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- EMDB-13206: Tetrameric building block of the human GID complex. -

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Entry
Database: EMDB / ID: EMD-13206
TitleTetrameric building block of the human GID complex.
Map dataPostprocessed map of the four building blocks of the tetrameric hGID complex, consisting of WDR26, RanBP9, TWA1, and MAEA or RMND5A.
Sample
  • Complex: hGID
    • Protein or peptide: RanBP9
    • Protein or peptide: WDR26
    • Protein or peptide: Twa1
    • Protein or peptide: MAEA
    • Protein or peptide: RMND5A
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsMohamed WI / Park SL / Rabl J / Leitner A / Boehringer D / Peter M
Funding supportEuropean Union, Switzerland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)ITN network grantEuropean Union
Swiss National Science Foundation Switzerland
Citation
Journal: EMBO Rep / Year: 2021
Title: The human GID complex engages two independent modules for substrate recruitment.
Authors: Weaam I Mohamed / Sophia L Park / Julius Rabl / Alexander Leitner / Daniel Boehringer / Matthias Peter /
Abstract: The human GID (hGID) complex is a conserved E3 ubiquitin ligase regulating diverse biological processes, including glucose metabolism and cell cycle progression. However, the biochemical function and ...The human GID (hGID) complex is a conserved E3 ubiquitin ligase regulating diverse biological processes, including glucose metabolism and cell cycle progression. However, the biochemical function and substrate recognition of the multi-subunit complex remain poorly understood. Using biochemical assays, cross-linking mass spectrometry, and cryo-electron microscopy, we show that hGID engages two distinct modules for substrate recruitment, dependent on either WDR26 or GID4. WDR26 and RanBP9 cooperate to ubiquitinate HBP1 in vitro, while GID4 is dispensable for this reaction. In contrast, GID4 functions as an adaptor for the substrate ZMYND19, which surprisingly lacks a Pro/N-end degron. GID4 substrate binding and ligase activity is regulated by ARMC8α, while the shorter ARMC8β isoform assembles into a stable hGID complex that is unable to recruit GID4. Cryo-EM reconstructions of these hGID complexes reveal the localization of WDR26 within a ring-like, tetrameric architecture and suggest that GID4 and WDR26/Gid7 utilize different, non-overlapping binding sites. Together, these data advance our mechanistic understanding of how the hGID complex recruits cognate substrates and provides insights into the regulation of its E3 ligase activity.
#1: Journal: Biorxiv / Year: 2021
Title: The human GID complex engages two independent modules for substrate recruitment
Authors: Mohamed WI / Park SL / Rabl J / Leitner A / Boehringer D / Peter M
History
DepositionJul 15, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13206.png

Downloads & links

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Map

FileDownload / File: emd_13206.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of the four building blocks of the tetrameric hGID complex, consisting of WDR26, RanBP9, TWA1, and MAEA or RMND5A.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.36 Å/pix.
x 180 pix.
= 604.8 Å		3.36 Å/pix.
x 180 pix.
= 604.8 Å		3.36 Å/pix.
x 180 pix.
= 604.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.09197822 - 0.3189951
Average (Standard dev.)0.00025773348 (±0.0050042705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 604.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.363.363.36
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z604.800604.800604.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0920.3190.000

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Supplemental data

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Mask #1

Fileemd_13206_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_13206_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13206_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13206_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : hGID

EntireName: hGID
Components
  • Complex: hGID
    • Protein or peptide: RanBP9
    • Protein or peptide: WDR26
    • Protein or peptide: Twa1
    • Protein or peptide: MAEA
    • Protein or peptide: RMND5A

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Supramolecule #1: hGID

SupramoleculeName: hGID / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Complex of subunits WDR26, RanBP9, TWA1, MAEA, and RMND5A. The map contains one subunit of WDR26, RanBP9, TWA1, and one subunit of MAEA or RMND5A.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: Sf9 / Recombinant cell: Sf9

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Macromolecule #1: RanBP9

MacromoleculeName: RanBP9 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDWSHPQFEK SAVDENLYFQ GGGRMSGQPP PPPPQQQQQQ QQLSPPPPAA LAPVSGVVLP APPAVSAGSS PAGSPGGGAG GEGLGAAAAA LLLHPPPPPP PATAAPPPPP PPPPPPASAA APASGPPAPP GLAAGPGPAG GAPTPALVAG SSAAAPFPHG DSALNEQEKE ...String:
MDWSHPQFEK SAVDENLYFQ GGGRMSGQPP PPPPQQQQQQ QQLSPPPPAA LAPVSGVVLP APPAVSAGSS PAGSPGGGAG GEGLGAAAAA LLLHPPPPPP PATAAPPPPP PPPPPPASAA APASGPPAPP GLAAGPGPAG GAPTPALVAG SSAAAPFPHG DSALNEQEKE LQRRLKRLYP AVDEQETPLP RSWSPKDKFS YIGLSQNNLR VHYKGHGKTP KDAASVRATH PIPAACGIYY FEVKIVSKGR DGYMGIGLSA QGVNMNRLPG WDKHSYGYHG DDGHSFCSSG TGQPYGPTFT TGDVIGCCVN LINNTCFYTK NGHSLGIAFT DLPPNLYPTV GLQTPGEVVD ANFGQHPFVF DIEDYMREWR TKIQAQIDRF PIGDREGEWQ TMIQKMVSSY LVHHGYCATA EAFARSTDQT VLEELASIKN RQRIQKLVLA GRMGEAIETT QQLYPSLLER NPNLLFTLKV RQFIEMVNGT DSEVRCLGGR SPKSQDSYPV SPRPFSSPSM SPSHGMNIHN LASGKGSTAH FSGFESCSNG VISNKAHQSY CHSNKHQSSN LNVPELNSIN MSRSQQVNNF TSNDVDMETD HYSNGVGETS SNGFLNGSSK HDHEMEDCDT EMEVDSSQLR RQLCGGSQAA IERMIHFGRE LQAMSEQLRR DCGKNTANKK MLKDAFSLLA YSDPWNSPVG NQLDPIQREP VCSALNSAIL ETHNLPKQPP LALAMGQATQ CLGLMARSGI GSCAFATVED YLH

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Macromolecule #2: WDR26

MacromoleculeName: WDR26 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGGRSQSDED VIRLIGQHLN GLGLNQTVDL LMQESGCRLE HPSATKFRNH VMEGDWDKAE NDLNELKPLV HSPHAIVVRG ALEISQTLLG IIVRMKFLLL QQKYLEYLED GKVLEALQVL RCELTPLKYN TERIHVLSGY LMCSHAEDLR ...String:
MGSSHHHHHH SAVDENLYFQ GGGRSQSDED VIRLIGQHLN GLGLNQTVDL LMQESGCRLE HPSATKFRNH VMEGDWDKAE NDLNELKPLV HSPHAIVVRG ALEISQTLLG IIVRMKFLLL QQKYLEYLED GKVLEALQVL RCELTPLKYN TERIHVLSGY LMCSHAEDLR AKAEWEGKGT ASRSKLLDKL QTYLPPSVML PPRRLQTLLR QAVELQRDRC LYHNTKLDNN LDSVSLLIDH VCSRRQFPCY TQQILTEHCN EVWFCKFSND GTKLATGSKD TTVIIWQVDP DTHLLKLLKT LEGHAYGVSY IAWSPDDNYL VACGPDDCSE LWLWNVQTGE LRTKMSQSHE DSLTSVAWNP DGKRFVTGGQ RGQFYQCDLD GNLLDSWEGV RVQCLWCLSD GKTVLASDTH QRIRGYNFED LTDRNIVQED HPIMSFTISK NGRLALLNVA TQGVHLWDLQ DRVLVRKYQG VTQGFYTIHS CFGGHNEDFI ASGSEDHKVY IWHKRSELPI AELTGHTRTV NCVSWNPQIP SMMASASDDG TVRIWGPAPF IDHQNIEEEC SSMDS

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Macromolecule #3: Twa1

MacromoleculeName: Twa1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGGRMSYAEK PDEITKDEWM EKLNNLHVQR ADMNRLIMNY LVTEGFKEAA EKFRMESGIE PSVDLETLDE RIKIREMILK GQIQEAIALI NSLHPELLDT NRYLYFHLQQ QHLIELIRQR ETEAALEFAQ TQLAEQGEES RECLTEMERT ...String:
MGSSHHHHHH SAVDENLYFQ GGGRMSYAEK PDEITKDEWM EKLNNLHVQR ADMNRLIMNY LVTEGFKEAA EKFRMESGIE PSVDLETLDE RIKIREMILK GQIQEAIALI NSLHPELLDT NRYLYFHLQQ QHLIELIRQR ETEAALEFAQ TQLAEQGEES RECLTEMERT LALLAFDSPE ESPFGDLLHT MQRQKVWSEV NQAVLDYENR ESTPKLAKLL KLLLWAQNEL DQKKVKYPKM TDLSKGVIEE PK

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Macromolecule #4: MAEA

MacromoleculeName: MAEA / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKS AVDENLYFQG GGRMAVQESA AQLSMTLKVQ EYPTLKVPYE TLNKRFRAAQ KNIDRETSHV TMVVAELEKT LSGCPAVDSV VSLLDGVVEK LSVLKRKAVE SIQAEDESAK LCKRRIEHLK EHSSDQPAAA SVWKRKRMDR MMVEHLLRCG YYNTAVKLAR ...String:
MDYKDDDDKS AVDENLYFQG GGRMAVQESA AQLSMTLKVQ EYPTLKVPYE TLNKRFRAAQ KNIDRETSHV TMVVAELEKT LSGCPAVDSV VSLLDGVVEK LSVLKRKAVE SIQAEDESAK LCKRRIEHLK EHSSDQPAAA SVWKRKRMDR MMVEHLLRCG YYNTAVKLAR QSGIEDLVNI EMFLTAKEVE ESLERRETAT CLAWCHDNKS RLRKMKSCLE FSLRIQEFIE LIRQNKRLDA VRHARKHFSQ AEGSQLDEVR QAMGMLAFPP DTHISPYKDL LDPARWRMLI QQFRYDNYRL HQLGNNSVFT LTLQAGLSAI KTPQCYKEDG SSKSPDCPVC SRSLNKLAQP LPMAHCANSR LVCKISGDVM NENNPPMMLP NGYVYGYNSL LSIRQDDKVV CPRTKEVFHF SQAEKVYIM

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Macromolecule #5: RMND5A

MacromoleculeName: RMND5A / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGGRMDQCVT VERELEKVLH KFSGYGQLCE RGLEELIDYT GGLKHEILQS HGQDAELSGT LSLVLTQCCK RIKDTVQKLA SDHKDIHSSV SRVGKAIDKN FDSDISSVGI DGCWQADSQR LLNEVMVEHF FRQGMLDVAE ELCQESGLSV ...String:
MGSSHHHHHH SAVDENLYFQ GGGRMDQCVT VERELEKVLH KFSGYGQLCE RGLEELIDYT GGLKHEILQS HGQDAELSGT LSLVLTQCCK RIKDTVQKLA SDHKDIHSSV SRVGKAIDKN FDSDISSVGI DGCWQADSQR LLNEVMVEHF FRQGMLDVAE ELCQESGLSV DPSQKEPFVE LNRILEALKV RVLRPALEWA VSNREMLIAQ NSSLEFKLHR LYFISLLMGG TTNQREALQY AKNFQPFALN HQKDIQVLMG SLVYLRQGIE NSPYVHLLDA NQWADICDIF TRDACALLGL SVESPLSVSF SAGCVALPAL INIKAVIEQR QCTGVWNQKD ELPIEVDLGK KCWYHSIFAC PILRQQTTDN NPPMKLVCGH IISRDALNKM FNGSKLKCPY CPMEQSPGDA KQIFF

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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

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMHEPES
200.0 mMsodium chlorideNaCl
1.0 mMTCEP
0.01 %NP40

Details: 50 mM HEPES pH 7.4, 200 mM NaCl, 1mM TCEP and 0.01% NP40
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 15mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThe complex was purified with gel filtration and subsequently crosslinked using the GraFix method.

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 1 / Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 26017 / Average exposure time: 1.5 sec. / Average electron dose: 78.0 e/Å2 / Details: magnification: 105000x, 0.84A/pix
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 19599 / Average exposure time: 8.5 sec. / Average electron dose: 78.0 e/Å2 / Details: magnification: 165000, 0.84A/pix
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
DetailsCombined datasets (K2 and K3)
Particle selectionNumber selected: 815538
CTF correctionSoftware - Name: Gctf
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Details: Focused refinement of symmetry expanded particles. / Number images used: 144536
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC / Details: stochastic gradient descent
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 10 / Software - Name: RELION
FSC plot (resolution estimation)

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