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- EMDB-42407: Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1) -

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Basic information

Entry
Database: EMDB / ID: EMD-42407
TitleStructure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1)
Map dataStructure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1)
Sample
  • Complex: Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1)
    • Complex: Bud32
      • Protein or peptide: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
    • Complex: Cgi121
      • Protein or peptide: Regulatory protein Cgi121
    • Complex: Kae1
      • Protein or peptide: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
    • Complex: Pcc1
    • Protein or peptide: KEOPS complex Pcc1-like subunit
KeywordstRNA / modification / t6A / RNA BINDING PROTEIN
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / protein serine/threonine/tyrosine kinase activity / metalloendopeptidase activity / non-specific serine/threonine protein kinase / iron ion binding / protein serine kinase activity / protein serine/threonine kinase activity ...N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / protein serine/threonine/tyrosine kinase activity / metalloendopeptidase activity / non-specific serine/threonine protein kinase / iron ion binding / protein serine kinase activity / protein serine/threonine kinase activity / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
: / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family ...: / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / CTAG/Pcc1 family / Transcription factor Pcc1 / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / : / RIO domain / ATPase, nucleotide binding domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Regulatory protein Cgi121 / KEOPS complex Pcc1-like subunit / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea) / Pyrococcus furiosus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsOna Chuquimarca SM / Beenstock J / Daou S / Keszei AFA / Yin Z / Sicheri F
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-178026 Canada
CitationJournal: Nat Commun / Year: 2024
Title: Structures of KEOPS bound to tRNA reveal functional roles of the kinase Bud32.
Authors: Samara Mishelle Ona Chuquimarca / Jonah Beenstock / Salima Daou / Jennifer Porat / Alexander F A Keszei / Jay Z Yin / Tobias Beschauner / Mark A Bayfield / Mohammad T Mazhab-Jafari / Frank Sicheri /
Abstract: The enzyme complex KEOPS (Kinase, Endopeptidase and Other Proteins of Small size) installs the universally conserved and essential N-threonylcarbamoyl adenosine modification (tA) on ANN-decoding ...The enzyme complex KEOPS (Kinase, Endopeptidase and Other Proteins of Small size) installs the universally conserved and essential N-threonylcarbamoyl adenosine modification (tA) on ANN-decoding tRNAs in eukaryotes and in archaea. KEOPS consists of Cgi121, Kae1, Pcc1, Gon7 and the atypical kinase/ATPase Bud32. Except Gon7, all KEOPS subunits are needed for tRNA modification, and in humans, mutations in all five genes underlie the lethal genetic disease Galloway Mowat Syndrome (GAMOS). Kae1 catalyzes the modification of tRNA, but the specific contributions of Bud32 and the other subunits are less clear. Here we solved cryogenic electron microscopy structures of KEOPS with and without a tRNA substrate. We uncover distinct flexibility of KEOPS-bound tRNA revealing a conformational change that may enable its modification by Kae1. We further identified a contact between a flipped-out base of the tRNA and an arginine residue in C-terminal tail of Bud32 that correlates with the conformational change in the tRNA. We also uncover contact surfaces within the KEOPS-tRNA holo-enzyme substrate complex that are required for Bud32 ATPase regulation and tA modification activity. Our findings uncover inner workings of KEOPS including a basis for substrate specificity and why Kae1 depends on all other subunits.
History
DepositionOct 19, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42407.png

Downloads & links

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Map

FileDownload / File: emd_42407.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.43
Minimum - Maximum-25.463825 - 52.126907000000003
Average (Standard dev.)0.000000000003026 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42407_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_42407_additional_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_42407_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_42407_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 : Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1)

EntireName: Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1)
Components
  • Complex: Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1)
    • Complex: Bud32
      • Protein or peptide: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
    • Complex: Cgi121
      • Protein or peptide: Regulatory protein Cgi121
    • Complex: Kae1
      • Protein or peptide: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
    • Complex: Pcc1
    • Protein or peptide: KEOPS complex Pcc1-like subunit

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Supramolecule #1: Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1)

SupramoleculeName: Structure of the KEOPS complex (Cgi121/Bud32/Kae1/Pcc1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)

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Supramolecule #2: Bud32

SupramoleculeName: Bud32 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)

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Supramolecule #3: Cgi121

SupramoleculeName: Cgi121 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)

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Supramolecule #4: Kae1

SupramoleculeName: Kae1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)

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Supramolecule #5: Pcc1

SupramoleculeName: Pcc1 / type: complex / ID: 5 / Parent: 1
Source (natural)Organism: Pyrococcus furiosus (archaea)

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Macromolecule #1: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesi...

MacromoleculeName: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Molecular weightTheoretical: 23.957547 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: KIPEHLIGKG AEADIKRDSY LDFDVIIKER VKKGYRDERL DENIRKSRTA REARYLALVK DFGIPAPYIF DVDLDNKRIM MSYINGKLA KDVIEDNLDI AYKIGEIVGK LHKNDVIHND LTTSNFIFDK DLYIIDFGLG KISNLDRDKA VDLIVFKKAV L STHHEKFD ...String:
KIPEHLIGKG AEADIKRDSY LDFDVIIKER VKKGYRDERL DENIRKSRTA REARYLALVK DFGIPAPYIF DVDLDNKRIM MSYINGKLA KDVIEDNLDI AYKIGEIVGK LHKNDVIHND LTTSNFIFDK DLYIIDFGLG KISNLDRDKA VDLIVFKKAV L STHHEKFD EIWERFLEGY KSVYDRWEII LELMKDVERR ARYVE

UniProtKB: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein

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Macromolecule #2: Regulatory protein Cgi121

MacromoleculeName: Regulatory protein Cgi121 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Molecular weightTheoretical: 16.717654 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
PMIIRGIRGA RINNEIFNLG LKFQILNADV VATKKHVLHA INQAKTKKPI AKSFWMEILV RASGQRQIHE AIKIIGAKDG NVCLICEDE ETFRKIYELI GGEIDDSVLE INEDKERLIR EIFKIRGFGN VVERVLEKIA LIELKKE

UniProtKB: Regulatory protein Cgi121

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Macromolecule #3: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesi...

MacromoleculeName: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Molecular weightTheoretical: 35.772293 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MICLGLEGTA EKTGVGIVTS DGEVLFNKTI MYKPPKQGIN PREAADHHAE TFPKLIKEAF EVVDKNEIDL IAFSQGPGLG PSLRVTATV ARTLSLTLKK PIIGVNHCIA HIEIGKLTTE AEDPLTLYVS GGNTQVIAYV SKKYRVFGET LDIAVGNCLD Q FARYVNLP ...String:
MICLGLEGTA EKTGVGIVTS DGEVLFNKTI MYKPPKQGIN PREAADHHAE TFPKLIKEAF EVVDKNEIDL IAFSQGPGLG PSLRVTATV ARTLSLTLKK PIIGVNHCIA HIEIGKLTTE AEDPLTLYVS GGNTQVIAYV SKKYRVFGET LDIAVGNCLD Q FARYVNLP HPGGPYIEEL ARKGKKLVDL PYTVKGMDIA FSGLLTAAMR AYDAGERLED ICYSLQEYAF SMLTEITERA LA HTNKGEV MLVGGVAANN RLREMLKAMC EGQNVDFYVP PKEFCGDNGA MIAWLGLLMH KNGRWMSLDE TKIIPNYRTD MVE VNWI

UniProtKB: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein

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Macromolecule #4: KEOPS complex Pcc1-like subunit

MacromoleculeName: KEOPS complex Pcc1-like subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus (archaea)
Molecular weightTheoretical: 9.410949 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKAKRVQAKI EIEFPSEDVA KVVYEAVLYE HLSVPYRRSE IDFKLEGKKI ILDIKATDSS ALRGTVNSYL RWIKAAIDVI EV

UniProtKB: KEOPS complex Pcc1-like subunit

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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-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.61 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 386585
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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