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- PDB-7l4v: C-terminal bZIP domain of human C/EBPbeta Bound to DNA with Conse... -

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Basic information

Entry
Database: PDB / ID: 7l4v
TitleC-terminal bZIP domain of human C/EBPbeta Bound to DNA with Consensus Recognition with GT Mismatch
Components
  • CCAAT/enhancer-binding protein beta
  • DNA Strand 1
  • DNA Strand 2
KeywordsTRANSCRIPTION/DNA / bZIP Transciption Factor DNA Methylation CpA methylation PROTEIN-DNA COMPLEX / TRANSCRIPTION / TRANSCRIPTION-DNA complex / G-T DNA Mismatch
Function / homology
Function and homology information


granuloma formation / regulation of odontoblast differentiation / positive regulation of sodium-dependent phosphate transport / CHOP-C/EBP complex / C/EBP complex / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / hepatocyte proliferation ...granuloma formation / regulation of odontoblast differentiation / positive regulation of sodium-dependent phosphate transport / CHOP-C/EBP complex / C/EBP complex / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / hepatocyte proliferation / Response of EIF2AK1 (HRI) to heme deficiency / ATF4 activates genes in response to endoplasmic reticulum stress / regulation of osteoclast differentiation / mammary gland epithelial cell differentiation / condensed chromosome, centromeric region / regulation of dendritic cell differentiation / regulation of interleukin-6 production / mammary gland epithelial cell proliferation / histone acetyltransferase binding / positive regulation of interleukin-4 production / regulation of cell differentiation / ubiquitin-like protein ligase binding / Transcriptional Regulation by VENTX / Response of EIF2AK4 (GCN2) to amino acid deficiency / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of fat cell differentiation / embryonic placenta development / positive regulation of osteoblast differentiation / brown fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / ovarian follicle development / negative regulation of T cell proliferation / response to endoplasmic reticulum stress / liver regeneration / acute-phase response / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to amino acid stimulus / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / kinase binding / histone deacetylase binding / RNA polymerase II transcription regulator complex / nuclear matrix / Transcriptional regulation of granulopoiesis / positive regulation of inflammatory response / neuron differentiation / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Senescence-Associated Secretory Phenotype (SASP) / negative regulation of neuron apoptotic process / response to lipopolysaccharide / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / defense response to bacterium / immune response / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
CCAAT/enhancer-binding protein, chordates / : / Basic region leucine zipper / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / CCAAT/enhancer-binding protein beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHorton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations.
Authors: Yang, J. / Horton, J.R. / Akdemir, K.C. / Li, J. / Huang, Y. / Kumar, J. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionDec 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CCAAT/enhancer-binding protein beta
B: CCAAT/enhancer-binding protein beta
C: DNA Strand 1
D: DNA Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7719
Polymers28,4614
Non-polymers3105
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-35 kcal/mol
Surface area14910 Å2
Unit cell
Length a, b, c (Å)101.452, 113.144, 75.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein CCAAT/enhancer-binding protein beta / C/EBP beta / Liver activator protein / LAP / Liver-enriched inhibitory protein / LIP / Nuclear ...C/EBP beta / Liver activator protein / LAP / Liver-enriched inhibitory protein / LIP / Nuclear factor NF-IL6 / Transcription factor 5 / TCF-5


Mass: 9325.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEBPB, TCF5, PP9092 / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: P17676
#2: DNA chain DNA Strand 1


Mass: 4961.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA Strand 2


Mass: 4848.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM ammonium sulfate, 50 mM BIS-TRIS pH 6.5, 30% (v/v) pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→37.77 Å / Num. obs: 44214 / % possible obs: 99.9 % / Redundancy: 30.6 % / Biso Wilson estimate: 39.94 Å2 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.025 / Net I/σ(I): 23.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 11.3 % / Rmerge(I) obs: 1.762 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4352 / CC1/2: 0.541 / Rpim(I) all: 0.496 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MG2

6mg2


Resolution: 1.75→37.77 Å / SU ML: 0.2549 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6213
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2213 1995 4.52 %
Rwork0.1994 42140 -
obs0.2004 44135 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.5 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 651 20 206 1987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531869
X-RAY DIFFRACTIONf_angle_d0.77292629
X-RAY DIFFRACTIONf_chiral_restr0.0342295
X-RAY DIFFRACTIONf_plane_restr0.0058226
X-RAY DIFFRACTIONf_dihedral_angle_d22.3088784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.43611380.45472913X-RAY DIFFRACTION97.98
1.79-1.840.3841420.36672980X-RAY DIFFRACTION99.78
1.84-1.90.29371410.2932977X-RAY DIFFRACTION99.94
1.9-1.960.25111410.23852984X-RAY DIFFRACTION99.87
1.96-2.030.28131420.22982995X-RAY DIFFRACTION99.97
2.03-2.110.26691420.24663007X-RAY DIFFRACTION99.97
2.11-2.20.26791400.23312959X-RAY DIFFRACTION100
2.2-2.320.21061440.20383016X-RAY DIFFRACTION100
2.32-2.470.21211420.21363010X-RAY DIFFRACTION100
2.47-2.660.231430.21012998X-RAY DIFFRACTION100
2.66-2.920.27651440.22483043X-RAY DIFFRACTION99.97
2.92-3.350.24491400.20633017X-RAY DIFFRACTION99.34
3.35-4.220.18091460.173072X-RAY DIFFRACTION99.72
4.22-37.770.19271500.17323169X-RAY DIFFRACTION99.82
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.395333280892-1.789842365990.9406704945625.48510624951-3.810572980522.11645123919-0.155448897413-0.128588044423-0.007475726327220.3158455815090.340844065420.117068488992-0.135888031117-0.14324952134-0.2196021704260.3887985673570.0177037984028-0.02987783633980.3519426129980.01256938537440.3916079764327.220265529852.782930768133.6631039624
20.264231373040.575308663616-0.1167883778732.69008364564-0.2284817008530.444920275009-0.106287223040.05635250608230.00774994549307-0.3691112407130.1554847224090.0626786876058-0.018818158008-0.115653647833-0.05255458230220.290737871016-0.00255046962499-0.02288299346420.3001242069310.01097685966690.2782766415924.470973531552.805356295825.359569777
39.210550755440.437272448908-1.73336958335.291828113923.402903591472.64349125933-0.462903542686-1.22035462117-0.3380178501440.8643198550530.558243508194-1.338964919350.4735391494091.54455803122-0.2332070083720.100261930049-0.04396523026340.08352389358770.884931952577-0.123531685940.82227756032244.635200028431.592406893542.8464386276
46.940146300176.124574740723.162557091345.441471140433.042610373573.49902182488-0.667417523340.4676300031810.0108307496834-1.20269408910.542421878618-0.1869838876210.06615225793440.4570232719550.04456535921870.3332714141940.0150665395030.00644512907590.4997934010620.00875408270040.38806673273730.21629813825.135316113732.9099826318
54.79099163363-6.220591236054.522631507959.40126266447-4.054178924466.70499585378-0.666853036971-0.7970491169030.2228184226910.929835481370.3618548873670.78141412377-0.511582938599-1.182675835210.2393409832010.2643319731210.01782254822860.02984875557770.565996667494-0.1065668367710.47412744775713.744629254228.249929530539.5823672753
65.516626726546.47962984271-0.8296528579488.77721941677-0.4608360364022.05178663807-0.3967549111760.6941329359910.258260042311-0.3348878554650.05190391237270.327692584802-0.24763227159-0.3978140399930.2479762087560.291632219563-0.0372721435155-0.07152504588381.179031707230.1221806311331.004024531754.9047707648732.410369562731.3752233683
77.7579101093-3.615910409752.976129173373.86832578314-1.050351616352.92853895528-0.342433813213-0.1262358680810.130913071561-0.0671957659871-0.09742341356320.5183889385350.181057911679-0.6261500370860.402607588830.2545800274110.0155399059767-0.02419470054440.486373678187-0.04868995475590.44188684904513.95808581329.447329342531.7472947693
88.8402760373.486946447360.904483621024.28551881918-0.2582694426725.03361529963-0.1784337833310.762238641286-0.2544179300020.0129948469929-0.125095543092-0.118892845360.0766558777552-0.153126547910.325255718130.2397632360090.0348938197945-0.01722225794240.413457147551-0.03741597609950.31940603550229.690683662126.207264150141.1182521507
92.811130949034.78847250456-0.2505113938578.55746269104-0.9923841571427.16495505926-0.901329189330.668264639593-0.776854472207-1.096848266890.515293278151-1.60117893418-0.3313592432410.8673165916950.2943123440430.323591585440.03540990684140.02314643747430.754649596734-0.06272284020980.67190992098745.7898286528.842591661135.6111607999
106.20581155183-6.31387127814-1.210901401577.69996513918-1.63378861487.91763029643-1.70674530546-1.144782457652.257500040810.540678443283-0.05919016383520.515939223915-2.63200652036-1.833782493181.863316945290.5414609214310.130068488949-0.3703685965981.05875864375-0.2474230645051.2040185875753.419394667235.899423578543.7136265488
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 268 through 333 )AA268 - 3331 - 66
22chain 'B' and (resid 268 through 336 )BB268 - 3361 - 69
33chain 'C' and (resid 2 through 6 )CC2 - 6
44chain 'C' and (resid 7 through 11 )CC7 - 11
55chain 'C' and (resid 12 through 16 )CC12 - 16
66chain 'C' and (resid 17 through 17 )CC17
77chain 'D' and (resid 102 through 106 )DD102 - 106
88chain 'D' and (resid 107 through 111 )DD107 - 111
99chain 'D' and (resid 112 through 116 )DD112 - 116
1010chain 'D' and (resid 117 through 117 )DD117

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