[English] 日本語
Yorodumi
- PDB-6wf5: Crystal structure of human Naa50 in complex with a truncated cofa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wf5
TitleCrystal structure of human Naa50 in complex with a truncated cofactor derived inhibitor (compound 2)
Components
  • ACE-MET-LEU-GLY-PRO-NH2
  • N-alpha-acetyltransferase 50
KeywordsTRANSFERASE/INHIBITOR / N-alpha-acetyltransferase 50 / Inhibitor complex / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / protein-lysine-acetyltransferase activity ...mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / protein-lysine-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / post-translational protein modification / nucleolus / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-U44 / N-alpha-acetyltransferase 50
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.04 Å
AuthorsGreasley, S.E. / Feng, J. / Deng, Y.-L. / Stewart, A.E.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Characterization of SpecificN-alpha-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library.
Authors: Kung, P.P. / Bingham, P. / Burke, B.J. / Chen, Q. / Cheng, X. / Deng, Y.L. / Dou, D. / Feng, J. / Gallego, G.M. / Gehring, M.R. / Grant, S.K. / Greasley, S. / Harris, A.R. / Maegley, K.A. / ...Authors: Kung, P.P. / Bingham, P. / Burke, B.J. / Chen, Q. / Cheng, X. / Deng, Y.L. / Dou, D. / Feng, J. / Gallego, G.M. / Gehring, M.R. / Grant, S.K. / Greasley, S. / Harris, A.R. / Maegley, K.A. / Meier, J. / Meng, X. / Montano, J.L. / Morgan, B.A. / Naughton, B.S. / Palde, P.B. / Paul, T.A. / Richardson, P. / Sakata, S. / Shaginian, A. / Sonnenburg, W.K. / Subramanyam, C. / Timofeevski, S. / Wan, J. / Yan, W. / Stewart, A.E.
History
DepositionApr 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N-alpha-acetyltransferase 50
B: N-alpha-acetyltransferase 50
C: ACE-MET-LEU-GLY-PRO-NH2
D: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5496
Polymers40,0244
Non-polymers5252
Water1,76598
1
A: N-alpha-acetyltransferase 50
C: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2743
Polymers20,0122
Non-polymers2621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-9 kcal/mol
Surface area9950 Å2
MethodPISA
2
B: N-alpha-acetyltransferase 50
D: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2743
Polymers20,0122
Non-polymers2621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-9 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.937, 52.339, 64.123
Angle α, β, γ (deg.)90.000, 97.380, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein N-alpha-acetyltransferase 50 / hNaa50p / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog ...hNaa50p / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog / hSAN / N-epsilon-acetyltransferase 50 / NatE catalytic subunit / Naa50


Mass: 19571.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA50, MAK3, NAT13, NAT5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GZZ1, N-terminal methionine Nalpha-acetyltransferase NatE, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide ACE-MET-LEU-GLY-PRO-NH2


Mass: 440.581 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-U44 / (2R)-2-hydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide


Mass: 262.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H22N2O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 286.15 K / Method: vapor diffusion, sitting drop
Details: Co-crystallization: Naa50 apo protein (14.3 mg/ml) was incubated with compound 2 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) ...Details: Co-crystallization: Naa50 apo protein (14.3 mg/ml) was incubated with compound 2 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein:ligand complex

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→63.59 Å / Num. obs: 21247 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.126 / Net I/σ(I): 7.9
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.723 / Num. unique obs: 3080 / CC1/2: 0.667 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
autoPROCdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6WF3

6wf3


Resolution: 2.04→50.52 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.846 / SU R Cruickshank DPI: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.237 / SU Rfree Blow DPI: 0.201 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1023 4.82 %RANDOM
Rwork0.222 ---
obs0.224 21219 98.6 %-
Displacement parametersBiso max: 111.48 Å2 / Biso mean: 35.3 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1--16.7048 Å20 Å2-6.558 Å2
2--5.5496 Å20 Å2
3---11.1552 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.04→50.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 96 98 2815
Biso mean--31.86 35.9 -
Num. residues----324
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d960SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes392HARMONIC5
X-RAY DIFFRACTIONt_it2766HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion345SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3152SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2766HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3730HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion19.13
LS refinement shellResolution: 2.04→2.14 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.292 142 5.14 %
Rwork0.245 2619 -
all0.247 2761 -
obs--97.55 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more