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

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Basic information

Entry
Database: PDB / ID: 2vpd
TitleDecoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex
Components
  • B-CELL CLL/LYMPHOMA 9 PROTEIN
  • 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 / histone H3K4me3 reader activity / myoblast differentiation / skeletal muscle cell differentiation / sarcoplasm / somatic stem cell population maintenance / protein localization to nucleus ...myotube differentiation involved in skeletal muscle regeneration / spermatid nucleus differentiation / beta-catenin-TCF complex / cis-Golgi network / histone H3K4me3 reader activity / myoblast differentiation / skeletal muscle cell differentiation / sarcoplasm / somatic stem cell population maintenance / protein localization to nucleus / canonical Wnt signaling pathway / hematopoietic progenitor cell differentiation / Deactivation of the beta-catenin transactivating complex / kidney development / Formation of the beta-catenin:TCF transactivating complex / beta-catenin binding / transcription by RNA polymerase II / transcription coactivator activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm
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
B-cell CLL/lymphoma 9 protein / Pygopus homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsFiedler, M. / Sanchez-Barrena, M.J. / Nekrasov, M. / Mieszczanek, J. / Rybin, V. / Muller, J. / Evans, P. / Bienz, M.
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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.5Dec 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_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 1
B: B-CELL CLL/LYMPHOMA 9 PROTEIN
C: PYGOPUS HOMOLOG 1
D: B-CELL CLL/LYMPHOMA 9 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2378
Polymers21,9754
Non-polymers2624
Water30617
1
A: PYGOPUS HOMOLOG 1
B: B-CELL CLL/LYMPHOMA 9 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1184
Polymers10,9872
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-13 kcal/mol
Surface area7330 Å2
MethodPQS
2
C: PYGOPUS HOMOLOG 1
D: B-CELL CLL/LYMPHOMA 9 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1184
Polymers10,9872
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-14 kcal/mol
Surface area8200 Å2
MethodPQS
Unit cell
Length a, b, c (Å)88.720, 100.890, 64.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PYGOPUS HOMOLOG 1 / HPYGO1


Mass: 7229.039 Da / Num. of mol.: 2 / Fragment: PHD DOMAIN, RESIDUES 333-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS(DE3)-RIL / References: UniProt: Q9Y3Y4
#2: Protein/peptide B-CELL CLL/LYMPHOMA 9 PROTEIN / BCL9 / B-CELL LYMPHOMA 9 PROTEIN / PROTEIN LEGLESS HOMOLOG


Mass: 3758.405 Da / Num. of mol.: 2 / Fragment: HD1 DOMAIN, RESIDUES 174-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS(DE3)-RIL / References: UniProt: O00512
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.1 Å3/Da / Density % sol: 60.34 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: HANGING-DROP VAPOUR-DIFFUSION METHOD AT 19 CELSIUS. CRYSTALLIZATION CONDITIONS: 1.3M (NH4)2SO4, 100MM TRIS PH6.5, 200MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 16, 2007 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.77→31.45 Å / Num. obs: 30994 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.5
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.2 / % possible all: 99.7

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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 2VPB

2vpb


Resolution: 2.77→66.67 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.905 / SU B: 16.298 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 0.682 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PHD RESIDUE S362 PRESENTS AN UNUSUAL CONFORMATION SINCE IT IS NEXT TO C363, WHICH IS PART OF THE ZN 2 BINDING SITE
RfactorNum. reflection% reflectionSelection details
Rfree0.267 352 4.6 %RANDOM
Rwork0.234 ---
obs0.235 7263 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.85 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å20 Å20 Å2
2--3.84 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.77→66.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 4 17 1473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221482
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.9272003
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0925190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85725.76359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25815237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.613152
X-RAY DIFFRACTIONr_chiral_restr0.0710.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021094
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.2556
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21049
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0340.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.471.5984
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.83221537
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9133576
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.334.5466
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: 2.77→2.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.424 23
Rwork0.295 518

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