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- PDB-7lh9: Crystal structure of BRPF2 PWWP domain in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 7lh9
TitleCrystal structure of BRPF2 PWWP domain in complex with DNA
Components
  • Bromodomain-containing protein 1
  • DNA
KeywordsDNA BINDING PROTEIN/DNA / BRPF2 / PWWP / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


histone H3-K14 acetyltransferase complex / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / erythrocyte maturation / response to immobilization stress / response to electrical stimulus / Regulation of TP53 Activity through Acetylation / histone reader activity / positive regulation of erythrocyte differentiation ...histone H3-K14 acetyltransferase complex / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / erythrocyte maturation / response to immobilization stress / response to electrical stimulus / Regulation of TP53 Activity through Acetylation / histone reader activity / positive regulation of erythrocyte differentiation / HATs acetylate histones / histone binding / perikaryon / nuclear speck / chromatin remodeling / dendrite / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
BRPF2, ePHD domain / BRPF2, PHD domain / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain ...BRPF2, ePHD domain / BRPF2, PHD domain / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Bromodomain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsZhang, M. / Lei, M. / Qin, S. / Dong, A. / Yang, A. / Li, Y. / Loppnau, P. / Hughes, T.R. / Arrowsmith, C.H. / Edwards, A.M. ...Zhang, M. / Lei, M. / Qin, S. / Dong, A. / Yang, A. / Li, Y. / Loppnau, P. / Hughes, T.R. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Liu, J. / Structural Genomics Consortium (SGC)
CitationJournal: Biochim Biophys Acta Gene Regul Mech / Year: 2021
Title: Crystal structure of the BRPF2 PWWP domain in complex with DNA reveals a different binding mode than the HDGF family of PWWP domains.
Authors: Zhang, M. / Lei, M. / Qin, S. / Dong, A. / Yang, A. / Li, Y. / Loppnau, P. / Hughes, T.R. / Min, J. / Liu, Y.
History
DepositionJan 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 1
B: Bromodomain-containing protein 1
C: Bromodomain-containing protein 1
D: Bromodomain-containing protein 1
E: DNA
F: DNA
G: DNA
H: DNA
I: DNA
J: DNA
K: DNA
L: DNA


Theoretical massNumber of molelcules
Total (without water)86,54212
Polymers86,54212
Non-polymers00
Water0
1
A: Bromodomain-containing protein 1
E: DNA
F: DNA

E: DNA
F: DNA


Theoretical massNumber of molelcules
Total (without water)28,9625
Polymers28,9625
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
2
B: Bromodomain-containing protein 1
G: DNA
H: DNA


Theoretical massNumber of molelcules
Total (without water)21,6363
Polymers21,6363
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 1
I: DNA
J: DNA


Theoretical massNumber of molelcules
Total (without water)21,6363
Polymers21,6363
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 1
K: DNA
L: DNA

K: DNA
L: DNA


Theoretical massNumber of molelcules
Total (without water)28,9625
Polymers28,9625
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Unit cell
Length a, b, c (Å)40.410, 216.113, 54.037
Angle α, β, γ (deg.)90.000, 109.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 3 / Auth seq-ID: 1026 - 1029 / Label seq-ID: 103 - 106

Dom-IDAuth asym-IDLabel asym-ID
1DD
2AA

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.461525, 0.863089, -0.205114), (-0.719455, 0.228881, -0.655742), (-0.519017, 0.450211, 0.726588)23.3783, 50.509892, 7.26127

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Components

#1: Protein
Bromodomain-containing protein 1 / BR140-like protein / Bromodomain and PHD finger-containing protein 2 / BRPF2


Mass: 14308.836 Da / Num. of mol.: 4 / Fragment: PWWP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD1, BRL, BRPF2 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O95696
#2: DNA chain
DNA /


Mass: 3663.392 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.57 Å3/Da / Density % sol: 52.17 % / Mosaicity: 0.913 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Magnesium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 25975 / % possible obs: 97.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.057 / Rrim(I) all: 0.11 / Χ2: 1.253 / Net I/σ(I): 7.5 / Num. measured all: 92761
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.643.50.86213390.5050.5341.0191.19298.5
2.64-2.693.60.7313240.5820.4390.8551.24597
2.69-2.743.70.64812520.6710.3870.7581.10398.4
2.74-2.83.60.57213020.7340.3440.6711.16297.4
2.8-2.863.60.47913110.6150.2930.5641.30196.8
2.86-2.933.60.4113130.8320.2490.4821.21998.4
2.93-33.50.36212610.8360.2190.4251.26794.7
3-3.083.40.26113080.9370.1630.3091.24997.2
3.08-3.173.20.22312470.9510.1450.2681.26394.5
3.17-3.283.70.15913080.990.0960.1861.36398.2
3.28-3.393.60.09813090.9960.060.1161.36497
3.39-3.533.70.12612820.9760.0760.1481.33297.5
3.53-3.693.60.10313090.9860.0630.1211.35795.7
3.69-3.883.60.09112430.9830.0560.1081.4196.1
3.88-4.133.30.0712880.9880.0440.0841.28295.5
4.13-4.453.70.06313150.9930.0370.0731.20997.6
4.45-4.893.70.05412910.9940.0320.0631.1296.9
4.89-5.63.60.05413100.9940.0330.0641.40397.7
5.6-7.053.50.05413090.9940.0330.0641.17797.1
7.05-503.80.05113540.9970.0290.0591.06898.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.05 Å41.6 Å
Translation4.05 Å41.6 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z02

4z02


Resolution: 2.6→41.64 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.055 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.744 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 1042 4 %RANDOM
Rwork0.2249 ---
obs0.227 24880 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 178.89 Å2 / Biso mean: 51.445 Å2 / Biso min: 23.01 Å2
Baniso -1Baniso -2Baniso -3
1--2.69 Å20 Å2-0.42 Å2
2--2.83 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 2.6→41.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 1959 0 0 5353
Num. residues----548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125675
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184291
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.4438113
X-RAY DIFFRACTIONr_angle_other_deg1.3041.9349977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1645445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36822.677127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12315540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1531512
X-RAY DIFFRACTIONr_chiral_restr0.0630.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021180
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: D / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
7LOOSE POSITIONAL0.035
24TIGHT THERMAL23.020.5
7LOOSE THERMAL20.9210
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 63 -
Rwork0.373 1854 -
all-1917 -
obs--96.72 %

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