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- PDB-2lq6: Solution structure of BRD1 PHD2 finger -

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Basic information

Entry
Database: PDB / ID: 2lq6
TitleSolution structure of BRD1 PHD2 finger
ComponentsBromodomain-containing protein 1
KeywordsMETAL BINDING PROTEIN / PHD finger
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
Bromodomain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsLiu, L. / Wu, J.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Solution structure of an atypical PHD finger in BRPF2 and its interaction with DNA
Authors: Liu, L. / Qin, S. / Zhang, J. / Ji, P. / Shi, Y. / Wu, J.
History
DepositionFeb 25, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7883
Polymers9,6571
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 9657.266 Da / Num. of mol.: 1 / Fragment: UNP residues 317-394 / Mutation: C338S, C393S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD1, BRL, BRPF2 / Production host: Escherichia coli (E. coli) / References: UniProt: O95696
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
1323D HN(CA)CB
1423D HNCO
1523D HN(CO)CA
1623D HBHA(CO)NH
1723D H(CCO)NH
1833D (H)CCH-COSY
1933D (H)CCH-TOCSY
11023D 1H-15N NOESY
11133D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-15N] protein-1, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-13C; U-15N] protein-2, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-13C; U-15N] protein-3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMprotein-1[U-15N]1
0.4 mMprotein-2[U-13C; U-15N]2
0.4 mMprotein-3[U-13C; U-15N]3
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
SPARKYGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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