[English] 日本語
Yorodumi
- PDB-7cvo: crystal structure of Arabidopsis CO CCT domain in complex with NF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cvo
Titlecrystal structure of Arabidopsis CO CCT domain in complex with NF-YB3/YC4 and FT CORE2 DNA
Components
  • Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS
  • FT CORE2 DNA forward strand
  • FT CORE2 DNA reverse strand
  • Nuclear transcription factor Y subunit B-3
KeywordsDNA BINDING PROTEIN/DNA / CONSTANS / transcription factor / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of starch metabolic process / far-red light signaling pathway / regulation of long-day photoperiodism, flowering / positive regulation of photomorphogenesis / CCAAT-binding factor complex / gibberellic acid mediated signaling pathway / regulation of flower development / regulation of seed germination / response to far red light / flower development ...negative regulation of starch metabolic process / far-red light signaling pathway / regulation of long-day photoperiodism, flowering / positive regulation of photomorphogenesis / CCAAT-binding factor complex / gibberellic acid mediated signaling pathway / regulation of flower development / regulation of seed germination / response to far red light / flower development / abscisic acid-activated signaling pathway / plastid / positive regulation of protein metabolic process / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Zinc finger protein CONSTANS-like / : / CCT domain / CCT motif / CCT domain profile. / 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 ...Zinc finger protein CONSTANS-like / : / CCT domain / CCT motif / CCT domain profile. / 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 / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear transcription factor Y subunit B-3 / Zinc finger protein CONSTANS / Nuclear transcription factor Y subunit C-4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLv, X. / Du, J.
CitationJournal: Plant Cell / Year: 2021
Title: Structural insights into the multivalent binding of the Arabidopsis FLOWERING LOCUS T promoter by the CO-NF-Y master transcription factor complex.
Authors: Lv, X. / Zeng, X. / Hu, H. / Chen, L. / Zhang, F. / Liu, R. / Liu, Y. / Zhou, X. / Wang, C. / Wu, Z. / Kim, C. / He, Y. / Du, J.
History
DepositionAug 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS
B: Nuclear transcription factor Y subunit B-3
D: FT CORE2 DNA forward strand
E: FT CORE2 DNA reverse strand
F: Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS
G: Nuclear transcription factor Y subunit B-3


Theoretical massNumber of molelcules
Total (without water)76,6696
Polymers76,6696
Non-polymers00
Water88349
1
A: Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS
B: Nuclear transcription factor Y subunit B-3
D: FT CORE2 DNA forward strand
E: FT CORE2 DNA reverse strand

F: Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS
G: Nuclear transcription factor Y subunit B-3


Theoretical massNumber of molelcules
Total (without water)76,6696
Polymers76,6696
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area17500 Å2
ΔGint-144 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.744, 139.944, 65.569
Angle α, β, γ (deg.)90.000, 108.380, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Chimera of Nuclear transcription factor Y subunit C-4 and Zinc finger protein CONSTANS / AtNF-YC-4


Mass: 18933.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NFYC4, At5g63470, MLE2.10, CO, At5g15840, F14F8_220 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9FMV5, UniProt: Q39057
#2: Protein Nuclear transcription factor Y subunit B-3 / AtNF-YB-3 / Transcriptional activator HAP3C


Mass: 11724.325 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NFYB3, HAP3C, At4g14540, dl3310w, FCAALL.252 / Plasmid: pET-Sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O23310
#3: DNA chain FT CORE2 DNA forward strand


Mass: 7752.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#4: DNA chain FT CORE2 DNA reverse strand


Mass: 7600.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M KI and 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2019
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 28875 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 21.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.664 / Num. unique obs: 2851 / CC1/2: 0.83 / CC star: 0.952 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AWL

4awl


Resolution: 2.6→48.016 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 1456 5.08 %
Rwork0.1962 27202 -
obs0.1974 28658 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.31 Å2 / Biso mean: 58.1874 Å2 / Biso min: 21.75 Å2
Refinement stepCycle: final / Resolution: 2.6→48.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 1019 0 49 4376
Biso mean---54.52 -
Num. residues----454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154498
X-RAY DIFFRACTIONf_angle_d1.4786260
X-RAY DIFFRACTIONf_chiral_restr0.075707
X-RAY DIFFRACTIONf_plane_restr0.008620
X-RAY DIFFRACTIONf_dihedral_angle_d22.4261817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.69290.26091300.25222721100
2.6929-2.80070.25741380.24652729100
2.8007-2.92820.30691540.24742708100
2.9282-3.08260.32351570.25142732100
3.0826-3.27560.2361500.23282727100
3.2756-3.52850.2431350.21462720100
3.5285-3.88340.23531530.1916267098
3.8834-4.4450.19381320.1668273699
4.445-5.59890.1781380.16942738100
5.5989-480.18381690.1717272199
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)
10.0342-0.13070.1720.643-0.82951.16780.44830.2429-0.0174-0.0311-0.3167-0.96421.13231.82840.3371.21210.1261-0.03751.26550.00741.0352.511-26.889-21.681
27.6426-1.32690.33157.1718-0.90386.5308-0.02340.25760.017-0.01740.2064-0.4637-0.53170.036-0.13060.3312-0.01230.07080.5197-0.0520.412113.411-31.806-12.528
32.16031.59791.26961.648-0.38763.06160.0379-0.30320.08540.854-0.0214-0.06160.18890.2402-0.08860.8419-0.060.03480.6194-0.07120.69933.749-17.46715.79
42.37610.86190.35395.5698-0.3672.46880.04440.03210.04840.1402-0.0065-0.1405-0.03930.1114-0.05970.36740.02130.0380.3234-0.0010.25230.525-33.315-3.958
57.2218-1.7251.07947.3610.37832.9935-0.4898-0.16010.73160.0101-0.14380.7835-0.8874-0.54070.40880.5420.067-0.14170.4767-0.04420.5927-12.234-25.431-8.387
63.05713.1055-3.15186.5146-0.42255.59170.1897-0.89990.00570.8172-0.15310.48460.684-0.03970.06290.6156-0.04340.01640.45780.0230.2931-0.714-29.1944.778
72.02211.09170.05086.07991.72872.7983-0.04710.038-0.0732-0.01540.0411-0.007-0.08180.10480.04740.2813-0.0043-0.02250.33790.02390.2625-2.307-34.808-5.245
84.3421.5379-3.10717.85-2.31337.4847-0.36160.0399-0.6766-0.40970.1076-0.24441.18440.04120.27090.30610.0080.02060.2592-0.02680.3437-0.071-53.162-8.764
95.80551.47940.39723.6712-0.67257.57080.20640.6657-0.3755-0.4843-0.3527-0.71270.5660.84430.00740.51740.0740.00850.5075-0.05040.54798.09-42.28-11.01
101.06021.4436-0.15164.9137-0.81510.75250.2885-0.2130.02010.2595-0.46340.00580.05370.06470.15360.60180.00630.04360.4699-0.01890.4519-1.613-20.43510.287
110.71941.1573-0.21824.5566-0.71591.37510.2402-0.1613-0.02470.5425-0.39630.0709-0.09870.17080.13090.538-0.01540.00240.4918-0.06760.5176-3.86-24.210.75
129.17620.63781.21426.16440.36340.414-0.28750.0482-0.93710.12160.30930.16580.3829-0.51840.07840.4320.0524-0.05520.6792-0.01390.618939.782-40.192-13.091
135.1214-2.5587-2.16647.2581.88066.63080.73091.02060.1173-0.2014-0.6951-0.489-0.0436-0.6755-0.17940.4564-0.001-0.02190.49270.08060.352321.687-27.172-28.671
145.8294-0.38960.39582.611-1.85126.5203-0.13670.5145-0.508-0.1558-0.1102-0.79730.24580.52830.31230.3191-0.01660.01290.5102-0.07950.440332.244-38.755-22.716
153.95130.56590.30442.3704-0.57034.8559-0.24270.2636-1.02250.0826-0.4199-0.14331.19140.52020.53840.61480.07770.1040.51460.01940.737429.126-50.719-16.862
166.85610.5561-0.01635.8697-1.08696.9641-0.32530.2843-0.8708-0.02940.20210.29971.5209-0.3460.18820.5997-0.06890.20240.50480.00360.728815.646-46.524-18.378
171.9735-1.1092.21336.0465-0.33987.39170.27771.4262-0.3561-1.48-0.5021-0.11730.2972-0.62480.26750.67710.05450.09710.7037-0.14520.516827.374-43.242-31.782
183.69392.29350.57874.8493-0.68083.193-0.09340.2142-0.5112-0.39430.0824-0.55890.29320.0463-0.04540.3054-0.00420.04220.471-0.00410.359825.105-37.018-21.6
194.1944-1.16271.27472.64514.06859.0230.1954-0.57391.66630.99590.28060.6048-1.498-0.3636-0.26150.89810.02650.07250.62020.06220.791123.193-14.043-19.724
205.788-1.21321.71642.1736-2.34928.111-0.50530.32931.14270.8570.4012-0.5598-0.97440.4061-0.28170.499-0.0197-0.04790.4565-0.04550.555930.607-22.674-16.455
219.48513.0615-2.74615.8591-0.97624.95420.0752-0.53860.59370.2492-0.4279-0.0757-0.46250.54160.36960.3385-0.0122-0.0460.6514-0.03610.423234.76-30.534-15.88
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 298:302 )A298 - 302
2X-RAY DIFFRACTION2( CHAIN A AND RESID 303:319 )A303 - 319
3X-RAY DIFFRACTION3( CHAIN A AND RESID 320:347 )A320 - 347
4X-RAY DIFFRACTION4( CHAIN B AND RESID 23:94 )B23 - 94
5X-RAY DIFFRACTION5( CHAIN B AND RESID 95:110 )B95 - 110
6X-RAY DIFFRACTION6( CHAIN A AND RESID 77:90 )A77 - 90
7X-RAY DIFFRACTION7( CHAIN A AND RESID 91:126 )A91 - 126
8X-RAY DIFFRACTION8( CHAIN A AND RESID 127:143 )A127 - 143
9X-RAY DIFFRACTION9( CHAIN A AND RESID 144:156 )A144 - 156
10X-RAY DIFFRACTION10( CHAIN D AND RESID 1:25 )D1 - 25
11X-RAY DIFFRACTION11( CHAIN E AND RESID 1:25 )E1 - 25
12X-RAY DIFFRACTION12( CHAIN F AND RESID 300:319 )F300 - 319
13X-RAY DIFFRACTION13( CHAIN G AND RESID 23:46 )G23 - 46
14X-RAY DIFFRACTION14( CHAIN G AND RESID 47:74 )G47 - 74
15X-RAY DIFFRACTION15( CHAIN G AND RESID 75:94 )G75 - 94
16X-RAY DIFFRACTION16( CHAIN G AND RESID 95:110 )G95 - 110
17X-RAY DIFFRACTION17( CHAIN F AND RESID 78:90 )F78 - 90
18X-RAY DIFFRACTION18( CHAIN F AND RESID 91:126 )F91 - 126
19X-RAY DIFFRACTION19( CHAIN F AND RESID 127:133 )F127 - 133
20X-RAY DIFFRACTION20( CHAIN F AND RESID 134:143 )F134 - 143
21X-RAY DIFFRACTION21( CHAIN F AND RESID 144:155 )F144 - 155

+
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://pdbjlvh1.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