[English] 日本語
Yorodumi
- PDB-7aw7: CCAAT-binding complex and HapX bound to Aspergillus nidulans cccA DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7aw7
TitleCCAAT-binding complex and HapX bound to Aspergillus nidulans cccA DNA
Components
  • (DNA) x 2
  • BZIP domain-containing protein
  • CBFD_NFYB_HMF domain-containing protein
  • HapB
  • Transcription factor HapC (Eurofung)
KeywordsTRANSCRIPTION / transcription factor / histone fold / basic leucine zipper / heteropentamer / protein-DNA complex
Function / homology
Function and homology information


negative regulation of iron ion transport / CCAAT-binding factor complex / regulation of carbohydrate metabolic process / RNA polymerase II transcription regulator complex / nucleosome / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding ...negative regulation of iron ion transport / CCAAT-binding factor complex / regulation of carbohydrate metabolic process / RNA polymerase II transcription regulator complex / nucleosome / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / intracellular iron ion homeostasis / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Hap4 transcription factor, heteromerisation domain / Minimal binding motif of Hap4 for binding to Hap2/3/5 / : / Nuclear transcription factor Y subunit A / CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B / NF-YA/HAP2 family profile. / CCAAT-Binding transcription Factor / Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. ...Hap4 transcription factor, heteromerisation domain / Minimal binding motif of Hap4 for binding to Hap2/3/5 / : / Nuclear transcription factor Y subunit A / CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B / NF-YA/HAP2 family profile. / CCAAT-Binding transcription Factor / Transcription factor, NFYB/HAP3, conserved site / Transcription factor NFYB/HAP3 / NF-YB/HAP3 subunit signature. / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / Basic-leucine zipper (bZIP) domain signature. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / BZIP domain-containing protein / Transcriptional activator HAP2 / Histone H2A/H2B/H3 domain-containing protein / Transcription factor HapC (Eurofung)
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
Emericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/8-1 Germany
German Research Foundation (DFG)SFB1309-325871075 Germany
CitationJournal: Structure / Year: 2022
Title: Structural insights into cooperative DNA recognition by the CCAAT-binding complex and its bZIP transcription factor HapX.
Authors: Huber, E.M. / Hortschansky, P. / Scheven, M.T. / Misslinger, M. / Haas, H. / Brakhage, A.A. / Groll, M.
History
DepositionNov 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: 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: HapB
B: Transcription factor HapC (Eurofung)
C: CBFD_NFYB_HMF domain-containing protein
D: BZIP domain-containing protein
E: BZIP domain-containing protein
F: DNA
G: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,79310
Polymers77,7127
Non-polymers813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23260 Å2
ΔGint-184 kcal/mol
Surface area35220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.150, 133.150, 199.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

-
Protein , 4 types, 5 molecules ABCDE

#1: Protein HapB


Mass: 7669.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ANIA_07545 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5EAZ0
#2: Protein Transcription factor HapC (Eurofung)


Mass: 10641.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: ANIA_04034 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5B5Z6
#3: Protein CBFD_NFYB_HMF domain-containing protein / HapE


Mass: 13666.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: AN6492.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5AYY8
#4: Protein BZIP domain-containing protein


Mass: 11479.957 Da / Num. of mol.: 2 / Mutation: C92K, C129S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: ANIA_08251 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5EAX9

-
DNA chain , 2 types, 2 molecules FG

#5: DNA chain DNA


Mass: 11426.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus nidulans FGSC A4 (mold)
#6: DNA chain DNA


Mass: 11347.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Aspergillus nidulans FGSC A4 (mold)

-
Non-polymers , 2 types, 3 molecules

#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium fluoride, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→47 Å / Num. obs: 14326 / % possible obs: 99.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.7
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1166 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y37, 5VPE

6y37

5vpe


Resolution: 3.4→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / SU B: 86.495 / SU ML: 0.574 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.627 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 716 5 %RANDOM
Rwork0.2521 ---
obs0.2544 13590 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 240.58 Å2 / Biso mean: 136.643 Å2 / Biso min: 84.92 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å2-0 Å2
2--8.72 Å20 Å2
3----6.27 Å2
Refinement stepCycle: final / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3533 1517 3 0 5053
Biso mean--118.17 --
Num. residues----502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0125382
X-RAY DIFFRACTIONr_bond_other_d0.0020.0184267
X-RAY DIFFRACTIONr_angle_refined_deg1.0221.497450
X-RAY DIFFRACTIONr_angle_other_deg1.1341.879921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4055.527785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.82720.256234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69615697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8471546
X-RAY DIFFRACTIONr_chiral_restr0.1730.226752
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024880
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021193
LS refinement shellResolution: 3.4→3.487 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 52 -
Rwork0.358 990 -
all-1042 -
obs--99.9 %
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)
10.299-0.32080.29170.3527-0.47643.46140.03420.08470.0008-0.0383-0.1416-0.010.11211.16010.10740.05680.00540.12050.4989-0.02970.2722-6.0006-49.8819-36.3841
20.7205-0.21170.93920.97190.17052.81020.03260.063-0.08040.0082-0.1023-0.0847-0.29610.28030.06970.3932-0.00990.10060.38480.00310.2418-17.9053-41.0851-30.7132
30.79860.19830.14820.43480.73681.5787-0.03170.0203-0.0436-0.0452-0.06660.0006-0.28150.0730.09820.47390.0660.0810.40670.00860.2663-21.0276-40.3394-37.7459
40.0721-0.16350.15590.8056-0.42730.49880.0170.00950.07320.0142-0.3197-0.17470.00090.29510.30280.3444-0.10.10170.58050.17040.2891-20.7045-12.0849-14.0288
50.09490.3051-0.22692.2053-1.76861.7409-0.14260.0334-0.1030.056-0.0454-0.4961-0.07520.11380.1880.3721-0.1690.03320.56730.18550.3596-7.5748-8.0451-13.1419
60.30010.16650.37331.51812.20753.47290.0782-0.0476-0.08990.1306-0.1260.00560.24840.04370.04780.39380.04670.05740.33270.06430.1634-19.2881-46.1575-10.7907
70.5739-0.10090.18990.92620.93552.57220.1822-0.1321-0.12990.1684-0.0369-0.26240.35160.0484-0.14530.34320.06620.04060.34260.09250.2251-17.8548-48.217-15.9251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A233 - 290
2X-RAY DIFFRACTION2B41 - 132
3X-RAY DIFFRACTION3C48 - 164
4X-RAY DIFFRACTION4D38 - 130
5X-RAY DIFFRACTION5E61 - 128
6X-RAY DIFFRACTION6F1 - 37
7X-RAY DIFFRACTION7G1 - 37

+
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