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- PDB-4qbm: Crystal structure of human BAZ2A bromodomain in complex with a di... -

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Basic information

Entry
Database: PDB / ID: 4qbm
TitleCrystal structure of human BAZ2A bromodomain in complex with a diacetylated histone 4 peptide (H4K16acK20ac)
Components
  • Bromodomain adjacent to zinc finger domain protein 2A
  • histone H4 peptide with sequence Gly-Ala-Lys(ac)-Arg-His-Arg-Lys(ac)-Val-Leu
KeywordsTRANSCRIPTION / Bromodomain adjacent to zinc finger domain protein 2A / Transcription termination factor I-interacting protein 5 / Tip5 / Bromodomain / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


NoRC complex / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / lysine-acetylated histone binding / NoRC negatively regulates rRNA expression ...NoRC complex / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / negative regulation of transcription by RNA polymerase I / DNA methylation-dependent constitutive heterochromatin formation / nuclear receptor binding / lysine-acetylated histone binding / NoRC negatively regulates rRNA expression / heterochromatin formation / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / DNA binding / RNA binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif ...Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTallant, C. / Nunez-Alonso, G. / Picaud, S. / Filippakopoulos, P. / Krojer, T. / Williams, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Tallant, C. / Nunez-Alonso, G. / Picaud, S. / Filippakopoulos, P. / Krojer, T. / Williams, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2015
Title: Molecular basis of histone tail recognition by human TIP5 PHD finger and bromodomain of the chromatin remodeling complex NoRC.
Authors: Cynthia Tallant / Erica Valentini / Oleg Fedorov / Lois Overvoorde / Fleur M Ferguson / Panagis Filippakopoulos / Dmitri I Svergun / Stefan Knapp / Alessio Ciulli /
Abstract: Binding of the chromatin remodeling complex NoRC to RNA complementary to the rDNA promoter mediates transcriptional repression. TIP5, the largest subunit of NoRC, is involved in recruitment to rDNA ...Binding of the chromatin remodeling complex NoRC to RNA complementary to the rDNA promoter mediates transcriptional repression. TIP5, the largest subunit of NoRC, is involved in recruitment to rDNA by interactions with promoter-bound TTF-I, pRNA, and acetylation of H4K16. TIP5 domains that recognize posttranslational modifications on histones are essential for recruitment of NoRC to chromatin, but how these reader modules recognize site-specific histone tails has remained elusive. Here, we report crystal structures of PHD zinc finger and bromodomains from human TIP5 and BAZ2B in free form and bound to H3 and/or H4 histones. PHD finger functions as an independent structural module in recognizing unmodified H3 histone tails, and the bromodomain prefers H3 and H4 acetylation marks followed by a key basic residue, KacXXR. Further low-resolution analyses of PHD-bromodomain modules provide molecular insights into their trans histone tail recognition, required for nucleosome recruitment and transcriptional repression of the NoRC complex.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2A
B: Bromodomain adjacent to zinc finger domain protein 2A
C: histone H4 peptide with sequence Gly-Ala-Lys(ac)-Arg-His-Arg-Lys(ac)-Val-Leu
D: histone H4 peptide with sequence Gly-Ala-Lys(ac)-Arg-His-Arg-Lys(ac)-Val-Leu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3835
Polymers27,3214
Non-polymers621
Water4,035224
1
A: Bromodomain adjacent to zinc finger domain protein 2A
C: histone H4 peptide with sequence Gly-Ala-Lys(ac)-Arg-His-Arg-Lys(ac)-Val-Leu


Theoretical massNumber of molelcules
Total (without water)13,6602
Polymers13,6602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-2 kcal/mol
Surface area7290 Å2
MethodPISA
2
B: Bromodomain adjacent to zinc finger domain protein 2A
D: histone H4 peptide with sequence Gly-Ala-Lys(ac)-Arg-His-Arg-Lys(ac)-Val-Leu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7233
Polymers13,6602
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-3 kcal/mol
Surface area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.869, 64.869, 71.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2A / Transcription termination factor I-interacting protein 5 / TTF-I-interacting protein 5 / Tip5 / hWALp3


Mass: 12509.048 Da / Num. of mol.: 2 / Fragment: unp residues 1796-1899
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, CB1_000449039, KIAA0314, TIP5 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: Q9UIF9
#2: Protein/peptide histone H4 peptide with sequence Gly-Ala-Lys(ac)-Arg-His-Arg-Lys(ac)-Val-Leu


Mass: 1151.385 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium phosphate monobasic, 0.1M potassium phosphate monobasic, 2 M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.65→29.01 Å / Num. all: 35633 / Num. obs: 35633 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 18.75 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.036 / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.8.0069refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4LZ2, BAZ2A

4lz2


Resolution: 1.65→64.87 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.974 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20495 1661 4.7 %RANDOM
Rwork0.18534 ---
obs0.18631 33458 98.22 %-
all-35633 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.668 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0 Å2
2--0.24 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.65→64.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 4 224 2133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191976
X-RAY DIFFRACTIONr_bond_other_d0.0010.021820
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9562656
X-RAY DIFFRACTIONr_angle_other_deg0.79534182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1365233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.84322.477109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07915333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7021523
X-RAY DIFFRACTIONr_chiral_restr0.0830.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02509
X-RAY DIFFRACTIONr_mcbond_it1.3591.803920
X-RAY DIFFRACTIONr_mcbond_other1.3531.801919
X-RAY DIFFRACTIONr_mcangle_it2.1322.6841145
X-RAY DIFFRACTIONr_mcangle_other2.1342.6861146
X-RAY DIFFRACTIONr_scbond_it2.2842.1941056
X-RAY DIFFRACTIONr_scbond_other2.2822.1941056
X-RAY DIFFRACTIONr_scangle_other3.6293.1681508
X-RAY DIFFRACTIONr_long_range_B_refined5.37716.2442539
X-RAY DIFFRACTIONr_long_range_B_other5.24815.6052405
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 121 -
Rwork0.187 2507 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6309-0.2571-0.30980.32320.13870.3777-0.04270.00360.0340.05490.0518-0.0610.0325-0.0387-0.00910.02810.0131-0.01050.0219-0.01320.012510.71992.9499-57.5868
20.4920.3377-0.20781.27370.03320.3995-0.04110.0110.033-0.03570.0541-0.03740.0783-0.0414-0.0130.0202-0.0080.00520.01670.00360.015529.7726-20.1779-74.5087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1794 - 1899
2X-RAY DIFFRACTION2B1794 - 1898

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