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- PDB-4u9w: Crystal Structure of NatD bound to H4/H2A peptide and CoA -

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Basic information

Entry
Database: PDB / ID: 4u9w
TitleCrystal Structure of NatD bound to H4/H2A peptide and CoA
Components
  • Histone H4/H2A N-terminus
  • N-alpha-acetyltransferase 40
KeywordsTRANSFERASE / Acetyltransferase / GNAT fold / N-terminal acetylation / acetyl-CoA
Function / homology
Function and homology information


N-terminal L-serine Nalpha-acetyltransferase NatD / histone H2A acetyltransferase activity / peptide-serine-alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / centriolar satellite / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends ...N-terminal L-serine Nalpha-acetyltransferase NatD / histone H2A acetyltransferase activity / peptide-serine-alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / centriolar satellite / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / lipid metabolic process / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
N-alpha-acetyltransferase 40 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold ...N-alpha-acetyltransferase 40 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold
Similarity search - Domain/homology
COENZYME A / Histone H4 / N-alpha-acetyltransferase 40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsMagin, R.S. / Liszczak, G.P. / Marmorstein, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM060293 United States
CitationJournal: Structure / Year: 2015
Title: The Molecular Basis for Histone H4- and H2A-Specific Amino-Terminal Acetylation by NatD.
Authors: Magin, R.S. / Liszczak, G.P. / Marmorstein, R.
History
DepositionAug 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.4Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-alpha-acetyltransferase 40
B: N-alpha-acetyltransferase 40
C: N-alpha-acetyltransferase 40
D: N-alpha-acetyltransferase 40
E: Histone H4/H2A N-terminus
F: Histone H4/H2A N-terminus
G: Histone H4/H2A N-terminus
H: Histone H4/H2A N-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,43820
Polymers97,9078
Non-polymers3,53012
Water7,728429
1
A: N-alpha-acetyltransferase 40
F: Histone H4/H2A N-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4526
Polymers24,4772
Non-polymers9754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-13 kcal/mol
Surface area10200 Å2
MethodPISA
2
B: N-alpha-acetyltransferase 40
E: Histone H4/H2A N-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2674
Polymers24,4772
Non-polymers7912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-11 kcal/mol
Surface area10300 Å2
MethodPISA
3
C: N-alpha-acetyltransferase 40
G: Histone H4/H2A N-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3595
Polymers24,4772
Non-polymers8833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-10 kcal/mol
Surface area9810 Å2
MethodPISA
4
D: N-alpha-acetyltransferase 40
H: Histone H4/H2A N-terminus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3595
Polymers24,4772
Non-polymers8833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-12 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.901, 93.288, 100.329
Angle α, β, γ (deg.)90.00, 96.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND SEGID B
211CHAIN B AND SEGID B
311CHAIN C AND SEGID B
411CHAIN D AND SEGID B
112CHAIN E AND SEGID
212CHAIN F AND SEGID
312CHAIN G AND SEGID
412CHAIN H AND SEGID

NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
N-alpha-acetyltransferase 40 / N-acetyltransferase 11 / NatD catalytic subunit


Mass: 23973.225 Da / Num. of mol.: 4 / Fragment: UNP residues 17-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA40, NAT11 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86UY6, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide
Histone H4/H2A N-terminus


Mass: 503.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805*PLUS

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Non-polymers , 4 types, 441 molecules

#3: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG 3350, 200 mM sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 9, 2013
RadiationMonochromator: Rigaku Osmic VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 33518 / % possible obs: 98.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 35.58 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 8
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.552 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000phasing
HKL-3000data scaling
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U9V

4u9v


Resolution: 2.49→26.24 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 3295 5.05 %
Rwork0.176 --
obs0.178 65272 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.59 Å2
Refinement stepCycle: LAST / Resolution: 2.49→26.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 220 429 7122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016829
X-RAY DIFFRACTIONf_angle_d1.2069220
X-RAY DIFFRACTIONf_dihedral_angle_d15.8442489
X-RAY DIFFRACTIONf_chiral_restr0.052951
X-RAY DIFFRACTIONf_plane_restr0.0061164
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A3750X-RAY DIFFRACTIONPOSITIONAL
12B3750X-RAY DIFFRACTIONPOSITIONAL
13C3750X-RAY DIFFRACTIONPOSITIONAL
14D3750X-RAY DIFFRACTIONPOSITIONAL
21E56X-RAY DIFFRACTIONPOSITIONAL
22F56X-RAY DIFFRACTIONPOSITIONAL
23G56X-RAY DIFFRACTIONPOSITIONAL
24H56X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.52490.33651230.24932284X-RAY DIFFRACTION85
2.5249-2.56260.30871350.25612509X-RAY DIFFRACTION96
2.5626-2.60260.34351410.25292555X-RAY DIFFRACTION96
2.6026-2.64520.32811360.23642564X-RAY DIFFRACTION97
2.6452-2.69080.30131370.24482596X-RAY DIFFRACTION98
2.6908-2.73960.25841370.23242579X-RAY DIFFRACTION98
2.7396-2.79230.29621350.23372573X-RAY DIFFRACTION98
2.7923-2.84920.27731370.23412590X-RAY DIFFRACTION98
2.8492-2.91110.34291350.23542626X-RAY DIFFRACTION98
2.9111-2.97870.28511320.25332550X-RAY DIFFRACTION98
2.9787-3.05310.32791380.21582588X-RAY DIFFRACTION98
3.0531-3.13550.21841390.20412631X-RAY DIFFRACTION99
3.1355-3.22760.26241340.19172590X-RAY DIFFRACTION99
3.2276-3.33160.2581430.17892614X-RAY DIFFRACTION99
3.3316-3.45040.25631360.17552623X-RAY DIFFRACTION99
3.4504-3.58820.18031440.15932632X-RAY DIFFRACTION99
3.5882-3.75110.21061370.15032575X-RAY DIFFRACTION98
3.7511-3.94830.21361390.14822596X-RAY DIFFRACTION99
3.9483-4.19470.17761420.13812608X-RAY DIFFRACTION99
4.1947-4.51710.17881420.12042598X-RAY DIFFRACTION98
4.5171-4.96880.15121350.12372599X-RAY DIFFRACTION99
4.9688-5.68150.19291400.15712657X-RAY DIFFRACTION100
5.6815-7.13420.17591390.1742644X-RAY DIFFRACTION99
7.1342-26.23910.16991390.16122596X-RAY DIFFRACTION99

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