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- PDB-2puy: Crystal Structure of the BHC80 PHD finger -

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Basic information

Entry
Database: PDB / ID: 2puy
TitleCrystal Structure of the BHC80 PHD finger
Components
  • Histone H3
  • PHD finger protein 21A
KeywordsTRANSCRIPTION / PHD finger / Histone code / BRAF-HDAC complex
Function / homology
Function and homology information


DNA repair complex / rRNA transcription / histone deacetylase complex / nucleosomal DNA binding / HDACs deacetylate histones / euchromatin / structural constituent of chromatin / nucleosome / chromatin organization / Factors involved in megakaryocyte development and platelet production ...DNA repair complex / rRNA transcription / histone deacetylase complex / nucleosomal DNA binding / HDACs deacetylate histones / euchromatin / structural constituent of chromatin / nucleosome / chromatin organization / Factors involved in megakaryocyte development and platelet production / positive regulation of cell growth / Potential therapeutics for SARS / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
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 ...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 / Histone H3.3C / PHD finger protein 21A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.43 Å
AuthorsHorton, J.R. / Cheng, X. / Collins, R.E.
CitationJournal: Nature / Year: 2007
Title: Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression.
Authors: Lan, F. / Collins, R.E. / De Cegli, R. / Alpatov, R. / Horton, J.R. / Shi, X. / Gozani, O. / Cheng, X. / Shi, Y.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: PHD finger protein 21A
B: PHD finger protein 21A
E: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4277
Polymers15,1653
Non-polymers2624
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.511, 25.386, 62.282
Angle α, β, γ (deg.)90.00, 96.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-43-

HOH

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Components

#1: Protein PHD finger protein 21A / / BRAF35-HDAC complex protein BHC80 / BHC80a


Mass: 7007.362 Da / Num. of mol.: 2 / Fragment: PHD Finger Residues: 486-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF21A, BHC80, KIAA1696 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q96BD5
#2: Protein/peptide Histone H3 /


Mass: 1150.332 Da / Num. of mol.: 1 / Fragment: H3 1-10 / Source method: obtained synthetically / Details: synthesized peptide / References: UniProt: P61836, UniProt: Q6NXT2*PLUS
#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 / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% Isopropanol, 5-10% polyethylene glycol 4000, 100mM MES 6.2-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97917, 1.28295, 1.28341
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
21.282951
31.283411
ReflectionResolution: 1.43→40 Å / Num. all: 23310 / Num. obs: 23287 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 16
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 8.5 / Num. unique all: 2295 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.43→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1114 -random
Rwork0.206 ---
all0.208 23310 --
obs0.208 23287 99.9 %-
Displacement parametersBiso mean: 15.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å2-1.41 Å2
2---0.15 Å20 Å2
3----0.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-40 Å
Luzzati sigma a--0.08 Å
Refinement stepCycle: LAST / Resolution: 1.43→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 4 88 1166
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 1.43→1.47 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.208 98 -
Rwork0.189 --
obs-2116 99.9 %

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