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- EMDB-49743: Get3(D57N)-Get4/5 Complex (ATP-bound) -

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Basic information

Entry
Database: EMDB / ID: EMD-49743
TitleGet3(D57N)-Get4/5 Complex (ATP-bound)
Map data
Sample
  • Complex: Get3D(D57N)-Get4/5 Complex
    • Protein or peptide: Ubiquitin-like protein MDY2
    • Protein or peptide: ATPase GET3
    • Protein or peptide: Golgi to ER traffic protein 4
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsmembrane protein targeting / ATPase / chaperone / protein complex
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / GET complex / TRC complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...cell morphogenesis involved in conjugation with cellular fusion / GET complex / TRC complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / vesicle-mediated transport / protein folding chaperone / guanyl-nucleotide exchange factor activity / cytoplasmic stress granule / unfolded protein binding / response to heat / cellular response to oxidative stress / protein-macromolecule adaptor activity / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / : / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain ...Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / : / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Golgi to ER traffic protein 4 / ATPase GET3 / Ubiquitin-like protein MDY2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsKim KH / Granados-Villanueva D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J Biol Chem / Year: 2025
Title: Get4/5-mediated remodeling of Get3's substrate-binding chamber: Insights into tail-anchored protein targeting by the GET pathway.
Authors: Diego Granados-Villanueva / Andrew Rossow / Kelly H Kim /
Abstract: The Guided Entry of Tail-Anchored Proteins (GET) pathway ensures accurate targeting of Tail-Anchored proteins (TAs)-a diverse class of membrane proteins-to the endoplasmic reticulum (ER) membrane. In ...The Guided Entry of Tail-Anchored Proteins (GET) pathway ensures accurate targeting of Tail-Anchored proteins (TAs)-a diverse class of membrane proteins-to the endoplasmic reticulum (ER) membrane. In yeast, newly synthesized TAs are captured by Sgt2 and transferred to Get3 for delivery to the ER, where they undergo subsequent membrane insertion. Efficient and protected handoff of hydrophobic TAs from Sgt2 to Get3 is facilitated by the Get4/5 complex, which is thought to act as a scaffold to position TA-bound Sgt2 and Get3 in proximity while trapping Get3 in an ATP-bound conformation necessary for TA binding. To define the molecular basis for this process, we determined the cryo-EM structure of the Saccharomyces cerevisiae Get3-Get4/5 complex at 3.2 Å resolution. Our structure shows that Get4/5 remodels Get3's TA-binding chamber by unfolding helices that form the lateral walls of the chamber. We termed this region the "lateral gate," as its helix-to-coil transition makes the TA-binding chamber more solvent accessible. Molecular dynamics simulations highlighted the flexibility of the lateral gate, indicating it is structurally dynamic and prone to conformational changes. Mutagenesis studies showed that the lateral gate residues influence both the binding affinity of Get3 for Get4/5 and its ATPase activity. Additionally, our cryo-EM map shows that the Sgt2-binding domain of Get5 is positioned near the lateral gate opening of Get3's TA-binding chamber. Based on these findings, we propose a model in which Get4/5 opens Get3's TA-binding chamber to form a lateral opening, enabling protected, lateral transfer of TAs from Sgt2 to Get3.
History
DepositionMar 15, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49743.png

Downloads & links

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Map

FileDownload / File: emd_49743.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 320 pix.
= 324. Å		1.01 Å/pix.
x 320 pix.
= 324. Å		1.01 Å/pix.
x 320 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.6336108 - 1.3087236
Average (Standard dev.)0.0008735353 (±0.018958474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49743_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49743_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Get3D(D57N)-Get4/5 Complex

EntireName: Get3D(D57N)-Get4/5 Complex
Components
  • Complex: Get3D(D57N)-Get4/5 Complex
    • Protein or peptide: Ubiquitin-like protein MDY2
    • Protein or peptide: ATPase GET3
    • Protein or peptide: Golgi to ER traffic protein 4
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Get3D(D57N)-Get4/5 Complex

SupramoleculeName: Get3D(D57N)-Get4/5 Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: Ubiquitin-like protein MDY2

MacromoleculeName: Ubiquitin-like protein MDY2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 23.768344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSTSASGPEH EFVSKFLTLA TLTEPKLPKS YTKPLKDVTN LGVPLPTLKY KYKQNRAKKL KLHQDQQGQD NAAVHLTLKK IQAPKFSIE HDFSPSDTIL QIKQHLISEE KASHISEIKL LLKGKVLHDN LFLSDLKVTP ANSTITVMIK PNPTISKEPE A EKSTNSPA ...String:
MSTSASGPEH EFVSKFLTLA TLTEPKLPKS YTKPLKDVTN LGVPLPTLKY KYKQNRAKKL KLHQDQQGQD NAAVHLTLKK IQAPKFSIE HDFSPSDTIL QIKQHLISEE KASHISEIKL LLKGKVLHDN LFLSDLKVTP ANSTITVMIK PNPTISKEPE A EKSTNSPA PAPPQELTVP WDDIEALLKN NFENDQAAVR QVMERLQKGW SLAK

UniProtKB: Ubiquitin-like protein MDY2

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Macromolecule #2: ATPase GET3

MacromoleculeName: ATPase GET3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 41.936328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGENLYFQG HMMDLTVEPN LHSLITSTTH KWIFVGGKGG VGKTTSSCSI AIQMALSQPN KQFLLISTNP AHNLSDAFG EKFGKDARKV TGMNNLSCME IDPSAALKDM NDMAVSRANN NGSDGQGDDL GSLLQGGALA DLTGSIPGID E ALSFMEVM ...String:
MGSSHHHHHH SSGENLYFQG HMMDLTVEPN LHSLITSTTH KWIFVGGKGG VGKTTSSCSI AIQMALSQPN KQFLLISTNP AHNLSDAFG EKFGKDARKV TGMNNLSCME IDPSAALKDM NDMAVSRANN NGSDGQGDDL GSLLQGGALA DLTGSIPGID E ALSFMEVM KHIKRQEQGE GETFDTVIFD TAPTGHTLRF LQLPNTLSKL LEKFGEITNK LGPMLNSFMG AGNVDISGKL NE LKANVET IRQQFTDPDL TTFVCVCISE FLSLYETERL IQELISYDMD VNSIIVNQLL FAENDQEHNC KRCQARWKMQ KKY LDQIDE LYEDFHVVKM PLCAGEIRGL NNLTKFSQFL NKEYNPITDG KVIYELEDKE

UniProtKB: ATPase GET3

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Macromolecule #3: Golgi to ER traffic protein 4

MacromoleculeName: Golgi to ER traffic protein 4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 38.604445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVPAESNAVQ AKLAKTLQRF ENKIKAGDYY EAHQTLRTIA NRYVRSKSYE HAIELISQGA LSFLKAKQGG SGTDLIFYLL EVYDLAEVK VDDISVARLV RLIAELDPSE PNLKDVITGM NNWSIKFSEY KFGDPYLHNT IGSKLLEGDF VYEAERYFML G THDSMIKY ...String:
MVPAESNAVQ AKLAKTLQRF ENKIKAGDYY EAHQTLRTIA NRYVRSKSYE HAIELISQGA LSFLKAKQGG SGTDLIFYLL EVYDLAEVK VDDISVARLV RLIAELDPSE PNLKDVITGM NNWSIKFSEY KFGDPYLHNT IGSKLLEGDF VYEAERYFML G THDSMIKY VDLLWDWLCQ VDDIEDSTVA EFFSRLVFNY LFISNISFAH ESKDIFLERF IEKFHPKYEK IDKNGYEIVF FE DYSDLNF LQLLLITCQT KDKSYFLNLK NHYLDFSQAY KSELEFLGQE YFNIVAPKQT NFLQDMMSGF LGGSKSGGGG GEN LYFQGG SSHHHHHH

UniProtKB: Golgi to ER traffic protein 4

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 149868
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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