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- PDB-4up0: Ternary crystal structure of the Pygo2 PHD finger in complex with... -

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Basic information

Entry
Database: PDB / ID: 4up0
TitleTernary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and a H3K4me2 peptide
Components
  • HISTONE H3.1Histone H3
  • PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN
KeywordsTRANSCRIPTION / WNT SIGNALLING / PHD FINGER / BCL9L / HD1 DOMAIN
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 / regulation of cell morphogenesis / myoblast differentiation / 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 / regulation of cell morphogenesis / myoblast differentiation / 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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / 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 / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / kidney development / Defective pyroptosis / Deactivation of the beta-catenin transactivating complex / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / fibrillar center / beta-catenin binding / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / gene expression / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / 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 / chromatin binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / 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. / 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
Histone H3.1 / B-cell CLL/lymphoma 9-like protein / Pygopus homolog 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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 11, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN
F: HISTONE H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3024
Polymers12,1722
Non-polymers1312
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-16.5 kcal/mol
Surface area5210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.910, 53.910, 57.940
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 327-387,235-263
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: Protein/peptide HISTONE H3.1 / Histone H3


Mass: 1633.872 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-16 / Source method: obtained synthetically / Details: DIMETHYLATED LYSINE 4 - K4ME2 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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) OF 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: 2.16 Å3/Da / Density % sol: 43.1 % / Description: NONE
Crystal growDetails: 1 M SODIUM CITRATE, 0.1 M TRIS PH 7, 0.2 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976219
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976219 Å / Relative weight: 1
ReflectionResolution: 1.28→39.47 Å / Num. obs: 22695 / % possible obs: 99.9 % / Observed criterion σ(I): 2.4 / Redundancy: 11.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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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: 1.28→39.47 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.222 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.041 / 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 A RESIDUE 1263 IS DISORDERED. CHAIN F RESIDUES 7-15 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.16611 1157 5.1 %RANDOM
Rwork0.13797 ---
obs0.13946 21476 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.28→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms692 0 2 94 788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019703
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.927954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50524.06332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25815102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.112154
X-RAY DIFFRACTIONr_chiral_restr0.1330.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02528
X-RAY DIFFRACTIONr_gen_planes_other
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_restr8.0793702
X-RAY DIFFRACTIONr_sphericity_free32.703533
X-RAY DIFFRACTIONr_sphericity_bonded19.1395756
LS refinement shellResolution: 1.279→1.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 83 -
Rwork0.255 1403 -
obs--99.4 %

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