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- PDB-6c95: The Human NatA (Naa10/Naa15) amino-terminal acetyltransferase com... -

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Basic information

Entry
Database: PDB / ID: 6c95
TitleThe Human NatA (Naa10/Naa15) amino-terminal acetyltransferase complex bound to HYPK
Components
  • Huntingtin-interacting protein K
  • N-alpha-acetyltransferase 10
  • N-alpha-acetyltransferase 15, NatA auxiliary subunit
KeywordsTRANSFERASE / NatA / HYPK / N-terminal acetylation / Huntingtin interacting protein / protein complex
Function / homology
Function and homology information


negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / : / N-acetyltransferase activity / internal protein amino acid acetylation ...negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-glutamate-alpha-N-acetyltransferase activity / NatA complex / peptide-serine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / : / N-acetyltransferase activity / internal protein amino acid acetylation / protein acetylation / chromosome organization / protein folding chaperone / microtubule cytoskeleton / ribosome binding / angiogenesis / transcription regulator complex / cell differentiation / nuclear body / protein stabilization / intracellular membrane-bounded organelle / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Huntingtin-interacting protein K, UBA-like domain / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / 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. ...Huntingtin-interacting protein K, UBA-like domain / Nascent polypeptide-associated complex subunit alpha-like, UBA domain / HYPK UBA domain / 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. / Acyl-CoA N-acyltransferase / Tetratricopeptide repeats / 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 / Huntingtin-interacting protein K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 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 25, 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

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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
D: Huntingtin-interacting protein K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,3004
Polymers142,6403
Non-polymers6601
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10490 Å2
ΔGint-55 kcal/mol
Surface area47030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.320, 182.320, 86.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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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.: 1
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.: 1
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: Protein Huntingtin-interacting protein K / Huntingtin yeast partner K / yeast two-hybrid protein K


Mass: 14689.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HYPK, C15orf63, HSPC136 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NX55
#4: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 19.5% PEG3350, 11% Tascimate, pH 6.5

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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: Apr 24, 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: 3.152→49.043 Å / Num. obs: 27025 / % possible obs: 95.3 % / Redundancy: 4.84 % / Rmerge(I) obs: 0.013 / Net I/σ(I): 11.43
Reflection shellResolution: 3.15→3.27 Å / Redundancy: 4.91 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 1.2 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→49.04 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1352 5 %
Rwork0.221 --
obs0.223 27022 95.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8384 0 36 34 8454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058586
X-RAY DIFFRACTIONf_angle_d0.94411579
X-RAY DIFFRACTIONf_dihedral_angle_d13.385277
X-RAY DIFFRACTIONf_chiral_restr0.1381257
X-RAY DIFFRACTIONf_plane_restr0.0061480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1522-3.26480.43611350.37682558X-RAY DIFFRACTION96
3.2648-3.39550.3551360.33612580X-RAY DIFFRACTION96
3.3955-3.550.30591350.30352566X-RAY DIFFRACTION96
3.55-3.73710.3651360.28112586X-RAY DIFFRACTION96
3.7371-3.97120.31281350.24862557X-RAY DIFFRACTION96
3.9712-4.27760.26791340.2122555X-RAY DIFFRACTION95
4.2776-4.70780.21831350.19442566X-RAY DIFFRACTION95
4.7078-5.38830.20891350.2012568X-RAY DIFFRACTION95
5.3883-6.78580.25251340.21342545X-RAY DIFFRACTION94
6.7858-49.04850.18791370.15622589X-RAY DIFFRACTION93
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)
11.2475-0.0896-0.25330.8027-0.03441.07010.0882-0.12550.1255-0.09450.03920.161-0.01690.0001-0.13020.39620.0053-0.050.4664-0.01380.4764115.072293.09612.1365
22.69280.0309-0.05063.1181-0.27982.5529-0.0562-0.1435-0.0818-0.36110.16310.89520.2657-0.3833-0.12670.5944-0.0563-0.1080.55610.10680.744597.08677.8674.3303
31.01010.026-0.52250.9683-0.16061.23830.2935-0.51510.09130.33160.01080.0528-0.08370.2886-0.22040.78540.0455-0.06390.87-0.21410.7695123.3276102.253225.6993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 5 THROUGH 841)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 1 THROUGH 160)
3X-RAY DIFFRACTION3(CHAIN 'D' AND RESID 35 THROUGH 129)

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