[English] 日本語
Yorodumi
- PDB-7l4v: C-terminal bZIP domain of human C/EBPbeta Bound to DNA with Conse... -

+
Open data


ID or keywords:

Loading...

-
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 1DNA
  • DNA Strand 2DNA
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


C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / Response of EIF2AK1 (HRI) to heme deficiency ...C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of biomineral tissue development / myeloid cell development / integrated stress response signaling / T-helper 1 cell activation / Response of EIF2AK1 (HRI) to heme deficiency / hepatocyte proliferation / 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 / regulation of cell differentiation / ubiquitin-like protein ligase binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / Transcriptional Regulation by VENTX / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of interleukin-4 production / embryonic placenta development / positive regulation of fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of osteoblast differentiation / Nuclear events stimulated by ALK signaling in cancer / brown fat cell differentiation / ovarian follicle development / negative regulation of T cell proliferation / response to endoplasmic reticulum stress / liver regeneration / acute-phase response / cellular response to amino acid stimulus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / chromatin DNA binding / nuclear matrix / DNA-binding transcription repressor activity, RNA polymerase II-specific / kinase binding / positive regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Transcriptional regulation of granulopoiesis / histone deacetylase binding / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / response to lipopolysaccharide / transcription by RNA polymerase II / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / immune response / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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 superfamily / Basic-leucine zipper domain
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / DNA


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


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 / Ethylene glycol


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


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

-
Experimental details

-
Experiment

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

-
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)

-
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

-
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

+
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