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- PDB-5y53: Crystal structure of AL2 PAL domain in complex with AtBMI1b bindi... -

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Basic information

Entry
Database: PDB / ID: 5y53
TitleCrystal structure of AL2 PAL domain in complex with AtBMI1b binding site
Components
  • AtBMI1b binding site
  • PHD finger protein ALFIN-LIKE 2
KeywordsGENE REGULATION / PRC1 interactor / alfin-like family protein / Complex
Function / homology
Function and homology information


response to water deprivation / protein autoubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / chromatin organization / histone binding / protein ubiquitination / regulation of DNA-templated transcription / zinc ion binding / metal ion binding / nucleus
Similarity search - Function
DRIP1/2, RAWUL domain / E3 ubiquitin protein ligase DRIP1-like / 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 ...DRIP1/2, RAWUL domain / E3 ubiquitin protein ligase DRIP1-like / 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
E3 ubiquitin protein ligase DRIP1 / PHD finger protein ALFIN-LIKE 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 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
DepositionAug 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Structure summary / Category: entity / entity_name_com / struct
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _struct.pdbx_descriptor / _struct.title
Revision 1.2Jan 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 1.3Nov 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

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Assembly

Deposited unit
A: PHD finger protein ALFIN-LIKE 2
B: PHD finger protein ALFIN-LIKE 2
D: AtBMI1b binding site
C: PHD finger protein ALFIN-LIKE 2
E: PHD finger protein ALFIN-LIKE 2
F: AtBMI1b binding site


Theoretical massNumber of molelcules
Total (without water)66,3416
Polymers66,3416
Non-polymers00
Water13,565753
1
A: PHD finger protein ALFIN-LIKE 2
B: PHD finger protein ALFIN-LIKE 2
D: AtBMI1b binding site


Theoretical massNumber of molelcules
Total (without water)33,1713
Polymers33,1713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PHD finger protein ALFIN-LIKE 2
E: PHD finger protein ALFIN-LIKE 2
F: AtBMI1b binding site


Theoretical massNumber of molelcules
Total (without water)33,1713
Polymers33,1713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.650, 49.232, 71.265
Angle α, β, γ (deg.)75.64, 82.97, 67.38
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 15508.561 Da / Num. of mol.: 4 / 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 AtBMI1b binding site / Peptide from E3 ubiquitin protein ligase DRIP1


Mass: 2153.509 Da / Num. of mol.: 2 / Fragment: UNP residues 269-286 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
References: UniProt: Q9M9Y4, RING-type E3 ubiquitin transferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 2000 MME, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.598→30 Å / Num. obs: 69212 / % possible obs: 98.6 % / Redundancy: 7.6 % / Net I/σ(I): 15.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 6945 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XVL

5xvl


Resolution: 1.598→28.603 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 16.5
RfactorNum. reflection% reflection
Rfree0.1891 2000 2.89 %
Rwork0.1548 --
obs0.1557 69207 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.598→28.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4394 0 0 753 5147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084726
X-RAY DIFFRACTIONf_angle_d0.9436469
X-RAY DIFFRACTIONf_dihedral_angle_d19.8221821
X-RAY DIFFRACTIONf_chiral_restr0.055699
X-RAY DIFFRACTIONf_plane_restr0.006864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5979-1.63790.20071420.18234782X-RAY DIFFRACTION97
1.6379-1.68220.20091430.1814814X-RAY DIFFRACTION98
1.6822-1.73170.21811420.17364758X-RAY DIFFRACTION99
1.7317-1.78750.20591430.17044774X-RAY DIFFRACTION98
1.7875-1.85140.22581410.17124782X-RAY DIFFRACTION98
1.8514-1.92550.21091420.16524777X-RAY DIFFRACTION97
1.9255-2.01320.16641430.16084789X-RAY DIFFRACTION99
2.0132-2.11930.1961450.14814847X-RAY DIFFRACTION99
2.1193-2.2520.16761430.15214856X-RAY DIFFRACTION99
2.252-2.42580.21591420.15614730X-RAY DIFFRACTION97
2.4258-2.66970.17811440.15454856X-RAY DIFFRACTION100
2.6697-3.05570.21411440.15194856X-RAY DIFFRACTION100
3.0557-3.84830.17011420.14214772X-RAY DIFFRACTION98
3.8483-28.60710.16771440.14354814X-RAY DIFFRACTION99

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