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- PDB-1fos: TWO HUMAN C-FOS:C-JUN:DNA COMPLEXES -

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Basic information

Entry
Database: PDB / ID: 1fos
TitleTWO HUMAN C-FOS:C-JUN:DNA COMPLEXES
Components
  • C-JUN PROTO-ONCOGENE PROTEIN
  • DNA (5'-D(*AP*AP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*AP*GP*GP*AP*GP*A)-3')
  • DNA (5'-D(*TP*TP*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*AP*T)-3')
  • P55-C-FOS PROTO-ONCOGENE PROTEIN
KeywordsTRANSCRIPTION/DNA / COILED-COIL / DNA-BINDING PROTEIN / HETERODIMER / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


mononuclear cell differentiation / cellular response to prolactin / medium-term memory / leading edge cell differentiation / cellular response to anisomycin / cAMP response element binding / transcription factor AP-1 complex / integrated stress response signaling / cellular response to zinc ion starvation / positive regulation of DNA-templated transcription initiation ...mononuclear cell differentiation / cellular response to prolactin / medium-term memory / leading edge cell differentiation / cellular response to anisomycin / cAMP response element binding / transcription factor AP-1 complex / integrated stress response signaling / cellular response to zinc ion starvation / positive regulation of DNA-templated transcription initiation / release from viral latency / skeletal muscle cell proliferation / negative regulation of DNA binding / WNT5:FZD7-mediated leishmania damping / neural retina development / cellular response to phorbol 13-acetate 12-myristate / SMAD protein signal transduction / conditioned taste aversion / NGF-stimulated transcription / positive regulation of osteoclast differentiation / host-mediated activation of viral transcription / response to steroid hormone / axon regeneration / cellular response to parathyroid hormone stimulus / response to corticosterone / nuclear chromosome / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Activation of the AP-1 family of transcription factors / response to gravity / eyelid development in camera-type eye / response to immobilization stress / outflow tract morphogenesis / R-SMAD binding / response to light stimulus / ubiquitin-like protein ligase binding / myoblast proliferation / monocyte differentiation / skeletal muscle cell differentiation / positive regulation of epithelial cell migration / general transcription initiation factor binding / host-mediated suppression of viral transcription / response to cAMP / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of vascular associated smooth muscle cell proliferation / JNK cascade / response to muscle stretch / NPAS4 regulates expression of target genes / positive regulation of endothelial cell proliferation / transcription repressor complex / transforming growth factor beta receptor signaling pathway / GTPase activator activity / cellular response to calcium ion / response to progesterone / osteoclast differentiation / cellular response to epidermal growth factor stimulus / response to endoplasmic reticulum stress / Regulation of PTEN gene transcription / response to activity / transcription coregulator binding / cellular response to reactive oxygen species / FCERI mediated MAPK activation / TP53 Regulates Transcription of DNA Repair Genes / promoter-specific chromatin binding / liver development / microglial cell activation / female pregnancy / euchromatin / protein-DNA complex / MAPK6/MAPK4 signaling / response to insulin / cerebral cortex development / positive regulation of miRNA transcription / response to toxic substance / Pre-NOTCH Transcription and Translation / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear matrix / positive regulation of fibroblast proliferation / neuron differentiation / sequence-specific double-stranded DNA binding / cellular response to tumor necrosis factor / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / angiogenesis / Interleukin-4 and Interleukin-13 signaling / Oxidative Stress Induced Senescence / response to lipopolysaccharide / transcription regulator complex / cellular response to hypoxia / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cell population proliferation
Similarity search - Function
AP-1 transcription factor / Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Transcription factor, Skn-1-like, 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. ...AP-1 transcription factor / Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Transcription factor, Skn-1-like, 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 / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Protein c-Fos / Transcription factor Jun
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.05 Å
AuthorsGlover, J.N.M. / Harrison, S.C.
CitationJournal: Nature / Year: 1995
Title: Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA.
Authors: Glover, J.N. / Harrison, S.C.
History
DepositionMar 7, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 10, 1995Provider: 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(*AP*AP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*AP*GP*GP*AP*GP*A)-3')
B: DNA (5'-D(*TP*TP*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*AP*T)-3')
C: DNA (5'-D(*AP*AP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*AP*GP*GP*AP*GP*A)-3')
D: DNA (5'-D(*TP*TP*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*AP*T)-3')
E: P55-C-FOS PROTO-ONCOGENE PROTEIN
F: C-JUN PROTO-ONCOGENE PROTEIN
G: P55-C-FOS PROTO-ONCOGENE PROTEIN
H: C-JUN PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)53,9348
Polymers53,9348
Non-polymers00
Water00
1
A: DNA (5'-D(*AP*AP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*AP*GP*GP*AP*GP*A)-3')
B: DNA (5'-D(*TP*TP*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*AP*T)-3')
E: P55-C-FOS PROTO-ONCOGENE PROTEIN
F: C-JUN PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,9674
Polymers26,9674
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*AP*AP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*AP*GP*GP*AP*GP*A)-3')
D: DNA (5'-D(*TP*TP*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*AP*T)-3')
G: P55-C-FOS PROTO-ONCOGENE PROTEIN
H: C-JUN PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,9674
Polymers26,9674
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)241.100, 48.690, 66.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

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


Mass: 6271.092 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*TP*CP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*AP*T)-3')


Mass: 5994.890 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein P55-C-FOS PROTO-ONCOGENE PROTEIN / CELLULAR ONCOGENE C-FOS / G0S7 PROTEIN


Mass: 7379.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PJUN(S)63 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3/PLYSS / References: UniProt: P01100
#4: Protein C-JUN PROTO-ONCOGENE PROTEIN


Mass: 7321.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PJUN(S)63 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3/PLYSS / References: GenBank: 386839, UniProt: P05412*PLUS
Sequence detailsFOS SEQUENCE EXPRESSED CORRESPONDS TO RESIDUES 139 - 200 OF HUMAN P55-C-FOS PROTO-ONCOGENE PROTEIN. ...FOS SEQUENCE EXPRESSED CORRESPONDS TO RESIDUES 139 - 200 OF HUMAN P55-C-FOS PROTO-ONCOGENE PROTEIN. JUN SEQUENCE EXPRESSED CORRESPONDS TO RESIDUES 263 - 324 OF HUMAN TRANSCRIPTION FACTOR AP-1 (C-JUN PROTO-ONCOGENE).

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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: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: pH 6.70, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 40011
3NH4 ACETATE11
4NACL11
5MGCL211
6SPERMINE11
7DTT11
8BIS-TRIS-PROPANE11
9WATER12
10PEG 40012
11NACL12
12MGCL212
13SPERMINE12
14BIS-TRIS-PROPANE12
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMFos63-jun631drop
20.6-0.8 mMDNA1drop
35.5-7.5 %PEG4001drop
4100-200 mMammonium acetate1drop
5150 mM1dropNaCl
627.5 mM1dropMgCl2
71.0 mMspermine1drop
85-10 mMdithiothreitol1drop
925 mMbis-Tris1drop
1011-15 %PEG4001reservoir
11300 mM1reservoirNaCl
1255 mM1reservoirMgCl2
1320. mMspermine1reservoir
145-10 mMdithiothreitol1reservoir
1550 mMbis-Tris1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 14316 / % possible obs: 91.1 % / Observed criterion σ(I): 1
Reflection
*PLUS
% possible obs: 91.1 % / Observed criterion σ(I): 0 / Num. measured all: 76796 / Rmerge(I) obs: 0.09

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Processing

Software
NameClassification
X-PLORrefinement
XDSdata reduction
RefinementResolution: 3.05→10 Å / Rfactor Rfree: 0.321 / Rfactor Rwork: 0.23 / Rfactor obs: 0.23 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 3.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 1628 0 0 3484
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.33
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.05 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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