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- PDB-4naa: Crystal structure of UVB photoreceptor UVR8 from Arabidopsis thal... -

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Basic information

Entry
Database: PDB / ID: 4naa
TitleCrystal structure of UVB photoreceptor UVR8 from Arabidopsis thaliana and UV-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 / RCC1-like domain / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation (RCC1) signature 2. / 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 / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsYang, X. / Zeng, X. / Ren, Z. / Zhao, K.H.
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 22, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)163,64810
Polymers163,5024
Non-polymers1466
Water28,5721586
1
A: Ultraviolet-B receptor UVR8
B: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7994
Polymers81,7512
Non-polymers492
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)81,8486
Polymers81,7512
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9002
Polymers40,8751
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9002
Polymers40,8751
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Ultraviolet-B receptor UVR8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9484
Polymers40,8751
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)40,9002
Polymers40,8751
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.521, 77.336, 189.312
Angle α, β, γ (deg.)90.00, 95.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-802-

HOH

21C-712-

HOH

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Components

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


Mass: 40875.438 Da / Num. of mol.: 4 / Fragment: UNP residues 13-382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: UVR8, At5g63860, MGI19.7 / 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.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1586 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 290 K / pH: 9.2
Details: protein 8mg/ml, 0.1M MgCl2 15-18% PEG8000 and 0.1M Tris HCl, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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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: Apr 12, 2013
RadiationMonochromator: DIAMOND LAUE MONOCHROMATORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 154616 / % possible obs: 82.8 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 23

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Processing

Software
NameVersionClassification
MD2data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DNW

4dnw


Resolution: 1.67→31.09 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 23.57 / 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
Rfree0.181 6744 5 %
Rwork0.147 --
obs0.149 134807 72.2 %
all-186972 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→31.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11200 0 6 1586 12792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611737
X-RAY DIFFRACTIONf_angle_d1.04615963
X-RAY DIFFRACTIONf_dihedral_angle_d13.4584166
X-RAY DIFFRACTIONf_chiral_restr0.081674
X-RAY DIFFRACTIONf_plane_restr0.0042110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6714-1.69040.203460.1719888X-RAY DIFFRACTION15
1.6904-1.71030.2336800.18551364X-RAY DIFFRACTION23
1.7103-1.73120.2021080.1881923X-RAY DIFFRACTION33
1.7312-1.75310.23131220.18562466X-RAY DIFFRACTION41
1.7531-1.77610.23421640.18092904X-RAY DIFFRACTION50
1.7761-1.80050.23141880.17773196X-RAY DIFFRACTION54
1.8005-1.82620.19931970.18513377X-RAY DIFFRACTION58
1.8262-1.85340.21461810.18453637X-RAY DIFFRACTION62
1.8534-1.88240.20321770.17763869X-RAY DIFFRACTION65
1.8824-1.91330.21411920.16994085X-RAY DIFFRACTION69
1.9133-1.94620.21142230.17514297X-RAY DIFFRACTION72
1.9462-1.98160.23262260.16774301X-RAY DIFFRACTION74
1.9816-2.01970.18942190.16064459X-RAY DIFFRACTION75
2.0197-2.0610.16852260.15774493X-RAY DIFFRACTION76
2.061-2.10580.19022360.1544549X-RAY DIFFRACTION77
2.1058-2.15470.1932300.15354625X-RAY DIFFRACTION78
2.1547-2.20860.19332430.15014638X-RAY DIFFRACTION79
2.2086-2.26830.20912380.15794727X-RAY DIFFRACTION79
2.2683-2.3350.20722710.1514674X-RAY DIFFRACTION80
2.335-2.41040.18662580.15484747X-RAY DIFFRACTION81
2.4104-2.49650.2122590.16274858X-RAY DIFFRACTION82
2.4965-2.59640.20552660.16374931X-RAY DIFFRACTION83
2.5964-2.71450.20662480.16525127X-RAY DIFFRACTION86
2.7145-2.85750.20672990.17135258X-RAY DIFFRACTION89
2.8575-3.03640.19392770.16435470X-RAY DIFFRACTION92
3.0364-3.27060.18993090.14895663X-RAY DIFFRACTION95
3.2706-3.59930.15283030.12685807X-RAY DIFFRACTION97
3.5993-4.11910.14193120.10995802X-RAY DIFFRACTION98
4.1191-5.18570.13183280.11245905X-RAY DIFFRACTION99
5.1857-31.09620.17623180.14496023X-RAY DIFFRACTION99
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)
11.12120.0992-0.15890.62370.04961.4080.01660.0307-0.0357-0.02220.0301-0.09360.01710.2315-0.04880.12760.0280.0010.21220.01350.130910.9206-7.5769-22.7774
21.2236-0.0624-0.2610.65050.09721.22920.10390.20890.2224-0.1168-0.02850.0817-0.2416-0.1953-0.05860.20180.0790.00080.23660.08030.2012-18.90997.9071-21.8521
31.0304-0.0443-0.16130.4314-0.01991.28870.0421-0.1224-0.00350.0303-0.02080.07820.0144-0.1935-0.02240.1277-0.05410.00530.1351-0.020.1471-1.2422-4.9732-71.4515
41.09690.0921-0.3280.5926-0.02090.87880.1302-0.24950.24480.0892-0.0801-0.0187-0.22830.1682-0.02630.1996-0.10030.01410.1703-0.07220.208528.378910.548-72.5833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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