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- EMDB-28744: Cryo-EM consensus map of the S. cerevisiae Arf-like protein Arl1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-28744
TitleCryo-EM consensus map of the S. cerevisiae Arf-like protein Arl1 bound to the Arf guanine nucleotide exchange factor Gea2
Map data
Sample
  • Complex: Gea2 homodimer in complex with two Arl1 monomers
    • Protein or peptide: ARF guanine-nucleotide exchange factor 2
    • Protein or peptide: ADP-ribosylation factor-like protein 1
Keywordssmall GTPase / guanine nucleotide exchange factor / membrane trafficking / lipid flippase / trans-Golgi network / protein transport / LIPID TRANSPORT
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsDuan HD / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA231466 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural insight into an Arl1-ArfGEF complex involved in Golgi recruitment of a GRIP-domain golgin.
Authors: H Diessel Duan / Bhawik K Jain / Hua Li / Todd R Graham / Huilin Li /
Abstract: Arl1 is an Arf-like (Arl) GTP-binding protein that interacts with the guanine nucleotide exchange factor Gea2 to recruit the golgin Imh1 to the Golgi. The Arl1-Gea2 complex also binds and activates ...Arl1 is an Arf-like (Arl) GTP-binding protein that interacts with the guanine nucleotide exchange factor Gea2 to recruit the golgin Imh1 to the Golgi. The Arl1-Gea2 complex also binds and activates the phosphatidylserine flippase Drs2 and these functions may be related, although the underlying molecular mechanism is unclear. Here we report high-resolution cryo-EM structures of the full-length Gea2 and the Arl1-Gea2 complex. Gea2 is a large protein with 1459 residues and is composed of six domains (DCB, HUS, SEC7, HDS1-3). We show that Gea2 assembles a stable dimer via an extensive interface involving hydrophobic and electrostatic interactions in the DCB and HUS region. Contrary to the previous report on a Gea2 homolog in which Arl1 binds to the dimerization surface of the DCB domain, implying a disrupted dimer upon Arl1 binding, we find that Arl1 binds to the outside surface of the Gea2 DCB domain, leaving the Gea2 dimer intact. The interaction between Arl1 and Gea2 involves the classic FWY aromatic residue triad as well as two Arl1-specific residues. We show that key mutations that disrupt the Arl1-Gea2 interaction abrogate Imh1 Golgi association. This work clarifies the Arl1-Gea2 interaction and improves our understanding of molecular events in the membrane trafficking.
History
DepositionNov 1, 2022-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28744.png

Downloads & links

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Map

FileDownload / File: emd_28744.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 423.936 Å		0.83 Å/pix.
x 512 pix.
= 423.936 Å		0.83 Å/pix.
x 512 pix.
= 423.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.027672121 - 1.9048703
Average (Standard dev.)0.0006522556 (±0.016357344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 423.936 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28744_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_28744_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 : Gea2 homodimer in complex with two Arl1 monomers

EntireName: Gea2 homodimer in complex with two Arl1 monomers
Components
  • Complex: Gea2 homodimer in complex with two Arl1 monomers
    • Protein or peptide: ARF guanine-nucleotide exchange factor 2
    • Protein or peptide: ADP-ribosylation factor-like protein 1

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Supramolecule #1: Gea2 homodimer in complex with two Arl1 monomers

SupramoleculeName: Gea2 homodimer in complex with two Arl1 monomers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: ARF guanine-nucleotide exchange factor 2

MacromoleculeName: ARF guanine-nucleotide exchange factor 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHSSG VDLGTENLYF QSNAMSDREF VTVDPVTIII KECINLSTAM RKYSKFTSQS GVAALLGGGS EIFSNQDDYL AHTFNNLNT NKHNDPFLSG FIQLRLMLNK LKNLDNIDSL TILQPFLLIV STSSISGYIT SLALDSLQKF FTLNIINESS Q NYIGAHRA ...String:
MHHHHHHSSG VDLGTENLYF QSNAMSDREF VTVDPVTIII KECINLSTAM RKYSKFTSQS GVAALLGGGS EIFSNQDDYL AHTFNNLNT NKHNDPFLSG FIQLRLMLNK LKNLDNIDSL TILQPFLLIV STSSISGYIT SLALDSLQKF FTLNIINESS Q NYIGAHRA TVNALTHCRF EGSQQLSDDS VLLKVVFLLR SIVDSPYGDL LSNSIIYDVL QTILSLACNN RRSEVLRNAA QS TMIAVTV KIFSKLKTIE PVNVNQIYIN DESYTNDVLK ADTIGTNVES KEEGSQEDPI GMKVNNEEAI SEDDGIEEEH IHS EKSTNG AEQLDIVQKT TRSNSRIQAY ADDNYGLPVV RQYLNLLLSL IAPENELKHS YSTRIFGLEL IQTALEISGD RLQL YPRLF TLISDPIFKS ILFIIQNTTK LSLLQATLQL FTTLVVILGN NLQLQIELTL TRIFSILLDD GTANNSSSEN KNKPS IIKE LLIEQISILW TRSPSFFTST FINFDCNLDR ADVSINFLKA LTKLALPESA LTTTESVPPI CLEGLVSLVD DMFDHM KDI DREEFGRQKN EMEILKKRDR KTEFIECTNA FNEKPKKGIP MLIEKGFIAS DSDKDIAEFL FNNNNRMNKK TIGLLLC HP DKVSLLNEYI RLFDFSGLRV DEAIRILLTK FRLPGESQQI ERIIEAFSSA YCENQDYDPS KISDNAEDDI STVQPDAD S VFILSYSIIM LNTDLHNPQV KEHMSFEDYS GNLKGCCNHK DFPFWYLDRI YCSIRDKEIV MPEEHHGNEK WFEDAWNNL ISSTTVITEI KKDTQSVMDK LTPLELLNFD RAIFKQVGPS IVSTLFNIYV VASDDHISTR MITSLDKCSY ISAFFDFKDL FNDILNSIA KGTTLINSSH DDELSTLAFE YGPMPLVQIK FEDTNTEIPV STDAVRFGRS FKGQLNTVVF FRIIRRNKDP K IFSKELWL NIVNIILTLY EDLILSPDIF PDLQKRLKLS NLPKPSPEIS INKSKESKGL LSTFASYLKG DEEPTEEEIK SS KKAMECI KSSNIAASVF GNESNITADL IKTLLDSAKT EKNADNSRYF EAELLFIIEL TIALFLFCKE EKELGKFILQ KVF QLSHTK GLTKRTVRRM LTYKILLISL CADQTEYLSK LINDELLKKG DIFTQKFFAT NQGKEFLKRL FSLTESEFYR GFLL GNENF WKFLRKVTAM KEQSESIFEY LNESIKTDSN ILTNENFMWV LGLLDEISSM GAVGNHWEIE YKKLTESGHK IDKEN PYKK SIELSLKSIQ LTSHLLEDNN DLRKNEIFAI IQALAHQCIN PCKQISEFAV VTLEQTLINK IEIPTNEMES VEELIE GGL LPLLNSSETQ EDQKILISSI LTIISNVYLH YLKLGKTSNE TFLKILSIFN KFVEDSDIEK KLQQLILDKK SIEKGNG SS SHGSAHEQTP ESNDVEIEAT APIDDNTDDD NKPKLSDVEK D

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Macromolecule #2: ADP-ribosylation factor-like protein 1

MacromoleculeName: ADP-ribosylation factor-like protein 1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ELRILILGLD GAGKTTILYR LQIGEVVTTK PTIGFNVETL SYKNLKLNVW DLGGLTSIRP YWRCYYADTA AVIFVVDSTD KDRMSTASK ELHLMLQEEE LQDAALLVFA NKQDQPGALS ASEVSKELNL VELKDRSWSI VASSAIKGEG ITEGLDWLID V IKEEQLAG ENLYFQSAGH HHHHH

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 69.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / Details: PDB 5EE5 was also used as a startup model.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 712548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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