[English] 日本語
Yorodumi
- EMDB-23110: Cryo-EM structure of S. Pombe NatC complex with a Bisubstrate inh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23110
TitleCryo-EM structure of S. Pombe NatC complex with a Bisubstrate inhibitor and inositol hexaphosphate
Map dataNatC complex with a Bisubstrate inhibitor and inositol hexaphosphate
Sample
  • Complex: heterotimeric S.pombe NatC complex with a bisubstrate inhibitor and inositol hexaphosphate
    • Complex: N-alpha-acetyltransferase NatC, catalytic subunit NAA30, auxiliary subunits NAA35 and NAA38
      • Protein or peptide: N-alpha-acetyltransferase 30
      • Protein or peptide: N-alpha-acetyltransferase 35, NatC auxiliary subunit
      • Protein or peptide: N-alpha-acetyltransferase 38, NatC auxiliary subunit
    • Complex: CoA-Ac-MLGP bi-substrate
      • Protein or peptide: MLGP peptide
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid
  • Ligand: CARBOXYMETHYL COENZYME *A
Function / homology
Function and homology information


N-terminal methionine Nalpha-acetyltransferase NatC / NatC complex / N-terminal peptidyl-methionine acetylation / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / membrane => GO:0016020 / endoplasmic reticulum membrane / endoplasmic reticulum / nucleus / cytosol
Similarity search - Function
LSM domain containing 1 / -alpha-acetyltransferase 35, NatC auxiliary subunit / N-alpha-acetyltransferase 30-like / Mak10 subunit, NatC N(alpha)-terminal acetyltransferase / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / LSM domain superfamily / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. ...LSM domain containing 1 / -alpha-acetyltransferase 35, NatC auxiliary subunit / N-alpha-acetyltransferase 30-like / Mak10 subunit, NatC N(alpha)-terminal acetyltransferase / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / LSM domain superfamily / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
N-alpha-acetyltransferase 38, NatC auxiliary subunit / N-alpha-acetyltransferase 30 / N-alpha-acetyltransferase 35, NatC auxiliary subunit
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast) / Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsDeng S / Marmorstein R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118090 United States
CitationJournal: Structure / Year: 2021
Title: Molecular mechanism of N-terminal acetylation by the ternary NatC complex.
Authors: Sunbin Deng / Leah Gottlieb / Buyan Pan / Julianna Supplee / Xuepeng Wei / E James Petersson / Ronen Marmorstein /
Abstract: Protein N-terminal acetylation is predominantly a ribosome-associated modification, with NatA-E serving as the major enzymes. NatC is the most unusual of these enzymes, containing one Naa30 catalytic ...Protein N-terminal acetylation is predominantly a ribosome-associated modification, with NatA-E serving as the major enzymes. NatC is the most unusual of these enzymes, containing one Naa30 catalytic subunit and two auxiliary subunits, Naa35 and Naa38; and substrate selectivity profile that overlaps with NatE. Here, we report the cryoelectron microscopy structure of S. pombe NatC with a NatE/C-type bisubstrate analog and inositol hexaphosphate (IP), and associated biochemistry studies. We find that the presence of three subunits is a prerequisite for normal NatC acetylation activity in yeast and that IP binds tightly to NatC to stabilize the complex. We also describe the molecular basis for IP-mediated NatC complex stabilization and the overlapping yet distinct substrate profiles of NatC and NatE.
History
DepositionDec 14, 2020-
Header (metadata) releaseMay 12, 2021-
Map releaseMay 12, 2021-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7l1k
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23110.png

Downloads & links

-
Map

FileDownload / File: emd_23110.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNatC complex with a Bisubstrate inhibitor and inositol hexaphosphate
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.252 / Movie #1: 0.45
Minimum - Maximum-1.4852304 - 2.416325
Average (Standard dev.)0.0013826761 (±0.11161481)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 168.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z168.000168.000168.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-1.4852.4160.001

-
Supplemental data

-
Mask #1

Fileemd_23110_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: NatC complex with a Bisubstrate inhibitor and inositol hexaphosphate

Fileemd_23110_half_map_1.map
AnnotationNatC complex with a Bisubstrate inhibitor and inositol hexaphosphate
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: NatC complex with a Bisubstrate inhibitor and inositol hexaphosphate

Fileemd_23110_half_map_2.map
AnnotationNatC complex with a Bisubstrate inhibitor and inositol hexaphosphate
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : heterotimeric S.pombe NatC complex with a bisubstrate inhibitor a...

EntireName: heterotimeric S.pombe NatC complex with a bisubstrate inhibitor and inositol hexaphosphate
Components
  • Complex: heterotimeric S.pombe NatC complex with a bisubstrate inhibitor and inositol hexaphosphate
    • Complex: N-alpha-acetyltransferase NatC, catalytic subunit NAA30, auxiliary subunits NAA35 and NAA38
      • Protein or peptide: N-alpha-acetyltransferase 30
      • Protein or peptide: N-alpha-acetyltransferase 35, NatC auxiliary subunit
      • Protein or peptide: N-alpha-acetyltransferase 38, NatC auxiliary subunit
    • Complex: CoA-Ac-MLGP bi-substrate
      • Protein or peptide: MLGP peptide
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid
  • Ligand: CARBOXYMETHYL COENZYME *A

-
Supramolecule #1: heterotimeric S.pombe NatC complex with a bisubstrate inhibitor a...

SupramoleculeName: heterotimeric S.pombe NatC complex with a bisubstrate inhibitor and inositol hexaphosphate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

-
Supramolecule #2: N-alpha-acetyltransferase NatC, catalytic subunit NAA30, auxiliar...

SupramoleculeName: N-alpha-acetyltransferase NatC, catalytic subunit NAA30, auxiliary subunits NAA35 and NAA38
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Supramolecule #3: CoA-Ac-MLGP bi-substrate

SupramoleculeName: CoA-Ac-MLGP bi-substrate / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4

-
Macromolecule #1: N-alpha-acetyltransferase 30

MacromoleculeName: N-alpha-acetyltransferase 30 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: N-terminal methionine Nalpha-acetyltransferase NatC
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 17.72135 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVTIVPYSHQ YLKDICQLIQ KDLSEPYSKY VYRYFVHQWP EFSFVALDND RFIGAVICKQ DVHRGTTLRG YIAMLAIVKE YRGQGIATK LTQASLDVMK NRGAQEIVLE TEVDNEAAMS FYERLGFCRY KRLYRYYLNG TDAFRYILYP N

-
Macromolecule #2: N-alpha-acetyltransferase 35, NatC auxiliary subunit

MacromoleculeName: N-alpha-acetyltransferase 35, NatC auxiliary subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 80.541312 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVKESLSLL NSMQGNVKIG NVEPAKGNEG YVDNAGYVDC TKSYFEATKS LKEEQLVCDP KFTLLDSISA FEIMEPKMDS GIDYQPLRV DFSRDLSYLE ILALMDLIVS AEKEWHYGSP LSESLLCSAH VFSICKSPIS QVGDSGFSSG SGRNTTDIVL F PFVLAVIK ...String:
MSVKESLSLL NSMQGNVKIG NVEPAKGNEG YVDNAGYVDC TKSYFEATKS LKEEQLVCDP KFTLLDSISA FEIMEPKMDS GIDYQPLRV DFSRDLSYLE ILALMDLIVS AEKEWHYGSP LSESLLCSAH VFSICKSPIS QVGDSGFSSG SGRNTTDIVL F PFVLAVIK CCDIVHREFL MGNLYDEEDI SSFSYHMSFL QNYPIEKLNY LLQSSIEYLA SEVIKFSAEL RQIIEGILNR IQ LRIGILR VYERSDIKTT IDALHLIKNL VPEIQNTVSV VDSSIKESIL KQYWDFRVQA QLVATAPVRN IPPTGIEHSY QRI LYFADD MLLILNSHTL ASSLAVYQFC LDFTRLNRTP EPYVRSSLQA LITANNAVNL RDQPTSYMLE CIREFSGLPS NFYN PNTRT VIEKNSISSA YGPLVESLIA HSTNIMVDLV RICSHNPCRF RRNLINLLPE ITVAHFEAEA LDLKFVAKSL PSNGP FSSF IYHVKLNAIE HILLSSFEQK LHQPYQWPHF FAVLDHVFSI HQTHLELHGK DRNTPPMAKT FVTYLHRILN AIKETY SGY LLLTVLCMRL NIIKTPSFTL DEKIQESYYM AHYRPLINLR QPKPLLRSEA DCIIKNLQNF STDDLIIKSN EKFTAAK NS LINVIKSGFE QNEFINPYFL QTNYLKNLLC CCITNLVSLA ILSKDHSANL KIVEIPGNPL PSLSRT

-
Macromolecule #3: N-alpha-acetyltransferase 38, NatC auxiliary subunit

MacromoleculeName: N-alpha-acetyltransferase 38, NatC auxiliary subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 13.258555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALHYFLQYD VQILCIALMF SIFRVCISTA IDFTSPKLDE FSLIMEMGEI LLTSWLNRSV HIEIFDERKF IGKFLCTDRE GAAILSNTT EYNKGFSRAL GLVVIPGKHI KSFSVRA

-
Macromolecule #4: MLGP peptide

MacromoleculeName: MLGP peptide / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 416.535 Da
SequenceString:
MLGP

-
Macromolecule #5: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

-
Macromolecule #6: CARBOXYMETHYL COENZYME *A

MacromoleculeName: CARBOXYMETHYL COENZYME *A / type: ligand / ID: 6 / Number of copies: 1 / Formula: CMC
Molecular weightTheoretical: 825.57 Da
Chemical component information

ChemComp-CMC:
CARBOXYMETHYL COENZYME *A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
200.0 mMNaClSodium chloridesodium cloride
25.0 mMHepes4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
1.0 mMDTTDithiothreitol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 (6k x 4k) / #0 - Average electron dose: 1.6 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Average electron dose: 1.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 3289528
CTF correctionSoftware - Name: CTFFIND
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v2)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. v2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v2)
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2) / Number images used: 607131
Details5397 images
Image recording ID1

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7l1k:
Cryo-EM structure of S. Pombe NatC complex with a Bisubstrate inhibitor and inositol hexaphosphate

+
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