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- PDB-4qc3: Crystal structure of human BAZ2B bromodomain in complex with a di... -

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Basic information

Entry
Database: PDB / ID: 4qc3
TitleCrystal structure of human BAZ2B bromodomain in complex with a diacetylated histone 4 peptide (H4K8acK12ac)
Components
  • Bromodomain adjacent to zinc finger domain protein 2B
  • diacetylated histone 4 peptide (H4K8acK12ac)
KeywordsTRANSCRIPTION / Bromodomain adjacent to zinc finger domain protein 2B / hWALp4 / KIAA1476 / transcriptional regulation / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus
Similarity search - Function
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 ...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 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTallant, C. / Jose, B. / Picaud, S. / Chaikuad, A. / Filippakopoulos, P. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Tallant, C. / Jose, B. / Picaud, S. / Chaikuad, A. / Filippakopoulos, P. / Burgess-Brown, N. / 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 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain adjacent to zinc finger domain protein 2B
B: Bromodomain adjacent to zinc finger domain protein 2B
C: diacetylated histone 4 peptide (H4K8acK12ac)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8656
Polymers25,6783
Non-polymers1863
Water5,098283
1
A: Bromodomain adjacent to zinc finger domain protein 2B
C: diacetylated histone 4 peptide (H4K8acK12ac)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3134
Polymers13,1892
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-1 kcal/mol
Surface area7230 Å2
MethodPISA
2
B: Bromodomain adjacent to zinc finger domain protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5512
Polymers12,4891
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.670, 32.402, 62.033
Angle α, β, γ (deg.)90.00, 109.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bromodomain adjacent to zinc finger domain protein 2B / hWALp4


Mass: 12489.299 Da / Num. of mol.: 2 / Fragment: unp residues 2062-2166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Plasmid: pNIC28-Bsa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q9UIF8
#2: Protein/peptide diacetylated histone 4 peptide (H4K8acK12ac)


Mass: 699.798 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG 8000, 0.2M calcium acetate, 0.1 M cacodylate, 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 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.6→29.18 Å / Num. all: 30743 / Num. obs: 30743 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 10.062 Å2 / Rmerge(I) obs: 0.019 / Rsym value: 0.015 / Net I/σ(I): 45.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value
1.6-1.72.330.0418.0993550.052
1.7-1.812.30.03321.4588280.042
1.81-1.962.320.02627.1582160.034
1.96-2.142.280.02233.7375900.028
2.14-2.392.30.0239.0567870.026
2.39-2.762.270.01942.3359870.023
2.76-3.372.270.01847.2350440.022
3.37-4.742.250.01750.8139100.022
4.74-29.182.280.01750.821830.024

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of PDB ENTRY 3G0L, 1DVV, 1X0J, 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2UOU, 3D7C, 3DWY

3g0l

1dvv

1x0j

3dai

3hmh

2grc

2oo1

2oss

2uou

3d7c

3dwy


Resolution: 1.6→29.179 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.298 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.087 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18697 1550 5 %RANDOM
Rwork0.16768 ---
obs0.16866 29184 99.17 %-
all-29184 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.502 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å20.03 Å2
2--0 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 12 283 2082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191853
X-RAY DIFFRACTIONr_bond_other_d0.0010.021753
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9812489
X-RAY DIFFRACTIONr_angle_other_deg0.75834066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5375222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72524.76284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.85215337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.022158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212044
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
X-RAY DIFFRACTIONr_mcbond_it0.7070.982891
X-RAY DIFFRACTIONr_mcbond_other0.7050.982890
X-RAY DIFFRACTIONr_mcangle_it1.161.4621112
X-RAY DIFFRACTIONr_mcangle_other1.161.4621113
X-RAY DIFFRACTIONr_scbond_it1.2131.129962
X-RAY DIFFRACTIONr_scbond_other1.2121.129962
X-RAY DIFFRACTIONr_scangle_other1.8751.6261378
X-RAY DIFFRACTIONr_long_range_B_refined4.4829.4172496
X-RAY DIFFRACTIONr_long_range_B_other4.3128.6272325
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 104 -
Rwork0.147 2101 -
obs--97.61 %
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)
10.0934-0.0520.01990.3252-0.24451.60540.04320.0001-0.0109-0.04390.09380.04730.0479-0.0604-0.1370.0212-0.0069-0.00990.03620.01570.016520.13198.63854.0516
21.002-0.21190.35120.4333-0.17610.32290.0530.0266-0.00540.0638-0.0635-0.04930.0036-0.02260.01050.0198-0.01-0.0120.02250.00530.015741.61686.191834.7572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2060 - 2166
2X-RAY DIFFRACTION2B2060 - 2166

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