / response to endoplasmic reticulum stress / GTPase activator activity / FCERI mediated Ca+2 mobilization / osteoclast differentiation / transforming growth factor beta receptor signaling pathway / response to activity / 14-3-3 protein binding / response to progesterone / Regulation of PTEN gene transcription / female pregnancy / transcription coregulator binding / protein-DNA complex / TP53 Regulates Transcription of DNA Repair Genes / FCERI mediated MAPK activation / B cell receptor signaling pathway / MAPK6/MAPK4 signaling / response to insulin / euchromatin / response to toxic substance / Pre-NOTCH Transcription and Translation / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to reactive oxygen species / positive regulation of miRNA transcription / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / cell migration / sequence-specific double-stranded DNA binding / cellular response to tumor necrosis factor / nervous system development / regulation of cell population proliferation / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / Oxidative Stress Induced Senescence / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / response to lipopolysaccharide / transcription by RNA polymerase II / molecular adaptor activity / transcription cis-regulatory region binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / inflammatory response / ribonucleoprotein complex
Similarity search - Function
AP-1 transcription factor / Nuclear factor of activated T cells (NFAT) / Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / Rel homology domain (RHD), DNA-binding domain / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain ...AP-1 transcription factor / Nuclear factor of activated T cells (NFAT) / Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / Rel homology domain (RHD), DNA-binding domain / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein c-Fos / Transcription factor Jun / Nuclear factor of activated T-cells, cytoplasmic 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR/MAD / Resolution: 2.7 Å
AuthorsChen, L. / Glover, J.N.M. / Hogan, P.G. / Rao, A. / Harrison, S.C.
CitationJournal: 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. / Hogan, P.G. / Rao, A. / Harrison, S.C.
History
DepositionDec 8, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*DTP*DTP*DGP*DGP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DTP*DCP*DAP*DTP*DAP*DG)-3')
B: DNA (5'-D(*DAP*DAP*DCP*DTP*DAP*DTP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DCP*DC)-3')
N: NUCLEAR FACTOR OF ACTIVATED T CELLS
F: AP-1 FRAGMENT FOS
J: AP-1 FRAGMENT JUN


Theoretical massNumber of molelcules
Total (without water)59,8455
Polymers59,8455
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-43 kcal/mol
Surface area26430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.660, 85.460, 83.370
Angle α, β, γ (deg.)90.00, 112.03, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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DNA chain , 2 types, 2 molecules AB

#1: DNA chain DNA (5'-D(*DTP*DTP*DGP*DGP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DTP*DCP*DAP*DTP*DAP*DG)-3')


Mass: 6178.024 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DAP*DAP*DCP*DTP*DAP*DTP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DCP*DC)-3')


Mass: 6084.993 Da / Num. of mol.: 1 / Source method: obtained synthetically

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AP-1 FRAGMENT ... , 2 types, 2 molecules FJ

#4: Protein AP-1 FRAGMENT FOS / FOS


Mass: 6727.733 Da / Num. of mol.: 1 / Fragment: FOS / Mutation: C154S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01100
#5: Protein AP-1 FRAGMENT JUN / JUN


Mass: 6583.826 Da / Num. of mol.: 1 / Fragment: JUN / Mutation: C279S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05412

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Protein / Non-polymers , 2 types, 89 molecules N

#3: Protein NUCLEAR FACTOR OF ACTIVATED T CELLS / NFAT


Mass: 34270.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: T-LYMPHOCYTE / Gene: NFAT1 / Plasmid: PLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q13469
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.54 Å3/Da / Density % sol: 68 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: THE COMPLEX WAS CRYSTALLIZED IN 300-400 MM AMMONIUM ACETATE SALT, PH 7.5 (10 MM)., VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2DTT11
3NACLSodium chloride11
4GLYCEROL11
5AMMINO ACETATE11
6HEPES12
7DTT12
8NACLSodium chloride12
9GLYCEROL12
10AMMINO ACETATE12
Crystal
*PLUS
Density % sol: 68 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2-0.4 mMDNA1drop
210 mMHEPES1reservoir
31 mMdithiothreitol1reservoir
4100 mM1reservoirNaCl
520 %glycerol1reservoir
6300 mM1reservoirNH4OAc
71
81
91
101

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 16, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 22079 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 61 Å2 / Rsym value: 0.08
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.7 % / Rsym value: 0.43 / % possible all: 93.3
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % possible obs: 98.3 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Biso Wilson estimate: 61 Å2
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 93.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
CCP4model building
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
X-PLORphasing
RefinementMethod to determine structure: MIR/MAD / Resolution: 2.7→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUES N 478 - N 485 AND N 628 - N 634 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1671 7.5 %RANDOM
Rwork0.246 ---
obs0.246 21643 90.1 %-
Displacement parametersBiso mean: 51 Å2
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 814 0 88 3975
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it2.52.5
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.369 188 6.6 %
Rwork0.369 1784 -
obs--69.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_NDBX.DNATOP_NDBX.DNA
X-RAY DIFFRACTION3PARAM_NDBX.INTTOPH19.SOL
X-RAY DIFFRACTION4PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.62
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.49
LS refinement shell
*PLUS
Rfactor obs: 0.369

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