[English] 日本語
Yorodumi
- PDB-4nc4: Crystal structure of photoreceptor AtUVR8 mutant W285F and light-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nc4
TitleCrystal structure of photoreceptor AtUVR8 mutant W285F and light-induced structural changes at 120K
ComponentsUltraviolet-B receptor UVR8
KeywordsSIGNALING PROTEIN / 7-blade beta-propeller
Function / homology
Function and homology information


entrainment of circadian clock / response to UV-B / plastid / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding ...entrainment of circadian clock / response to UV-B / plastid / photoreceptor activity / response to UV / guanyl-nucleotide exchange factor activity / chromatin binding / chromatin / protein homodimerization activity / identical protein binding / nucleus / cytosol
Similarity search - Function
: / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 7 Propeller / Methylamine Dehydrogenase; Chain H / Mainly Beta
Similarity search - Domain/homology
Ultraviolet-B receptor UVR8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.75 Å
AuthorsYang, X. / Zeng, X. / Zhao, K.-H. / Ren, Z.
CitationJournal: Nat Plants / Year: 2015
Title: Dynamic Crystallography Reveals Early Signalling Events in Ultraviolet Photoreceptor UVR8.
Authors: Zeng, X. / Ren, Z. / Wu, Q. / Fan, J. / Peng, P.P. / Tang, K. / Zhang, R. / Zhao, K.H. / Yang, X.
History
DepositionOct 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Ultraviolet-B receptor UVR8
B: Ultraviolet-B receptor UVR8
C: Ultraviolet-B receptor UVR8
D: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,78322
Polymers163,3464
Non-polymers43718
Water29,5991643
1
A: Ultraviolet-B receptor UVR8
B: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,94013
Polymers81,6732
Non-polymers26711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ultraviolet-B receptor UVR8
D: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8439
Polymers81,6732
Non-polymers1707
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9827
Polymers40,8361
Non-polymers1466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9586
Polymers40,8361
Non-polymers1225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9094
Polymers40,8361
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9345
Polymers40,8361
Non-polymers974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.798, 79.119, 189.340
Angle α, β, γ (deg.)90.00, 95.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-921-

HOH

21A-923-

HOH

-
Components

#1: Protein
Ultraviolet-B receptor UVR8 / Protein UV-B RESISTANCE 8 / RCC1 domain-containing protein UVR8


Mass: 40836.398 Da / Num. of mol.: 4 / Fragment: UNP residues 13-382 / Mutation: W285F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g63860, MGI19.7, UVR8 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9FN03
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1643 / 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: 51.82 %
Crystal growTemperature: 290 K / pH: 9.2
Details: protein concentration 8mg/ml, mother liquor 0.1M MgCl2 15-18% PEG8000 and 0.1M Tris HCl pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 5, 2013
RadiationMonochromator: DIAMOND LAUE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 164911 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.047

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 4NAA

4naa


Resolution: 1.75→28.49 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 25.21 / Stereochemistry target values: ML
Details: THE AUTHOR STATES THAT ENTRIES 4NAA, 4NBM, AND 4NC4 WERE DERIVED FROM DYNAMIC CRYSTALLOGRAPHIC DATA SETS. SPECIFICALLY, EACH ENTRY PROVIDES THREE ASPECTS OF EXPERIMENTAL DATA THAT ARE NEEDED ...Details: THE AUTHOR STATES THAT ENTRIES 4NAA, 4NBM, AND 4NC4 WERE DERIVED FROM DYNAMIC CRYSTALLOGRAPHIC DATA SETS. SPECIFICALLY, EACH ENTRY PROVIDES THREE ASPECTS OF EXPERIMENTAL DATA THAT ARE NEEDED TO REPRODUCE AND VALIDATE OUR SCIENTIFIC FINDINGS. THEY INCLUDE: A) COORDINATES OF THE REFERENCE "DARK" STRUCTURE AS WE HAD DEPOSITED IN PDB; B) STRUCTURE FACTOR AMPLITUDES ACQUIRED IN THE "DARK" STATE; AND C) STRUCTURE FACTOR AMPLITUDES ACQUIRED IN THE "LIGHT" STATE. DATA SETS B) AND C) WERE COLLECTED FROM THE SAME CRYSTAL. OUR DEPOSITED MTZ FILE THUS CONTAINS DATA FROM BOTH B) AND C), AS WELL AS CALCULATED PHASES FROM A), WITH WHICH PDB USERS ARE ABLE TO GENERATE DIFFERENCE FOURIER MAPS TO EXAMINE LIGHT-INDUCED STRUCTURAL CHANGES.
RfactorNum. reflection% reflection
Rfree0.184 6434 5.04 %
Rwork0.149 --
obs0.15 127770 77.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11188 0 18 1643 12849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611730
X-RAY DIFFRACTIONf_angle_d1.05515954
X-RAY DIFFRACTIONf_dihedral_angle_d13.4144168
X-RAY DIFFRACTIONf_chiral_restr0.0811673
X-RAY DIFFRACTIONf_plane_restr0.0042116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.3074400.2109713X-RAY DIFFRACTION14
1.7699-1.79080.2811680.1995975X-RAY DIFFRACTION19
1.7908-1.81260.2102590.22281342X-RAY DIFFRACTION26
1.8126-1.83550.2288910.20851717X-RAY DIFFRACTION33
1.8355-1.85970.24741340.2012113X-RAY DIFFRACTION41
1.8597-1.88520.26871280.20422477X-RAY DIFFRACTION47
1.8852-1.91210.22851460.19572959X-RAY DIFFRACTION57
1.9121-1.94060.21081590.23319X-RAY DIFFRACTION63
1.9406-1.97090.21152290.19713826X-RAY DIFFRACTION73
1.9709-2.00320.23822330.18834274X-RAY DIFFRACTION82
2.0032-2.03780.22212510.1744705X-RAY DIFFRACTION90
2.0378-2.07480.21152570.17344979X-RAY DIFFRACTION94
2.0748-2.11470.19952670.1744873X-RAY DIFFRACTION95
2.1147-2.15790.20952970.16964973X-RAY DIFFRACTION96
2.1579-2.20480.20492620.16215014X-RAY DIFFRACTION95
2.2048-2.2560.22092620.16054981X-RAY DIFFRACTION96
2.256-2.31240.22452680.15914958X-RAY DIFFRACTION95
2.3124-2.37490.19732390.15895018X-RAY DIFFRACTION95
2.3749-2.44480.21182820.15625004X-RAY DIFFRACTION95
2.4448-2.52360.22182480.16144955X-RAY DIFFRACTION95
2.5236-2.61380.19352670.16194924X-RAY DIFFRACTION94
2.6138-2.71830.22612570.16354953X-RAY DIFFRACTION94
2.7183-2.84190.22550.17144931X-RAY DIFFRACTION94
2.8419-2.99160.21662640.16854856X-RAY DIFFRACTION93
2.9916-3.17880.17472690.1514853X-RAY DIFFRACTION92
3.1788-3.42390.17552450.13134870X-RAY DIFFRACTION92
3.4239-3.76780.13712480.11584788X-RAY DIFFRACTION91
3.7678-4.31130.12852440.10724702X-RAY DIFFRACTION88
4.3113-5.42570.12382270.11284667X-RAY DIFFRACTION88
5.4257-28.4960.17442380.14644617X-RAY DIFFRACTION85
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)
11.00060.0398-0.12620.6661-0.00051.20730.02610.0585-0.0371-0.0418-0.0075-0.09280.0460.1334-0.0220.12060.03340.00610.15220.01610.13210.8304-7.7192-22.9718
21.1806-0.0527-0.24790.7570.00420.92770.07580.1750.1968-0.0944-0.02630.1012-0.1502-0.1866-0.03940.16420.0565-0.00890.20350.0540.1926-18.91367.8297-22.0396
30.9258-0.0795-0.13610.58610.09321.1070.0229-0.1105-0.01330.0591-0.02780.09040.058-0.10490.00320.1204-0.04320.01050.1457-0.01760.1368-1.8067-5.1475-71.442
41.13010.0322-0.29090.6523-0.00410.78840.0855-0.20.20970.0779-0.0441-0.0475-0.14910.1618-0.03220.1556-0.06280.00610.1927-0.05130.18727.615210.6215-72.5299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain 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