[English] 日本語
Yorodumi
- PDB-4csr: High resolution crystal structure of the histone fold dimer (NF-Y... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4csr
TitleHigh resolution crystal structure of the histone fold dimer (NF-YB)-(NF-YC)
Components
  • NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA
  • NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA
KeywordsTRANSCRIPTION / NF-Y / DNA-BINDING / CCAAT-BOX
Function / homology
Function and homology information


CCAAT-binding factor complex / ATF6 (ATF6-alpha) activates chaperone genes / ATF4 activates genes in response to endoplasmic reticulum stress / FOXO-mediated transcription of cell death genes / Activation of gene expression by SREBF (SREBP) / cellular response to leukemia inhibitory factor / protein-DNA complex / PPARA activates gene expression / RNA polymerase II transcription regulator complex / protein folding ...CCAAT-binding factor complex / ATF6 (ATF6-alpha) activates chaperone genes / ATF4 activates genes in response to endoplasmic reticulum stress / FOXO-mediated transcription of cell death genes / Activation of gene expression by SREBF (SREBP) / cellular response to leukemia inhibitory factor / protein-DNA complex / PPARA activates gene expression / RNA polymerase II transcription regulator complex / protein folding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
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 / Histone, subunit A / Histone, subunit A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 ...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 / Histone, subunit A / Histone, subunit A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear transcription factor Y subunit beta / Nuclear transcription factor Y subunit gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGnesutta, N. / Cocolo, S. / Mantovani, R. / Bolognesi, M. / Nardini, M.
Citation
Journal: To be Published
Title: High Resolution Crystal Structure of the Histone Fold Dimer (NF-Yb)-(NF-Yc)
Authors: Gnesutta, N. / Cocolo, S. / Mantovani, R. / Bolognesi, M. / Nardini, M.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2013
Title: Sequence-Specific Transcription Factor NF-Y Displays Histone-Like DNA Binding and H2B-Like Ubiquitination.
Authors: Nardini, M. / Gnesutta, N. / Donati, G. / Gatta, R. / Forni, C. / Fossati, A. / Vonrhein, C. / Moras, D. / Romier, C. / Bolognesi, M. / Mantovani, R.
History
DepositionMar 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA
B: NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2345
Polymers21,9582
Non-polymers2763
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-47.2 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.670, 60.800, 61.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA / CCAAT BOX DNA-BINDING PROTEIN SUBUNIT B / NUCLEAR TRANSCRIPTION FACTORY SUBUNIT B / NF-YB / NUCLEAR ...CCAAT BOX DNA-BINDING PROTEIN SUBUNIT B / NUCLEAR TRANSCRIPTION FACTORY SUBUNIT B / NF-YB / NUCLEAR TRANSCRIPTION FACTORY SUBUNIT B


Mass: 10853.485 Da / Num. of mol.: 1 / Fragment: RESIDUES 49-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25208
#2: Protein NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA / CCAAT BOX DNA-BINDING PROTEIN SUBUNIT C / NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C / NF-YC / ...CCAAT BOX DNA-BINDING PROTEIN SUBUNIT C / NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C / NF-YC / TRANSACTIVATOR HSM-1/2 / NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C


Mass: 11104.061 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q13952
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.6 % / Description: NONE
Crystal growpH: 8.2
Details: 28% PEG 4K, 100 MM TRIS PH 8.2, 200 MM MG(OAC)2, 100 MM NA(OAC)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→33.18 Å / Num. obs: 31692 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N1J

1n1j


Resolution: 1.5→33.18 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.998 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18432 1594 5 %RANDOM
Rwork0.14462 ---
obs0.1466 30042 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.5 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 18 191 1590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191496
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9832027
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6555193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04624.36671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48515302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2671512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211104
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5331.616704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0382.433883
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8182.11792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.92131496
X-RAY DIFFRACTIONr_sphericity_free28.155551
X-RAY DIFFRACTIONr_sphericity_bonded12.80851613
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 110 -
Rwork0.209 2186 -
obs--100 %

+
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