[English] 日本語
Yorodumi
- EMDB-34717: Cryo-EM structure of yeast Erf2/Erf4 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34717
TitleCryo-EM structure of yeast Erf2/Erf4 complex
Map datathe yeast refined map
Sample
  • Complex: Erf2/Erf4 complex
    • Protein or peptide: Palmitoyltransferase ERF2
    • Protein or peptide: Ras modification protein ERF4
  • Ligand: PALMITIC ACID
  • Ligand: ZINC ION
Keywordspalmitoyltransferase / Saccaromyces cerevisiae / palmitoylation / RAS2 / TRANSFERASE
Function / homology
Function and homology information


endoplasmic reticulum palmitoyltransferase complex / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / protein targeting to membrane / Neutrophil degranulation / endoplasmic reticulum membrane ...endoplasmic reticulum palmitoyltransferase complex / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / perinuclear endoplasmic reticulum / cortical endoplasmic reticulum / protein targeting to membrane / Neutrophil degranulation / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
Golgin subfamily A member 7/ERF4 / Golgin subfamily A member 7/ERF4 family / Palmitoyltransferase, DHHC domain / DHHC palmitoyltransferase / DHHC domain profile.
Similarity search - Domain/homology
Ras modification protein ERF4 / Palmitoyltransferase ERF2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWu J / Hu Q / Zhang Y / Yang A / Liu S
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Regulation of RAS palmitoyltransferases by accessory proteins and palmitoylation.
Authors: Anlan Yang / Shengjie Liu / Yuqi Zhang / Jia Chen / Yujing Fan / Fengxiang Wang / Yilong Zou / Shan Feng / Jianping Wu / Qi Hu /
Abstract: Palmitoylation of cysteine residues at the C-terminal hypervariable regions in human HRAS and NRAS, which is necessary for RAS signaling, is catalyzed by the acyltransferase DHHC9 in complex with its ...Palmitoylation of cysteine residues at the C-terminal hypervariable regions in human HRAS and NRAS, which is necessary for RAS signaling, is catalyzed by the acyltransferase DHHC9 in complex with its accessory protein GCP16. The molecular basis for the acyltransferase activity and the regulation of DHHC9 by GCP16 is not clear. Here we report the cryo-electron microscopy structures of the human DHHC9-GCP16 complex and its yeast counterpart-the Erf2-Erf4 complex, demonstrating that GCP16 and Erf4 are not directly involved in the catalytic process but stabilize the architecture of DHHC9 and Erf2, respectively. We found that a phospholipid binding to an arginine-rich region of DHHC9 and palmitoylation on three residues (C24, C25 and C288) were essential for the catalytic activity of the DHHC9-GCP16 complex. Moreover, we showed that GCP16 also formed complexes with DHHC14 and DHHC18 to catalyze RAS palmitoylation. These findings provide insights into the regulatory mechanism of RAS palmitoyltransferases.
History
DepositionNov 10, 2022-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_34717.png

Downloads & links

-
Map

FileDownload / File: emd_34717.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe yeast refined map
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-5.843999 - 8.156653
Average (Standard dev.)0.0037406317 (±0.14511682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 208.70401 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map B

Fileemd_34717_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_34717_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Erf2/Erf4 complex

EntireName: Erf2/Erf4 complex
Components
  • Complex: Erf2/Erf4 complex
    • Protein or peptide: Palmitoyltransferase ERF2
    • Protein or peptide: Ras modification protein ERF4
  • Ligand: PALMITIC ACID
  • Ligand: ZINC ION

-
Supramolecule #1: Erf2/Erf4 complex

SupramoleculeName: Erf2/Erf4 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

-
Macromolecule #1: Palmitoyltransferase ERF2

MacromoleculeName: Palmitoyltransferase ERF2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein S-acyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 43.811672 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGHHHHHHHH HHHHGSDEVD AHMALVSRRS TRSESTSITK EEHTGEGSLT KLFFRWLVTL EGDQDINDGK GYISLPNVSN YIFFLGGRF RTVKGAKPLW LGVLLAIVCP MVLFSIFEAH KLWHTQNGYK VLVIFFYYFW VITLASFIRT ATSDPGVLPR N IHLSQLRN ...String:
MGHHHHHHHH HHHHGSDEVD AHMALVSRRS TRSESTSITK EEHTGEGSLT KLFFRWLVTL EGDQDINDGK GYISLPNVSN YIFFLGGRF RTVKGAKPLW LGVLLAIVCP MVLFSIFEAH KLWHTQNGYK VLVIFFYYFW VITLASFIRT ATSDPGVLPR N IHLSQLRN NYQIPQEYYN LITLPTHSSI SKDITIKYCP SCRIWRPPRS SHCSTCNVCV MVHDHHCIWV NNCIGKRNYR FF LIFLLGA ILSSVILLTN CAIHIARESG GPRDCPVAIL LLCYAGLTLW YPAILFTYHI FMAGNQQTTR EFLKGIGSKK NPV FHRVVK EENIYNKGSF LKNMGHLMLE PRGPSFVSAR KPHEAGDWRF MDLSPAHSFE KIQKI

UniProtKB: Palmitoyltransferase ERF2

-
Macromolecule #2: Ras modification protein ERF4

MacromoleculeName: Ras modification protein ERF4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 29.652705 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKG SDYKDDDDKG SDEVDAHMCD SHQKEEDNAN TSERALFFNY HEFSYSFYED LGSEDAKPTE HDEDHKLCIT HFPNVYAAR GSAEFQVTRV VRVPRRFDES RSSLETPQFS TQLPGSEPAA IVGDDGTSFV RCGRYDIGDH VFGCSSVSPL S EYLSAAEL ...String:
MDYKDDDDKG SDYKDDDDKG SDEVDAHMCD SHQKEEDNAN TSERALFFNY HEFSYSFYED LGSEDAKPTE HDEDHKLCIT HFPNVYAAR GSAEFQVTRV VRVPRRFDES RSSLETPQFS TQLPGSEPAA IVGDDGTSFV RCGRYDIGDH VFGCSSVSPL S EYLSAAEL AEVVHRVNGF LLREEGEVFG WRNLSGLLLD MLTGGLWSWV LGPLLSRPVF QESLALEQYV AQLNSPGGLL HE RGVRLVL PRRSGCLSLD FVVPRPK

UniProtKB: Ras modification protein ERF4

-
Macromolecule #3: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 3 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 191610
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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://pdbjlvh1.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