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- PDB-5y21: Crystal structure of AL2 PAL domain in complex with AtRing1a prox... -

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Basic information

Entry
Database: PDB / ID: 5y21
TitleCrystal structure of AL2 PAL domain in complex with AtRing1a proximal site
Components
  • AtRing1a proximal binding site peptide
  • PHD finger protein ALFIN-LIKE 2
KeywordsGENE REGULATION / PRC1 interactor / Alfin-like family protein / Complex
Function / homology
Function and homology information


maintenance of floral meristem identity / maintenance of inflorescence meristem identity / maintenance of shoot apical meristem identity / seed germination / PRC1 complex / root development / cell fate determination / negative regulation of gene expression, epigenetic / RING-type E3 ubiquitin transferase / transferase activity ...maintenance of floral meristem identity / maintenance of inflorescence meristem identity / maintenance of shoot apical meristem identity / seed germination / PRC1 complex / root development / cell fate determination / negative regulation of gene expression, epigenetic / RING-type E3 ubiquitin transferase / transferase activity / chromatin organization / histone binding / protein ubiquitination / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / zinc ion binding / nucleus
Similarity search - Function
Putative E3 ubiquitin-protein ligase RING1a/b / Alfin, N-terminal / Alfin1-like, PHD finger / Alfin / Alfin / Zinc finger, C3HC4 type (RING finger) / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...Putative E3 ubiquitin-protein ligase RING1a/b / Alfin, N-terminal / Alfin1-like, PHD finger / Alfin / Alfin / Zinc finger, C3HC4 type (RING finger) / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
RING 1A / Putative E3 ubiquitin-protein ligase RING1a / PHD finger protein ALFIN-LIKE 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.769 Å
AuthorsPeng, L. / Wang, L.L. / Huang, Y.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structural Analysis of the Arabidopsis AL2-PAL and PRC1 Complex Provides Mechanistic Insight into Active-to-Repressive Chromatin State Switch
Authors: Peng, L. / Wang, L. / Zhang, Y. / Dong, A. / Shen, W.H. / Huang, Y.
History
DepositionJul 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein ALFIN-LIKE 2
B: PHD finger protein ALFIN-LIKE 2
C: AtRing1a proximal binding site peptide
D: AtRing1a proximal binding site peptide


Theoretical massNumber of molelcules
Total (without water)34,6634
Polymers34,6634
Non-polymers00
Water8,773487
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-18 kcal/mol
Surface area13220 Å2
Unit cell
Length a, b, c (Å)46.114, 70.563, 55.324
Angle α, β, γ (deg.)90.00, 112.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHD finger protein ALFIN-LIKE 2 / Protein AL2


Mass: 15508.561 Da / Num. of mol.: 2 / Fragment: UNP residues 10-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AL2, At3g11200, F11B9.12, F9F8.2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9SRM4
#2: Protein/peptide AtRing1a proximal binding site peptide / RING 1A


Mass: 1823.156 Da / Num. of mol.: 2 / Fragment: UNP residues 307-320 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: F4K8U4, UniProt: Q9FKW0*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG2000 MME, 0.1 M Tris, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97907 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.769→50 Å / Num. obs: 31734 / % possible obs: 99.3 % / Redundancy: 3.7 % / Net I/σ(I): 35.4
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 14.4 / Num. unique obs: 3179 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XVL

5xvl


Resolution: 1.769→27.791 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 17.96
RfactorNum. reflection% reflection
Rfree0.1929 1996 6.29 %
Rwork0.1618 --
obs0.1638 31709 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.769→27.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 0 487 2808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052373
X-RAY DIFFRACTIONf_angle_d0.7463208
X-RAY DIFFRACTIONf_dihedral_angle_d17.692910
X-RAY DIFFRACTIONf_chiral_restr0.041342
X-RAY DIFFRACTIONf_plane_restr0.005421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7694-1.81360.23451370.18492103X-RAY DIFFRACTION100
1.8136-1.86260.21211530.17182126X-RAY DIFFRACTION100
1.8626-1.91740.21231360.16662143X-RAY DIFFRACTION100
1.9174-1.97930.20571420.16252109X-RAY DIFFRACTION100
1.9793-2.050.21531470.16192132X-RAY DIFFRACTION100
2.05-2.13210.18421320.1572143X-RAY DIFFRACTION100
2.1321-2.22910.23451490.15692114X-RAY DIFFRACTION100
2.2291-2.34660.18081460.15652129X-RAY DIFFRACTION100
2.3466-2.49350.20311410.16752136X-RAY DIFFRACTION100
2.4935-2.68590.19641450.15492123X-RAY DIFFRACTION100
2.6859-2.95590.17421380.16262151X-RAY DIFFRACTION100
2.9559-3.3830.16971460.15512126X-RAY DIFFRACTION99
3.383-4.25970.17051410.15172103X-RAY DIFFRACTION97
4.2597-27.79480.20031430.1772075X-RAY DIFFRACTION95

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