[English] 日本語
Yorodumi
- PDB-6r0m: Histone fold domain of AtNF-YB2/NF-YC3 in P212121 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r0m
TitleHistone fold domain of AtNF-YB2/NF-YC3 in P212121
Components
  • NF-YB2
  • NF-YC3
KeywordsTRANSCRIPTION / NF-Y / Transcription factor / arabidopsis
Function / homology
Function and homology information


positive regulation of photomorphogenesis / long-day photoperiodism, flowering / CCAAT-binding factor complex / gibberellic acid mediated signaling pathway / regulation of seed germination / response to water deprivation / abscisic acid-activated signaling pathway / plastid / transcription coregulator activity / DNA-binding transcription activator activity, RNA polymerase II-specific ...positive regulation of photomorphogenesis / long-day photoperiodism, flowering / CCAAT-binding factor complex / gibberellic acid mediated signaling pathway / regulation of seed germination / response to water deprivation / abscisic acid-activated signaling pathway / plastid / transcription coregulator activity / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / protein heterodimerization activity / DNA binding / 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 H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
(thale cress) hypothetical protein / (thale cress) hypothetical protein / Nuclear transcription factor Y subunit B-2 / Nuclear transcription factor Y subunit C-3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChaves-Sanjuan, A. / Gnesutta, N. / Chiara, M. / Bernardini, A. / Fornara, F. / Horner, D. / Nardini, M. / Mantovani, R.
CitationJournal: Plant J. / Year: 2021
Title: Structural determinants for NF-Y subunit organization and NF-Y/DNA association in plants.
Authors: Chaves-Sanjuan, A. / Gnesutta, N. / Gobbini, A. / Martignago, D. / Bernardini, A. / Fornara, F. / Mantovani, R. / Nardini, M.
History
DepositionMar 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
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 1.2Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NF-YB2
B: NF-YC3
C: NF-YB2
D: NF-YC3


Theoretical massNumber of molelcules
Total (without water)44,5754
Polymers44,5754
Non-polymers00
Water2,126118
1
A: NF-YB2
B: NF-YC3


Theoretical massNumber of molelcules
Total (without water)22,2882
Polymers22,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-47 kcal/mol
Surface area9620 Å2
MethodPISA
2
C: NF-YB2
D: NF-YC3


Theoretical massNumber of molelcules
Total (without water)22,2882
Polymers22,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-46 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.023, 74.980, 86.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein NF-YB2


Mass: 11160.813 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At5g46140 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178UPH7, UniProt: Q9FGJ3*PLUS
#2: Protein NF-YC3


Mass: 11126.929 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At1g49320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A178WGU5, UniProt: Q9ZVL3*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 3350, 0.1 M MES pH 6.5 and 0.3 M lithium citrate

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.010876 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.010876 Å / Relative weight: 1
ReflectionResolution: 2.3→44.07 Å / Num. obs: 20843 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2054 / CC1/2: 0.575 / Rpim(I) all: 0.215 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G49

5g49


Resolution: 2.3→44.07 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.276 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.209
RfactorNum. reflection% reflectionSelection details
Rfree0.241 967 4.64 %RANDOM
Rwork0.2 ---
obs0.202 20849 99.8 %-
Displacement parametersBiso mean: 63.91 Å2
Baniso -1Baniso -2Baniso -3
1--2.8816 Å20 Å20 Å2
2---1.4079 Å20 Å2
3---4.2895 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.3→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 0 118 2966
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132906HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963910HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1084SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes410HARMONIC5
X-RAY DIFFRACTIONt_it2906HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.07
X-RAY DIFFRACTIONt_other_torsion19.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion390SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3529SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.268 170 5.63 %
Rwork0.257 2848 -
all0.258 3018 -
obs--99.93 %
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)
12.69750.35960.85672.30880.46641.8987-0.26810.03870.21350.00730.1090.1145-0.2562-0.350.1592-0.00090.0316-0.0746-0.0481-0.0283-0.106514.630315.80079.7448
24.88750.75870.3322.23820.21683.6397-0.1066-0.11660.0360.0189-0.08970.2324-0.1817-0.54390.1963-0.00660.0807-0.0151-0.0151-0.0535-0.15567.842813.091811.4314
32.7692-0.98660.0772.8665-0.42673.47740.15620.09320.0563-0.0022-0.2861-0.2719-0.23290.12410.12990.0111-0.0204-0.0252-0.07790.0679-0.110133.39743.556232.0188
42.6713-0.6232-0.32874.0135-1.11653.15950.0258-0.10970.23730.1339-0.1065-0.0862-0.54420.04310.08070.0305-0.0273-0.0443-0.067-0.0158-0.140130.34489.908433.5496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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