[English] 日本語
Yorodumi
- PDB-8k8c: Crystal structure of C/EBPalpha BZIP domain bound to a high affin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k8c
TitleCrystal structure of C/EBPalpha BZIP domain bound to a high affinity DNA
Components
  • CCAAT/enhancer-binding protein alpha
  • DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*A)-3')
  • DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*T)-3')
KeywordsDNA BINDING PROTEIN/DNA / C/EBPalpha / DNA binding / bZIP / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of hematopoietic stem cell proliferation / CHOP-C/EBP complex / C/EBP complex / RNA polymerase I transcription regulatory region sequence-specific DNA binding / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / granulocyte differentiation / urea cycle / myeloid cell differentiation / positive regulation of macrophage activation ...negative regulation of hematopoietic stem cell proliferation / CHOP-C/EBP complex / C/EBP complex / RNA polymerase I transcription regulatory region sequence-specific DNA binding / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / granulocyte differentiation / urea cycle / myeloid cell differentiation / positive regulation of macrophage activation / epithelial cell maturation / STAT family protein binding / cellular response to lithium ion / interleukin-6-mediated signaling pathway / hematopoietic stem cell proliferation / lipid homeostasis / fat cell differentiation / : / inner ear development / macrophage differentiation / white fat cell differentiation / negative regulation of cell cycle / positive regulation of fat cell differentiation / embryonic placenta development / positive regulation of osteoblast differentiation / transcription by RNA polymerase I / brown fat cell differentiation / energy homeostasis / Notch signaling pathway / cholesterol metabolic process / liver development / generation of precursor metabolites and energy / mitochondrion organization / lung development / cytokine-mediated signaling pathway / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / kinase binding / RNA polymerase II transcription regulator complex / Transcriptional regulation of granulopoiesis / positive regulation of inflammatory response / glucose homeostasis / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to tumor necrosis factor / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
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 alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsMin, J.R. / Chen, S.Z. / Liu, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural basis for specific DNA sequence recognition by the transcription factor NFIL3.
Authors: Chen, S. / Lei, M. / Liu, K. / Min, J.
History
DepositionJul 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CCAAT/enhancer-binding protein alpha
B: CCAAT/enhancer-binding protein alpha
C: DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*A)-3')
D: DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8076
Polymers22,6234
Non-polymers1842
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-38 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.382, 63.366, 128.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CCAAT/enhancer-binding protein alpha


Mass: 7341.220 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEBPA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49715
#2: DNA chain DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*A)-3')


Mass: 3974.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*AP*TP*TP*AP*CP*GP*TP*AP*AP*TP*GP*T)-3')


Mass: 3965.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.015 M Calcium chloride dihydrate,0.1 M Sodium acetate trihydrate pH 4.6, 30% v/v 2-Methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.06→64.27 Å / Num. obs: 20836 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 1 / Net I/σ(I): 18.9
Reflection shellResolution: 2.06→2.17 Å / Num. unique obs: 2979 / CC1/2: 0.938

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→19.96 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 1986 9.61 %
Rwork0.2255 --
obs0.2308 20673 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 527 12 55 1598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081604
X-RAY DIFFRACTIONf_angle_d1.0732250
X-RAY DIFFRACTIONf_dihedral_angle_d25.259398
X-RAY DIFFRACTIONf_chiral_restr0.049248
X-RAY DIFFRACTIONf_plane_restr0.011207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.110.50431390.4971311X-RAY DIFFRACTION100
2.11-2.160.47341400.44361305X-RAY DIFFRACTION99
2.16-2.230.42741360.40081307X-RAY DIFFRACTION99
2.23-2.30.37161410.33141314X-RAY DIFFRACTION99
2.3-2.380.35551380.31031298X-RAY DIFFRACTION100
2.38-2.480.32871440.25561358X-RAY DIFFRACTION100
2.48-2.590.26721380.24021291X-RAY DIFFRACTION100
2.59-2.720.29741410.24521322X-RAY DIFFRACTION100
2.72-2.890.30661420.24351335X-RAY DIFFRACTION100
2.89-3.120.27411400.23681334X-RAY DIFFRACTION100
3.12-3.430.23521420.20451334X-RAY DIFFRACTION99
3.43-3.920.28351450.18781355X-RAY DIFFRACTION99
3.92-4.930.21381460.1781375X-RAY DIFFRACTION100
4.93-19.960.27271540.18871448X-RAY DIFFRACTION100
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)
10.19420.01220.56080.1833-0.50331.0803-0.19090.0847-0.18520.0317-0.0084-0.15510.0353-0.1833-0.0010.44440.06090.03360.32950.03870.37046.0155.620133.7934
20.15560.0629-0.37840.6074-0.90320.9392-0.11310.15720.17640.1844-0.1662-0.1538-0.27460.121-0.00060.46950.0259-0.02410.3656-0.00470.399-0.091913.595537.63
30.5465-0.27820.03551.81670.30012.0134-0.2884-0.05240.22550.0335-0.03460.19420.085-0.2185-0.00030.39120.00590.05870.42920.00080.42060.110614.690113.6178
41.1921-0.9712-0.40420.9404-0.19731.7618-0.0924-0.3242-0.18010.1185-0.04160.05760.03330.1633-0.00040.39160.00560.00380.4678-0.02640.38934.699416.980814.6827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 281:402)
2X-RAY DIFFRACTION2(chain B and resseq 283:340)
3X-RAY DIFFRACTION3(chain C and resseq 1:13)
4X-RAY DIFFRACTION4(chain D and resseq 1:13)

+
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