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- PDB-2vpg: Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signa... -

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Basic information

Entry
Database: PDB / ID: 2vpg
TitleDecoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex
Components
  • B-CELL CLL/LYMPHOMA 9 PROTEIN
  • HISTONE H3 TAIL
  • PYGOPUS HOMOLOG 1
KeywordsGENE REGULATION / WNT SIGNALING PATHWAY / WNT SIGNALING COMPLEX / CHROMOSOMAL REARRANGEMENT / SIGNALING PROTEIN / BCL9 HD1 DOMAIN / HPYGO1 PHD DOMAIN / PROTO-ONCOGENE / PHOSPHOPROTEIN / HISTONE H3K4ME2 / ZINC / NUCLEUS / ZINC-FINGER / METAL-BINDING
Function / homology
Function and homology information


myotube differentiation involved in skeletal muscle regeneration / spermatid nucleus differentiation / beta-catenin-TCF complex / cis-Golgi network / myoblast differentiation / skeletal muscle cell differentiation / somatic stem cell population maintenance / protein localization to nucleus / sarcoplasm / canonical Wnt signaling pathway ...myotube differentiation involved in skeletal muscle regeneration / spermatid nucleus differentiation / beta-catenin-TCF complex / cis-Golgi network / myoblast differentiation / skeletal muscle cell differentiation / somatic stem cell population maintenance / protein localization to nucleus / sarcoplasm / canonical Wnt signaling pathway / hematopoietic progenitor cell differentiation / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / kidney development / HDACs deacetylate histones / Deactivation of the beta-catenin transactivating complex / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / beta-catenin binding / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription by RNA polymerase II / transcription coactivator activity / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding
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. / Zinc finger, PHD-finger ...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 / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
B-cell CLL/lymphoma 9 protein / Histone H3.1 / Pygopus homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFiedler, M. / Sanchez-Barrena, M.J. / Nekrasov, M. / Mieszczanek, J. / Rybin, V. / Muller, J. / Bienz, M. / Evans, P.
CitationJournal: Mol.Cell / Year: 2008
Title: Decoding of Methylated Histone H3 Tail by the Pygo- Bcl9 Wnt Signaling Complex.
Authors: Fiedler, M. / Sanchez-Barrena, M.J. / Nekrasov, M. / Mieszczanek, J. / Rybin, V. / Muller, J. / Evans, P. / Bienz, M.
History
DepositionFeb 27, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 2.0May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other / Polymer sequence
Category: entity_poly / exptl_crystal_grow ...entity_poly / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.temp ..._entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 2.2Dec 13, 2023Group: 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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 1
B: B-CELL CLL/LYMPHOMA 9 PROTEIN
C: PYGOPUS HOMOLOG 1
D: B-CELL CLL/LYMPHOMA 9 PROTEIN
P: HISTONE H3 TAIL
R: HISTONE H3 TAIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,77011
Polymers24,4166
Non-polymers3545
Water4,666259
1
A: PYGOPUS HOMOLOG 1
B: B-CELL CLL/LYMPHOMA 9 PROTEIN
P: HISTONE H3 TAIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4316
Polymers12,2083
Non-polymers2233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-20.2 kcal/mol
Surface area6460 Å2
MethodPISA
2
C: PYGOPUS HOMOLOG 1
D: B-CELL CLL/LYMPHOMA 9 PROTEIN
R: HISTONE H3 TAIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3395
Polymers12,2083
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-22.6 kcal/mol
Surface area6780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.750, 105.750, 51.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein PYGOPUS HOMOLOG 1 / HPYGO1


Mass: 6759.612 Da / Num. of mol.: 2 / Fragment: PHD DOMAIN, RESIDUES 340-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: Q9Y3Y4

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Protein/peptide , 2 types, 4 molecules BDPR

#2: Protein/peptide B-CELL CLL/LYMPHOMA 9 PROTEIN / B-CELL LYMPHOMA 9 PROTEIN / BCL-9 / PROTEIN LEGLESS HOMOLOG / BCL9


Mass: 3444.991 Da / Num. of mol.: 2 / Fragment: HD1 DOMAIN, RESIDUES 177-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL / References: UniProt: O00512
#3: Protein/peptide HISTONE H3 TAIL


Mass: 2003.377 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: 18-MER H3R2ME2AK4ME2, DIMETHYLATION AT LYS K4, ASYMMETRIC DIMETHYLATION AT R2
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431*PLUS

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Non-polymers , 3 types, 264 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.84 Å3/Da / Density % sol: 56.74 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: HANGING-DROP VAPOUR-DIFFUSION METHOD AT 19 CELSIUS. CRYSTALLIZATION CONDITIONS: 20% PEG-4000, 20% ISO-PROPANOL, 0.1 M NA CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 16, 2007
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→26.44 Å / Num. obs: 37079 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VPE

2vpe


Resolution: 1.6→74.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.706 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1953 5 %RANDOM
Rwork0.201 ---
obs0.202 37079 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.6→74.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 10 259 1746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221514
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.211.9572047
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3575194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32326.20758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37915228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.252152
X-RAY DIFFRACTIONr_chiral_restr0.0840.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021109
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.2720
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21049
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8221.51003
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40621557
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.043593
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1254.5490
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 113
Rwork0.272 2732

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