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- PDB-4up5: Crystal structure of the Pygo2 PHD finger in complex with the B9L... -

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Basic information

Entry
Database: PDB / ID: 4up5
TitleCrystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and a chemical fragment
ComponentsPYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN
KeywordsTRANSCRIPTION / PYGO / WNT SIGNALLING / HISTONE H3 / FRAGMENT SCREENING
Function / homology
Function and homology information


histone acetyltransferase regulator activity / spermatid nucleus differentiation / regulation of mammary gland epithelial cell proliferation / beta-catenin-TCF complex / mammary gland development / myoblast differentiation / regulation of cell morphogenesis / lens development in camera-type eye / roof of mouth development / skeletal muscle cell differentiation ...histone acetyltransferase regulator activity / spermatid nucleus differentiation / regulation of mammary gland epithelial cell proliferation / beta-catenin-TCF complex / mammary gland development / myoblast differentiation / regulation of cell morphogenesis / lens development in camera-type eye / roof of mouth development / skeletal muscle cell differentiation / somatic stem cell population maintenance / developmental growth / canonical Wnt signaling pathway / positive regulation of epithelial to mesenchymal transition / Deactivation of the beta-catenin transactivating complex / kidney development / negative regulation of transforming growth factor beta receptor signaling pathway / Formation of the beta-catenin:TCF transactivating complex / brain development / beta-catenin binding / fibrillar center / histone binding / transcription by RNA polymerase II / transcription coactivator activity / chromatin binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
B Cell Lymphoma 9 / B-cell lymphoma 9, beta-catenin binding domain / : / B-cell lymphoma 9 protein / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. ...B Cell Lymphoma 9 / B-cell lymphoma 9, beta-catenin binding domain / : / B-cell lymphoma 9 protein / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
6-methoxy-1,3-benzothiazol-2-amine / B-cell CLL/lymphoma 9-like protein / Pygopus homolog 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMiller, T.C.R. / Fiedler, M. / Rutherford, T.J. / Birchall, K. / Chugh, J. / Bienz, M.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Competitive Binding of a Benzimidazole to the Histone-Binding Pocket of the Pygo Phd Finger.
Authors: Miller, T.C.R. / Rutherford, T.J. / Birchall, K. / Chugh, J. / Fiedler, M. / Bienz, M.
History
DepositionJun 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_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_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_conn.ptnr2_label_seq_id / _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: PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8494
Polymers10,5381
Non-polymers3113
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.270, 54.270, 57.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN / PYGO2 / B9L / B-CELL LYMPHOMA 9-LIKE PROTEIN / BCL9-LIKE PROTEIN / PROTEIN BCL9-2


Mass: 10537.676 Da / Num. of mol.: 1 / Fragment: PHD FINGER, HD1,RESIDUES 327-387,240-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL / References: UniProt: Q9BRQ0, UniProt: Q86UU0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-94W / 6-methoxy-1,3-benzothiazol-2-amine


Mass: 180.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGLYCINE (REMNANT OF TEV CLEAVAGE SITE), PYGO2 PHD FINGER ( AAS 327-387), ARTIFICIAL LINKER (8AA ...GLYCINE (REMNANT OF TEV CLEAVAGE SITE), PYGO2 PHD FINGER ( AAS 327-387), ARTIFICIAL LINKER (8AA LINKER-GSGSGSGS), B9L HD1 DOMAIN (AAS 235-263) IS MAPPED TO ISOFORM 2 OF Q86UU0

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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: 2.31 Å3/Da / Density % sol: 46.81 % / Description: NONE
Crystal growDetails: 60% TACSIMATE, PH 7.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0332
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.65→31.95 Å / Num. obs: 10894 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.7
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0002refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XB1

2xb1


Resolution: 1.65→39.52 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.86 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A RESIDUES 383-387 AND 8AA GSGSGSGS LINKER ARE DISORDERED CHAIN B RESIDUE 263 IS DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.21117 523 4.8 %RANDOM
Rwork0.1819 ---
obs0.18333 10327 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.805 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms642 0 14 36 692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.019667
X-RAY DIFFRACTIONr_bond_other_d0.0050.02588
X-RAY DIFFRACTIONr_angle_refined_deg2.0971.94908
X-RAY DIFFRACTIONr_angle_other_deg1.03931331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.966583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07224.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5361595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.569153
X-RAY DIFFRACTIONr_chiral_restr0.1310.2102
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02151
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 34 -
Rwork0.268 655 -
obs--100 %

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