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- EMDB-34717: Cryo-EM structure of yeast Erf2/Erf4 complex -

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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 / cortical endoplasmic reticulum / palmitoyltransferase activity / perinuclear 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 / cortical endoplasmic reticulum / palmitoyltransferase activity / perinuclear 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: To Be Published
Title: Cryo-EM structure of Yeast Erf2/Erf4 complex
Authors: Wu J / Hu Q / Zhang Y / Liu S / Yang A
History
DepositionNov 10, 2022-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34717.png

Downloads & links

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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 °

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Supplemental data

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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)

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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)

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Sample components

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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

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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)

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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

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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

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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 / Palmitic acid

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Macromolecule #4: ZINC ION

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

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

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