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- PDB-6c9m: The Human NatA (Naa10/Naa15) amino-terminal acetyltransferase complex -

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Basic information

Entry
Database: PDB / ID: 6c9m
TitleThe Human NatA (Naa10/Naa15) amino-terminal acetyltransferase complex
Components
  • N-alpha-acetyltransferase 10
  • N-alpha-acetyltransferase 15, NatA auxiliary subunit
KeywordsTRANSFERASE / NatA / N-terminal acetylation / protein complex
Function / homology
Function and homology information


negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / N-acetyltransferase activity / internal protein amino acid acetylation / protein acetylation ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / N-acetyltransferase activity / internal protein amino acid acetylation / protein acetylation / chromosome organization / ribosome binding / angiogenesis / transcription regulator complex / cell differentiation / protein stabilization / nuclear body / intracellular membrane-bounded organelle / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / RNA binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Tetratricopeptide repeat / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / TPR repeat region circular profile. / TPR repeat profile. ...N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Tetratricopeptide repeat / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Acyl-CoA N-acyltransferase / Tetratricopeptide repeat / Aminopeptidase / Tetratricopeptide-like helical domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / N-alpha-acetyltransferase 10 / N-alpha-acetyltransferase 15, NatA auxiliary subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGottlieb, L. / Marmorstein, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118090-01 United States
CitationJournal: Structure / Year: 2018
Title: Structure of Human NatA and Its Regulation by the Huntingtin Interacting Protein HYPK.
Authors: Gottlieb, L. / Marmorstein, R.
History
DepositionJan 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.3Jul 21, 2021Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
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 15, NatA auxiliary subunit
B: N-alpha-acetyltransferase 10
C: N-alpha-acetyltransferase 15, NatA auxiliary subunit
D: N-alpha-acetyltransferase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,4597
Polymers255,9004
Non-polymers1,5583
Water1629
1
A: N-alpha-acetyltransferase 15, NatA auxiliary subunit
B: N-alpha-acetyltransferase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6103
Polymers127,9502
Non-polymers6601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-33 kcal/mol
Surface area43240 Å2
MethodPISA
2
C: N-alpha-acetyltransferase 15, NatA auxiliary subunit
D: N-alpha-acetyltransferase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8484
Polymers127,9502
Non-polymers8982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-31 kcal/mol
Surface area42650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.110, 171.830, 178.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-alpha-acetyltransferase 15, NatA auxiliary subunit / Gastric cancer antigen Ga19 / N-terminal acetyltransferase / NMDA receptor-regulated protein 1 / ...Gastric cancer antigen Ga19 / N-terminal acetyltransferase / NMDA receptor-regulated protein 1 / Protein tubedown-1 / Tbdn100


Mass: 101427.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA15, GA19, NARG1, NATH, TBDN100 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BXJ9
#2: Protein N-alpha-acetyltransferase 10 / / N-terminal acetyltransferase complex ARD1 subunit homolog A / hARD1 / NatA catalytic subunit Naa10


Mass: 26522.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA10, ARD1, ARD1A, TE2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P41227, N-terminal amino-acid Nalpha-acetyltransferase NatA
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16% PEG3350, 10% Tascimate, pH 7.5, 2% acetone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 28, 2017
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→48.95 Å / Num. obs: 72780 / % possible obs: 99.8 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 20.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 1.44 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4KVO

4kvo


Resolution: 2.8→48.95 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.6 / Phase error: 26.12
RfactorNum. reflection% reflection
Rfree0.242 3640 5 %
Rwork0.187 --
obs0.19 72771 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15234 0 88 9 15331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115645
X-RAY DIFFRACTIONf_angle_d1.26921111
X-RAY DIFFRACTIONf_dihedral_angle_d12.2929573
X-RAY DIFFRACTIONf_chiral_restr0.1452273
X-RAY DIFFRACTIONf_plane_restr0.0062692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83690.41341370.31572600X-RAY DIFFRACTION100
2.8369-2.87570.3261400.28642651X-RAY DIFFRACTION100
2.8757-2.91680.31921380.27142621X-RAY DIFFRACTION100
2.9168-2.96030.3471370.27912615X-RAY DIFFRACTION100
2.9603-3.00660.34981380.26992622X-RAY DIFFRACTION100
3.0066-3.05590.38561390.28492623X-RAY DIFFRACTION100
3.0559-3.10860.3621380.292639X-RAY DIFFRACTION100
3.1086-3.16510.36421390.29042640X-RAY DIFFRACTION100
3.1651-3.2260.32491370.25642605X-RAY DIFFRACTION100
3.226-3.29180.29631400.23222643X-RAY DIFFRACTION100
3.2918-3.36330.28741390.21912648X-RAY DIFFRACTION100
3.3633-3.44160.26431400.21392650X-RAY DIFFRACTION100
3.4416-3.52760.26891370.20392618X-RAY DIFFRACTION100
3.5276-3.6230.231390.19862640X-RAY DIFFRACTION100
3.623-3.72950.25981400.20082655X-RAY DIFFRACTION100
3.7295-3.84990.25491400.18842651X-RAY DIFFRACTION100
3.8499-3.98740.2271390.17682641X-RAY DIFFRACTION100
3.9874-4.1470.21691400.16442677X-RAY DIFFRACTION100
4.147-4.33560.21341400.15722661X-RAY DIFFRACTION100
4.3356-4.5640.19371410.15172663X-RAY DIFFRACTION100
4.564-4.84970.18561400.15652659X-RAY DIFFRACTION100
4.8497-5.22380.22871410.16172695X-RAY DIFFRACTION100
5.2238-5.74880.23221420.17552691X-RAY DIFFRACTION100
5.7488-6.57890.23551430.18752708X-RAY DIFFRACTION100
6.5789-8.28220.21971440.16482748X-RAY DIFFRACTION100
8.2822-48.95760.21611520.1622868X-RAY DIFFRACTION100
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)
11.0530.1633-0.15240.9669-0.00110.89520.0071-0.2611-0.06950.1759-0.0824-0.13910.31030.28640.08260.61820.1059-0.03740.6773-0.03320.492938.2686-5.72713.2896
23.9928-0.3158-0.29083.53060.36674.7997-0.030.1563-0.1989-0.4630.0238-0.08890.1697-0.1105-0.00120.4744-0.00090.03140.3633-0.0610.398430.9398-2.23-18.5831
30.52230.10510.07761.57280.27050.69050.0640.0204-0.0047-0.1301-0.11810.04870.08490.01930.07310.50510.0204-0.00050.57920.03810.508456.390441.865-35.0646
43.37030.6049-0.60553.2283-0.77924.61870.01760.15410.0008-0.8339-0.0468-0.33820.12050.474-0.02770.61130.05620.15580.44330.03480.486568.674140.6449-55.2178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 1 THROUGH 841)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 1 THROUGH 160)
3X-RAY DIFFRACTION3(CHAIN 'C' AND RESID 3 THROUGH 841)
4X-RAY DIFFRACTION4(CHAIN 'D' AND RESID 1 THROUGH 160)

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