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- PDB-1ci6: TRANSCRIPTION FACTOR ATF4-C/EBP BETA BZIP HETERODIMER -

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Basic information

Entry
Database: PDB / ID: 1ci6
TitleTRANSCRIPTION FACTOR ATF4-C/EBP BETA BZIP HETERODIMER
Components
  • TRANSCRIPTION FACTOR ATF-4
  • TRANSCRIPTION FACTOR C/EBP BETA
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / BZIP
Function / homology
Function and homology information


L-asparagine metabolic process / ATF1-ATF4 transcription factor complex / CHOP-ATF4 complex / Lewy body core / ATF4-CREB1 transcription factor complex / regulation of odontoblast differentiation / positive regulation of sodium-dependent phosphate transport / granuloma formation / CHOP-C/EBP complex / C/EBP complex ...L-asparagine metabolic process / ATF1-ATF4 transcription factor complex / CHOP-ATF4 complex / Lewy body core / ATF4-CREB1 transcription factor complex / regulation of odontoblast differentiation / positive regulation of sodium-dependent phosphate transport / granuloma formation / CHOP-C/EBP complex / C/EBP complex / positive regulation of biomineral tissue development / myeloid cell development / leucine zipper domain binding / Senescence-Associated Secretory Phenotype (SASP) / integrated stress response signaling / T-helper 1 cell activation / cAMP response element binding protein binding / HRI-mediated signaling / ATF6 (ATF6-alpha) activates chaperone genes / response to manganese-induced endoplasmic reticulum stress / hepatocyte proliferation / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / PERK regulates gene expression / lens fiber cell morphogenesis / cellular response to leucine starvation / ATF4 activates genes in response to endoplasmic reticulum stress / nuclear glucocorticoid receptor binding / regulation of osteoclast differentiation / mammary gland epithelial cell differentiation / NFE2L2 regulating ER-stress associated genes / condensed chromosome, centromeric region / regulation of dendritic cell differentiation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of interleukin-6 production / embryonic hemopoiesis / negative regulation of cold-induced thermogenesis / mammary gland epithelial cell proliferation / NFE2L2 regulating anti-oxidant/detoxification enzymes / positive regulation of vascular associated smooth muscle cell apoptotic process / regulation of osteoblast differentiation / histone acetyltransferase binding / gamma-aminobutyric acid signaling pathway / positive regulation of interleukin-4 production / bone mineralization / fat cell differentiation / positive regulation of transcription by RNA polymerase I / negative regulation of potassium ion transport / ubiquitin-like protein ligase binding / positive regulation of vascular endothelial growth factor production / general transcription initiation factor binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to interleukin-1 / embryonic placenta development / positive regulation of fat cell differentiation / positive regulation of osteoblast differentiation / brown fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / endoplasmic reticulum unfolded protein response / ovarian follicle development / cellular response to glucose starvation / negative regulation of T cell proliferation / dendrite membrane / liver regeneration / nuclear periphery / cellular response to amino acid starvation / response to endoplasmic reticulum stress / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to amino acid stimulus / response to nutrient levels / promoter-specific chromatin binding / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / regulation of synaptic plasticity / chromatin DNA binding / response to toxic substance / DNA-binding transcription repressor activity, RNA polymerase II-specific / kinase binding / RNA polymerase II transcription regulator complex / memory / histone deacetylase binding / nuclear matrix / neuron differentiation / intracellular calcium ion homeostasis / positive regulation of inflammatory response / sequence-specific double-stranded DNA binding / cellular response to UV / positive regulation of neuron apoptotic process / positive regulation of cold-induced thermogenesis / cellular response to lipopolysaccharide / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / response to lipopolysaccharide / cellular response to hypoxia / sequence-specific DNA binding / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding
Similarity search - Function
CCAAT/enhancer-binding protein, chordates / : / bZIP transcription factor / Basic region leucine zipper / 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 ...CCAAT/enhancer-binding protein, chordates / : / bZIP transcription factor / Basic region leucine zipper / 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
BETA-MERCAPTOETHANOL / : / Cyclic AMP-dependent transcription factor ATF-4 / CCAAT/enhancer-binding protein beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPodust, L.M. / Kim, Y.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of the CCAAT box/enhancer-binding protein beta activating transcription factor-4 basic leucine zipper heterodimer in the absence of DNA
Authors: Podust, L.M. / Krezel, A.M. / Kim, Y.
History
DepositionApr 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTION FACTOR ATF-4
B: TRANSCRIPTION FACTOR C/EBP BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4636
Polymers15,2182
Non-polymers2464
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-20 kcal/mol
Surface area8300 Å2
MethodPISA
2
A: TRANSCRIPTION FACTOR ATF-4
B: TRANSCRIPTION FACTOR C/EBP BETA
hetero molecules

A: TRANSCRIPTION FACTOR ATF-4
B: TRANSCRIPTION FACTOR C/EBP BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,92712
Polymers30,4354
Non-polymers4918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5840 Å2
ΔGint-66 kcal/mol
Surface area15570 Å2
MethodPISA
3
A: TRANSCRIPTION FACTOR ATF-4
B: TRANSCRIPTION FACTOR C/EBP BETA
hetero molecules

A: TRANSCRIPTION FACTOR ATF-4
B: TRANSCRIPTION FACTOR C/EBP BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,92712
Polymers30,4354
Non-polymers4918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area6540 Å2
ΔGint-61 kcal/mol
Surface area14870 Å2
MethodPISA
4
A: TRANSCRIPTION FACTOR ATF-4
B: TRANSCRIPTION FACTOR C/EBP BETA
hetero molecules

A: TRANSCRIPTION FACTOR ATF-4
B: TRANSCRIPTION FACTOR C/EBP BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,92712
Polymers30,4354
Non-polymers4918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546x,-y-1,-z+11
Buried area5740 Å2
ΔGint-61 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.628, 81.152, 35.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Cell settingorthorhombic
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-402-

FE

21B-400-

FE

31B-401-

FE

41B-7-

HOH

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Components

#1: Protein TRANSCRIPTION FACTOR ATF-4


Mass: 7471.692 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P18848
#2: Protein TRANSCRIPTION FACTOR C/EBP BETA


Mass: 7746.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P28033
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.5 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0 M (NH4)2SO4, 100 MM SODIUM CACODYLATE, PH 6.5, 10.0 % DIOXANE AT 15 DEGREES C, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 15 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.3 mMC/EBP beta-ATF4 heterodimer1drop
21 Mammonium sulfate1drop
350 mMsodium cacodylate1drop
45 %dioxane1drop
510 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 15, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 6800 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 53.8 Å2 / Rsym value: 0.082 / Net I/σ(I): 8.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.48 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 58744 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.475

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNS0.4refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FOS

1fos


Resolution: 2.6→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high rms absF: 303496.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.273 638 9.7 %RANDOM
Rwork0.217 ---
obs-5890 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 87.74 Å2 / ksol: 0.48 e/Å3
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1-12.4 Å20 Å20 Å2
2---14 Å20 Å2
3---1.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-8 Å
Luzzati sigma a0.37 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 3 90 933
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d14.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.59
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.861.5
X-RAY DIFFRACTIONc_mcangle_it5.672
X-RAY DIFFRACTIONc_scbond_it6.722
X-RAY DIFFRACTIONc_scangle_it9.982.5
LS refinement shellResolution: 2.6→2.67 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.363 37 9.6 %
Rwork0.294 350 -
obs--73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4SEO.PARSEO.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.92
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg13.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.56

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