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- PDB-4qqg: Crystal structure of an N-terminal HTATIP fragment -

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Basic information

Entry
Database: PDB / ID: 4qqg
TitleCrystal structure of an N-terminal HTATIP fragment
ComponentsHistone acetyltransferase KAT5
KeywordsTRANSFERASE / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H2AK5 acetyltransferase activity / peptide crotonyltransferase activity / histone H2A acetyltransferase activity / positive regulation of mitotic sister chromatid segregation / positive regulation of protein acetylation / piccolo histone acetyltransferase complex / Sensing of DNA Double Strand Breaks / MSL complex / peptide butyryltransferase activity / histone H4K16 acetyltransferase activity ...histone H2AK5 acetyltransferase activity / peptide crotonyltransferase activity / histone H2A acetyltransferase activity / positive regulation of mitotic sister chromatid segregation / positive regulation of protein acetylation / piccolo histone acetyltransferase complex / Sensing of DNA Double Strand Breaks / MSL complex / peptide butyryltransferase activity / histone H4K16 acetyltransferase activity / lipid droplet disassembly / sperm DNA condensation / peptide 2-hydroxyisobutyryltransferase activity / positive regulation of attachment of mitotic spindle microtubules to kinetochore / peptidyl-lysine acetylation / positive regulation of triglyceride biosynthetic process / Swr1 complex / histone H4 acetyltransferase activity / regulation of double-strand break repair / Impaired BRCA2 binding to PALB2 / positive regulation of circadian rhythm / positive regulation of regulatory T cell differentiation / positive regulation of innate immune response / positive regulation of aggrephagy / Cardiogenesis / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / neural tube development / DNA repair-dependent chromatin remodeling / regulation of hematopoietic stem cell differentiation / Resolution of D-loop Structures through Holliday Junction Intermediates / negative regulation of interleukin-2 production / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / HDR through Single Strand Annealing (SSA) / peptide-lysine-N-acetyltransferase activity / Impaired BRCA2 binding to RAD51 / response to ionizing radiation / NuA4 histone acetyltransferase complex / mitotic spindle pole / establishment of mitotic spindle orientation / Presynaptic phase of homologous DNA pairing and strand exchange / acetyltransferase activity / positive regulation of double-strand break repair via homologous recombination / spermatid development / positive regulation of myoblast differentiation / negative regulation of double-strand break repair via homologous recombination / cellular response to glucose starvation / positive regulation of autophagy / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / neurogenesis / cellular response to estradiol stimulus / nucleotide-excision repair / cellular response to glucose stimulus / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / Formation of the beta-catenin:TCF transactivating complex / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / DNA Damage/Telomere Stress Induced Senescence / kinetochore / cellular senescence / nucleosome / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / HATs acetylate histones / Processing of DNA double-strand break ends / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / transcription coactivator activity / regulation of cell cycle / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain ...MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Acyl-CoA N-acyltransferase / SH3 type barrels. / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Histone acetyltransferase KAT5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsLiu, Y. / Tempel, W. / Wernimont, A.K. / Dobrovetsky, E. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: FEBS Lett. / Year: 2018
Title: Structural and histone binding studies of the chromo barrel domain of TIP60.
Authors: Zhang, Y. / Lei, M. / Yang, X. / Feng, Y. / Yang, Y. / Loppnau, P. / Li, Y. / Yang, Y. / Min, J. / Liu, Y.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
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_alt_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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT5
B: Histone acetyltransferase KAT5
C: Histone acetyltransferase KAT5
D: Histone acetyltransferase KAT5
E: Histone acetyltransferase KAT5
F: Histone acetyltransferase KAT5
G: Histone acetyltransferase KAT5


Theoretical massNumber of molelcules
Total (without water)67,29120
Polymers67,2917
Non-polymers013
Water00
1
A: Histone acetyltransferase KAT5


Theoretical massNumber of molelcules
Total (without water)9,6135
Polymers9,6131
Non-polymers04
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone acetyltransferase KAT5


Theoretical massNumber of molelcules
Total (without water)9,6132
Polymers9,6131
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Histone acetyltransferase KAT5


Theoretical massNumber of molelcules
Total (without water)9,6131
Polymers9,6131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Histone acetyltransferase KAT5


Theoretical massNumber of molelcules
Total (without water)9,6133
Polymers9,6131
Non-polymers02
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Histone acetyltransferase KAT5


Theoretical massNumber of molelcules
Total (without water)9,6132
Polymers9,6131
Non-polymers01
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Histone acetyltransferase KAT5


Theoretical massNumber of molelcules
Total (without water)9,6133
Polymers9,6131
Non-polymers02
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Histone acetyltransferase KAT5


Theoretical massNumber of molelcules
Total (without water)9,6134
Polymers9,6131
Non-polymers03
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.544, 59.986, 101.638
Angle α, β, γ (deg.)90.000, 100.650, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17B
27C
18B
28D
19B
29E
110B
210F
111B
211G
112C
212D
113C
213E
114C
214F
115C
215G
116D
216E
117D
217F
118D
218G
119E
219F
120E
220G
121F
221G

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDBeg label alt-ID
11GLUGLUPROPROAA3 - 714 - 72
21GLUGLUPROPROBB3 - 714 - 72
12ALAALAPHEPHEAA2 - 703 - 71
22ALAALAPHEPHECC2 - 703 - 71A
13GLUGLUPHEPHEAA3 - 704 - 71
23GLUGLUPHEPHEDD3 - 704 - 71
14METMETPHEPHEAA1 - 702 - 71
24METMETPHEPHEEE1 - 702 - 71
15GLUGLUPHEPHEAA3 - 704 - 71
25GLUGLUPHEPHEFF3 - 704 - 71
16METMETPHEPHEAA1 - 702 - 71
26METMETPHEPHEGG1 - 702 - 71
17GLUGLULYSLYSBB3 - 724 - 73
27GLUGLULYSLYSCC3 - 724 - 73
18GLUGLUPROPROBB3 - 714 - 72
28GLUGLUPROPRODD3 - 714 - 72
19GLUGLULYSLYSBB3 - 724 - 73
29GLUGLULYSLYSEE3 - 724 - 73
110GLUGLULYSLYSBB3 - 724 - 73
210GLUGLULYSLYSFF3 - 724 - 73
111GLUGLULYSLYSBB3 - 724 - 73
211GLUGLULYSLYSGG3 - 724 - 73
112GLUGLUPHEPHECC3 - 704 - 71
212GLUGLUPHEPHEDD3 - 704 - 71
113ALAALALYSLYSCC2 - 723 - 73A
213ALAALALYSLYSEE2 - 723 - 73
114GLUGLULYSLYSCC3 - 724 - 73
214GLUGLULYSLYSFF3 - 724 - 73
115ALAALAPROPROCC2 - 713 - 72A
215ALAALAPROPROGG2 - 713 - 72
116GLUGLUPHEPHEDD3 - 704 - 71
216GLUGLUPHEPHEEE3 - 704 - 71
117GLUGLUPHEPHEDD3 - 704 - 71
217GLUGLUPHEPHEFF3 - 704 - 71
118GLUGLUPHEPHEDD3 - 704 - 71
218GLUGLUPHEPHEGG3 - 704 - 71
119GLUGLUPROPROEE3 - 714 - 72
219GLUGLUPROPROFF3 - 714 - 72
120METMETPROPROEE1 - 712 - 72
220METMETPROPROGG1 - 712 - 72
121GLUGLUPROPROFF3 - 714 - 72
221GLUGLUPROPROGG3 - 714 - 72

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
DetailsAUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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Components

#1: Protein
Histone acetyltransferase KAT5 / 60 kDa Tat-interactive protein / Tip60 / Histone acetyltransferase HTATIP / HIV-1 Tat interactive ...60 kDa Tat-interactive protein / Tip60 / Histone acetyltransferase HTATIP / HIV-1 Tat interactive protein / Lysine acetyltransferase 5 / cPLA(2)-interacting protein


Mass: 9613.062 Da / Num. of mol.: 7 / Fragment: unp residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT5, HTATIP, TIP60 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q92993, histone acetyltransferase
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically

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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: 1.94 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 20% PEG3350, 0.2 M calcium acetate. The protein sample may have been treated with trypsin, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.283 Å
DetectorType: adsc q315 / Detector: CCD / Date: Feb 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2.8→42.26 Å / Num. obs: 12878 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.8-2.953.70.5652.86923187999.9
8.85-42.263.40.03424146642998.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.3.6data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2EKO

2eko


Resolution: 2.8→99.89 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.2245 / WRfactor Rwork: 0.1991 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7826 / SU B: 43.352 / SU ML: 0.378 / SU R Cruickshank DPI: 0.3992 / SU Rfree: 0.4265 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: molecular replacement coordinates, based on an nmr model, were initially processed by the program phaser, before input to MOLREP. PARROT was used for NCS- and solvent-based density ...Details: molecular replacement coordinates, based on an nmr model, were initially processed by the program phaser, before input to MOLREP. PARROT was used for NCS- and solvent-based density modification. BUCCANEER was used for automated model building. During interactive re-building, we experienced problems with the interpretation of electron density for some loops. Poor geometry of the model region between residues 17 and 23 of chain F is noted in particular. The pogram COOT and the MOLPROBITY server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 771 6 %THIN SHELLS (SFTOOLS)
Rwork0.2257 ---
obs0.2277 12868 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.49 Å2 / Biso mean: 36.3753 Å2 / Biso min: 2.31 Å2
Baniso -1Baniso -2Baniso -3
1--3.69 Å20 Å2-1.77 Å2
2--3.72 Å2-0 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.8→99.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 13 0 3969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194070
X-RAY DIFFRACTIONr_bond_other_d0.0090.023853
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9585520
X-RAY DIFFRACTIONr_angle_other_deg1.38938806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1965484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.81423.713202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2715694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8771532
X-RAY DIFFRACTIONr_chiral_restr0.0740.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214533
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02939
X-RAY DIFFRACTIONr_mcbond_it1.2821.6871960
X-RAY DIFFRACTIONr_mcbond_other1.2821.6871961
X-RAY DIFFRACTIONr_mcangle_it2.1772.5282437
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A36930.11
12B36930.11
21A38370.1
22C38370.1
31A38000.1
32D38000.1
41A38780.11
42E38780.11
51A35940.11
52F35940.11
61A37230.13
62G37230.13
71B37960.09
72C37960.09
81B37320.08
82D37320.08
91B37340.09
92E37340.09
101B35440.1
102F35440.1
111B35800.11
112G35800.11
121C36810.11
122D36810.11
131C39030.08
132E39030.08
141C36520.1
142F36520.1
151C36690.11
152G36690.11
161D37310.09
162E37310.09
171D35760.1
172F35760.1
181D36410.11
182G36410.11
191E36100.11
192F36100.11
201E37230.12
202G37230.12
211F35930.12
212G35930.12
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 113 -
Rwork0.343 858 -
all-971 -
obs--99.9 %
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)
16.7502-1.02581.05121.58010.86016.7437-0.2087-0.06520.2557-0.02330.08040.045-0.3386-0.02990.12830.1263-0.013-0.00870.0160.02150.063736.26830.3838-3.9589
22.1332-0.01133.66166.0278-0.51898.3575-0.03870.01940.21220.25530.02820.0579-0.2643-0.21080.01060.09240.04580.01260.08330.00370.110841.64441.569429.6134
36.5404-0.15221.84323.26732.28717.3166-0.0946-0.2384-0.22270.2698-0.0083-0.02640.3324-0.08710.10290.12750.02060.02270.08420.01240.066912.534528.224854.1374
43.5811-0.42462.01553.1497-0.75475.0117-0.07510.18040.1018-0.4057-0.0214-0.128-0.11850.42060.09650.14920.0142-0.01940.2132-0.10120.145326.136828.432423.3913
56.2040.66021.16115.26840.77836.0549-0.0788-0.2530.15040.36230.19450.02420.21810.2647-0.11560.17550.0119-0.02920.0388-0.01580.020749.918427.206313.1172
66.9835-1.0471.69884.5588-2.36816.0467-0.0277-0.0788-0.2089-0.14-0.027-0.13250.22810.21010.05460.09190.01560.00760.115-0.04410.139625.773956.796615.0826
76.06831.46282.10825.5189-1.9542.88560.0151-0.0783-0.06170.1353-0.0150.0724-0.14550.0235-00.15270.0010.00630.0994-0.04040.028137.832531.041241.3517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 71
2X-RAY DIFFRACTION2B3 - 72
3X-RAY DIFFRACTION3C2 - 72
4X-RAY DIFFRACTION4D3 - 71
5X-RAY DIFFRACTION5E1 - 72
6X-RAY DIFFRACTION6F3 - 72
7X-RAY DIFFRACTION7G0 - 72

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