[English] 日本語
Yorodumi
- EMDB-44118: Actin-bound Legionella pneumophila AMPylase LnaB with AMPylated c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44118
TitleActin-bound Legionella pneumophila AMPylase LnaB with AMPylated catalytic histidine
Map data
Sample
  • Complex: Actin-bound Legionella pneumophila AMPylase LnaB with AMPylated catalytic histidine
    • Complex: LnaB
      • Protein or peptide: Type IV secretion protein Dot
    • Complex: Actin
      • Protein or peptide: Actin, cytoplasmic 1
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: CALCIUM ION
  • Ligand: LATRUNCULIN B
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsAMPylase / antitoxin / actin / ubiquitin / TRANSFERASE
Function / homology
Function and homology information


positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / regulation of transepithelial transport / nBAF complex / brahma complex / morphogenesis of a polarized epithelium / protein localization to adherens junction / postsynaptic actin cytoskeleton ...positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / regulation of transepithelial transport / nBAF complex / brahma complex / morphogenesis of a polarized epithelium / protein localization to adherens junction / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / Formation of the dystrophin-glycoprotein complex (DGC) / GBAF complex / Formation of annular gap junctions / Tat protein binding / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / dense body / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / apical protein localization / regulation of double-strand break repair / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / regulation of norepinephrine uptake / transporter regulator activity / apical junction complex / nitric-oxide synthase binding / positive regulation of double-strand break repair / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / cortical cytoskeleton / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / regulation of synaptic vesicle endocytosis / regulation of G1/S transition of mitotic cell cycle / brush border / kinesin binding / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / calyx of Held / axonogenesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / adherens junction / positive regulation of cell differentiation / actin filament / FCGR3A-mediated phagocytosis / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / Schaffer collateral - CA1 synapse / B-WICH complex positively regulates rRNA expression / kinetochore / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / tau protein binding / VEGFA-VEGFR2 Pathway / platelet aggregation / cytoplasmic ribonucleoprotein granule / nuclear matrix / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / UCH proteinases / Signaling by BRAF and RAF1 fusions / nucleosome / cell-cell junction / lamellipodium / actin cytoskeleton / presynapse / Clathrin-mediated endocytosis / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / regulation of apoptotic process
Similarity search - Function
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin, cytoplasmic 1 / Type IV secretion protein Dot
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsZhang Z / Das C
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI171709 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM126296 United States
CitationJournal: J Mol Biol / Year: 2025
Title: Cryo-EM Detection of AMPylated Histidine Implies Covalent Catalysis in AMPylation Mediated by a Bacterial Effector.
Authors: Zhengrui Zhang / Rishi Patel / Zhao-Qing Luo / Chittaranjan Das /
Abstract: AMPylation is a post-translational modification (PTM) whereby adenosine monophosphate (AMP) from adenosine triphosphate (ATP) is transferred onto protein hydroxyl groups of serine, threonine, or ...AMPylation is a post-translational modification (PTM) whereby adenosine monophosphate (AMP) from adenosine triphosphate (ATP) is transferred onto protein hydroxyl groups of serine, threonine, or tyrosine. Recently, an actin-dependent AMPylase namely LnaB from the bacterial pathogen Legionella pneumophila was found to AMPylate phosphate groups of phosphoribosylated ubiquitin and Src family kinases. LnaB represents an evolutionarily distinct family of AMPylases with conserved active site Ser-His-Glu residues. Here, we capture the structure of the LnaB-actin complex in a putative intermediate state via single-particle cryogenic electron microscopy (cryo-EM) and find that the catalytic histidine of LnaB is covalently attached to AMP through a phosphoramidate linkage at the Nδ1 atom. This observation provides direct structural evidence of histidine AMPylation as a PTM and implies the possibility of covalent catalysis in LnaB-mediated AMPylation, a mechanism distinct from known AMPylases. Subsequent biochemical studies confirm the observed AMP binding site and provide additional insights into the catalytic properties of LnaB. Together, our work highlights the power of cryo-EM in capturing labile PTMs and transient species during enzymatic reactions, while opening new avenues of mechanistic investigation into the LnaB family.
History
DepositionMar 18, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateJan 8, 2025-
Current statusJan 8, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44118.png

Downloads & links

-
Map

FileDownload / File: emd_44118.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.432 Å		0.82 Å/pix.
x 256 pix.
= 210.432 Å		0.82 Å/pix.
x 256 pix.
= 210.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.2043028 - 1.6041691
Average (Standard dev.)0.00044130848 (±0.03602745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.432 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_44118_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_44118_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Actin-bound Legionella pneumophila AMPylase LnaB with AMPylated c...

EntireName: Actin-bound Legionella pneumophila AMPylase LnaB with AMPylated catalytic histidine
Components
  • Complex: Actin-bound Legionella pneumophila AMPylase LnaB with AMPylated catalytic histidine
    • Complex: LnaB
      • Protein or peptide: Type IV secretion protein Dot
    • Complex: Actin
      • Protein or peptide: Actin, cytoplasmic 1
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: CALCIUM ION
  • Ligand: LATRUNCULIN B
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Actin-bound Legionella pneumophila AMPylase LnaB with AMPylated c...

SupramoleculeName: Actin-bound Legionella pneumophila AMPylase LnaB with AMPylated catalytic histidine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

-
Supramolecule #2: LnaB

SupramoleculeName: LnaB / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)

-
Supramolecule #3: Actin

SupramoleculeName: Actin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Type IV secretion protein Dot

MacromoleculeName: Type IV secretion protein Dot / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Molecular weightTheoretical: 58.642035 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSYQKIELSI SLSLDSPKLD ESDFILLSVK YLEKSLGKKK EFSGFFEDIE KLYFKQNYKE AIEKILDFCK KNESLLSEQV VQRLAEVAP RLKSNPKDNE SRRLYETLYA DHLESVIKQE SDLSVFNELR DSYNAVKPEY AVTHETEIKT LDEAKQFILS F VMLNDNVE ...String:
MSYQKIELSI SLSLDSPKLD ESDFILLSVK YLEKSLGKKK EFSGFFEDIE KLYFKQNYKE AIEKILDFCK KNESLLSEQV VQRLAEVAP RLKSNPKDNE SRRLYETLYA DHLESVIKQE SDLSVFNELR DSYNAVKPEY AVTHETEIKT LDEAKQFILS F VMLNDNVE LPLKAQSERY PKKDRSREEL GNTPSANPGI MKPNSPNFTD NLVPVRDVPK IAINEKVAGG YSKTKPTTPF VA SLAGTTY SLMVVLTDYI EKHKTDKDIE KKVNQIINLW ISSYIKEGYH SYSEVVDVLT EPFLQSIFDK ANIKLNYGVL DDT HAEFRK AQDYVFGLTI QSAMHHELQE RFKNKEKLQE EVKNFESGLN KLNQNVENTG RHREALNKLN EVFQDWSAGK KSYD AFKSE SNQLIHDIES EEQKSNRGLG SMLKNLGNYL LYLITLRFLK EDYPKPSSPV TMLVTELRGT LEQIDHFHKT SLSLK KATQ PDPKNTSSSD ETADVRKSAH HHHHH

UniProtKB: Type IV secretion protein Dot

-
Macromolecule #2: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.78266 KDa
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

-
Macromolecule #3: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

-
Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #5: LATRUNCULIN B

MacromoleculeName: LATRUNCULIN B / type: ligand / ID: 5 / Number of copies: 1 / Formula: LAB
Molecular weightTheoretical: 395.513 Da
Chemical component information

ChemComp-LAB:
LATRUNCULIN B / toxin*YM

-
Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 536510
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
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