[English] 日本語
Yorodumi
- EMDB-23863: Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23863
TitleCryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex
Map data
Sample
  • Complex: Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex
    • Complex: SidJ-SdeC
      • Protein or peptide: Calmodulin-dependent glutamylase SidJ
      • Protein or peptide: SdeC
    • Complex: Calmodulin
      • Protein or peptide: Calmodulin
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: SODIUM IONSodium
  • Ligand: CALCIUM IONCalcium
  • Ligand: ADENOSINE MONOPHOSPHATE
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase activity => GO:0106274 / Ligases / negative regulation of calcium ion transmembrane transporter activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein deubiquitination / protein phosphatase activator activity / ligase activity ...NAD+-protein-arginine ADP-ribosyltransferase activity => GO:0106274 / Ligases / negative regulation of calcium ion transmembrane transporter activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein deubiquitination / protein phosphatase activator activity / ligase activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / voltage-gated potassium channel complex / titin binding / positive regulation of protein autophosphorylation / cysteine-type peptidase activity / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / positive regulation of protein serine/threonine kinase activity / spindle microtubule / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / transferase activity / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / nucleotide binding / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / proteolysis / membrane / metal ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
SidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...SidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-2 / Calmodulin-dependent glutamylase SidJ / SdeC
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsOsinski A / Black MH / Pawlowski K / Chen Z / Li Y / Tagliabracci VS
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137419 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F30HL143859 United States
Welch FoundationI-1911 United States
CitationJournal: Mol Cell / Year: 2021
Title: Structural and mechanistic basis for protein glutamylation by the kinase fold.
Authors: Adam Osinski / Miles H Black / Krzysztof Pawłowski / Zhe Chen / Yang Li / Vincent S Tagliabracci /
Abstract: The kinase domain transfers phosphate from ATP to substrates. However, the Legionella effector SidJ adopts a kinase fold, yet catalyzes calmodulin (CaM)-dependent glutamylation to inactivate the SidE ...The kinase domain transfers phosphate from ATP to substrates. However, the Legionella effector SidJ adopts a kinase fold, yet catalyzes calmodulin (CaM)-dependent glutamylation to inactivate the SidE ubiquitin ligases. The structural and mechanistic basis in which the kinase domain catalyzes protein glutamylation is unknown. Here we present cryo-EM reconstructions of SidJ:CaM:SidE reaction intermediate complexes. We show that the kinase-like active site of SidJ adenylates an active-site Glu in SidE, resulting in the formation of a stable reaction intermediate complex. An insertion in the catalytic loop of the kinase domain positions the donor Glu near the acyl-adenylate for peptide bond formation. Our structural analysis led us to discover that the SidJ paralog SdjA is a glutamylase that differentially regulates the SidE ligases during Legionella infection. Our results uncover the structural and mechanistic basis in which the kinase fold catalyzes non-ribosomal amino acid ligations and reveal an unappreciated level of SidE-family regulation.
History
DepositionApr 17, 2021-
Header (metadata) releaseAug 18, 2021-
Map releaseAug 18, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7mis
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23863.png

Downloads & links

-
Map

FileDownload / File: emd_23863.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.09069091 - 0.20380887
Average (Standard dev.)-9.013509e-06 (±0.0047395453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0910.204-0.000

-
Supplemental data

-
Sample components

+
Entire : Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex

EntireName: Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex
Components
  • Complex: Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex
    • Complex: SidJ-SdeC
      • Protein or peptide: Calmodulin-dependent glutamylase SidJ
      • Protein or peptide: SdeC
    • Complex: Calmodulin
      • Protein or peptide: Calmodulin
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: SODIUM IONSodium
  • Ligand: CALCIUM IONCalcium
  • Ligand: ADENOSINE MONOPHOSPHATE

+
Supramolecule #1: Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex

SupramoleculeName: Cryo-EM structure of SidJ-SdeC-CaM reaction intermediate complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

+
Supramolecule #2: SidJ-SdeC

SupramoleculeName: SidJ-SdeC / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3
Source (natural)Organism: Legionella pneumophila (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

+
Supramolecule #3: Calmodulin

SupramoleculeName: Calmodulin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

+
Macromolecule #1: Calmodulin-dependent glutamylase SidJ

MacromoleculeName: Calmodulin-dependent glutamylase SidJ / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Ligases
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 87.374031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGHVKQYYFA RRGETSTHDT SLPPPVKVLS GRSIPLKEIP FEATRNELVQ IYLTSIDKLI KSNKLNSIPS QQIASHYLFL RSLANSETD GIKKNQILSL AKPLGTYLAS KEPHVWKMIN ELIEKSEYPI IHYLKNNRAH SNFMLALIHE YHKEPLTKNQ S AFVQKFRD ...String:
SGHVKQYYFA RRGETSTHDT SLPPPVKVLS GRSIPLKEIP FEATRNELVQ IYLTSIDKLI KSNKLNSIPS QQIASHYLFL RSLANSETD GIKKNQILSL AKPLGTYLAS KEPHVWKMIN ELIEKSEYPI IHYLKNNRAH SNFMLALIHE YHKEPLTKNQ S AFVQKFRD SSVFLFPNPI YTAWLAHSYD EDSSFNPMFR ERLSTNFYHS TLTDNLLLRT EPKEVTLSSE HHYKKEKGPI DS SFRYQMS SDRLLRIQGR TLLFSTPQND VVAVKVQKKG EPKSTLEEEF EMADYLLKHQ RRLDVHSKLP QPLGQYSVKK SEI LEISRG SLDFERFKTL IDDSKDLEVY VYKAPQSYFT YLHDKNQDLE DLTASVKTNV HDLFVLLREG IVFPQLADIF HTHF GEDER EDKGRYQALV QLLNVLQFQL GRIDKWQKAV EYVNLRSSGL ADLGDSLPIT SLFTSSDFTK HYFSELLTGG YHPTF FDKS SGTANSLFTG KRRLFGNYLY LNTIAEYLLV IQLTLGSYGD KVTRDMMDKP KKEAVWRELA NVMFTSCAEA IHIMTG IPQ SRALTLLKQR ANIEKHFRQT QFWMTPDYSK LDEDTLQMEQ YSIYSGEPEY EFTDKLVSGV GLSVDGVHQD LGGYNRE SP LRELEKLLYA TVTLIEGTMQ LDKEFFKQLE QVEKILSGEI KTDANSCFEA VAQLLDLARP GCHFQKRLVL SYYEEAKL K YPSAPTDAYD SRFQVVARTN AAITIQRFWR EARKN

+
Macromolecule #2: Calmodulin

MacromoleculeName: Calmodulin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.939623 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SMADQLTEEQ IAEFKEAFSL FDKDGDGTIT TKELGTVMRS LGQNPTEAEL QDMINEVDAD GNGTIDFPEF LTMMARKMKD TDSEEEIRE AFRVFDKDGN GYISAAELRH VMTNLGEKLT DEEVDEMIRE ADIDGDGQVN YEEFVQMMTA K

+
Macromolecule #3: SdeC

MacromoleculeName: SdeC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 112.775297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMGSSKLLE NDDDVLDTIK YVHKEYLGKP YPGPLKNPKA PEEGRLPPNE GPDRGPHGLA HTVRTMACAE VMIEEARKAQ LRGETLGKA KNGQTLADVT PEELKKILIA QAFFVVGRDD ERSGYDDVHK RNFYAEYHEK SEQAFRKYVE DNKLIGKIFK D QKEVDFYA ...String:
GAMGSSKLLE NDDDVLDTIK YVHKEYLGKP YPGPLKNPKA PEEGRLPPNE GPDRGPHGLA HTVRTMACAE VMIEEARKAQ LRGETLGKA KNGQTLADVT PEELKKILIA QAFFVVGRDD ERSGYDDVHK RNFYAEYHEK SEQAFRKYVE DNKLIGKIFK D QKEVDFYA AIILDKNHEW DATPAHILIN QGHMVDLMRT KAPAEVALER TYNTLKGTVG SKGAEVVLKA HRDFFFATGA VV PLVNPEA IDDPSRGGPY ENPYSGEKFV IVDDKVPASK KDLPKAVNRD YKLKDNERFL TIKEYYAFPD VQQTYPGYKT RLE ASSYYF PTPFAGECEQ NPAKCLGAIQ KARSKLQTDA IKNGFQSSSE KERRQPNMDE IAAARIIQQI MANPDCIHDD HVLI NGQKL EEKFFRDLLA KCDMAVVGSL LNDTDIKNID TLMRHEKNTE FHSTDPKAVP VKIGDAWENR IRTKGGDVTQ MKHDL IFLM QNDAWYFSRV NAIAQNRDKG SNFKEVLFTT LMTPLTNKSL IDTSHVPAPK KLYRGLNLPQ EFTNKLINQS NAIIAN TEN TLFTDLSAEA FKQIKLNDFS QMSGKTCAST TKNMKLLTDI WGSNVIFEML DPDGLLHPKQ VGTHMAGSED EFSVYLP ED VALVPTKVTL EGKTDTGEDR YIFTLVAVKS PDFIPRHESG YAVEPFMKMQ KEKVTQALDA IEKDKDSYNI DEQLKSLR T EMVRQAKLPL REGVFDRLSH RLSLETSDNK ISPERRDFLN QHVIPVLQEC HIALRANDMD MMQKALAKFP TDKQWSAFK SGEAVRAKAQ MDVLKQQIEK KIMLQTQIIP ALTECGEALD KQNVTEALQA LNKLPAEKEI GKVKTIGQEL RGQIVGVKQE LTGNLEPLQ RATTTPIVQD AEKIKVRYET LLTDVTKRVT DFEKIKPANL DGYNKAIADL NNIQQELNLL RNEKIRMHTD K DKAVDFSD IEALDKRLQD VQSKLPTQLL EQTSKDVAK

+
Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

+
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #6: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 6 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

+
Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

+
Macromolecule #8: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.35 mg/mL
BufferpH: 6.5
Details: 25 mM Bis-tris pH 6.5, 100 mM NaCl, 1 mM TCEP, 2 mM MgCl2, 1 mM ATP
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
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

-
Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152589

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more