[English] 日本語
Yorodumi
- EMDB-37593: Vibrio vulnificus MARTX effector duet (RDTND-RID) complexed with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37593
TitleVibrio vulnificus MARTX effector duet (RDTND-RID) complexed with human Rac1 Q61L and calmodulin
Map datapixel size: 0.66extraction box size: 500 pixel (500 x 0.66 = 330 A)
Sample
  • Complex: RDTND-RID effector duet complexed with Ca2+CaM and Rac1Q61L
    • Complex: RDTND-RID
      • Protein or peptide: RDTND-RID
    • Complex: Calmodulin
      • Protein or peptide: Calmodulin
    • Complex: Rac1
      • Protein or peptide: Rac1
KeywordsMARTX toxin / RDTND-RID / NADase / N-fatty acyl transferase / CaM / Rac1 / TOXIN
Function / homology
Function and homology information


negative regulation of calcium ion transmembrane transporter activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / regulation of respiratory burst / regulation of neutrophil migration / localization within membrane / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / ruffle assembly / regulation of hydrogen peroxide metabolic process ...negative regulation of calcium ion transmembrane transporter activity / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / regulation of respiratory burst / regulation of neutrophil migration / localization within membrane / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / ruffle assembly / regulation of hydrogen peroxide metabolic process / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / respiratory burst / cortical cytoskeleton organization / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / hepatocyte growth factor receptor signaling pathway / ruffle organization / regulation of stress fiber assembly / thioesterase binding / cell projection assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / regulation of nitric oxide biosynthetic process / PCP/CE pathway / Activation of RAC1 / motor neuron axon guidance / positive regulation of neutrophil chemotaxis / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / Azathioprine ADME / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / host cell cytosol / positive regulation of cyclic-nucleotide phosphodiesterase activity / small GTPase-mediated signal transduction / regulation of cell size / negative regulation of calcium ion export across plasma membrane / Rho GDP-dissociation inhibitor binding / positive regulation of Rho protein signal transduction / Activation of RAC1 downstream of NMDARs / establishment or maintenance of cell polarity / NRAGE signals death through JNK / acyltransferase activity / positive regulation of ryanodine-sensitive calcium-release channel activity / Rac protein signal transduction / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / negative regulation of ryanodine-sensitive calcium-release channel activity / ligase activity / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / : / Sema3A PAK dependent Axon repulsion / semaphorin-plexin signaling pathway / adenylate cyclase binding / ficolin-1-rich granule membrane / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / positive regulation of lamellipodium assembly / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / voltage-gated potassium channel complex / positive regulation of substrate adhesion-dependent cell spreading / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / RHO GTPases activate PKNs / : / titin binding / positive regulation of protein autophosphorylation / cysteine-type peptidase activity / regulation of calcium-mediated signaling / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / sperm midpiece / positive regulation of microtubule polymerization / calcium channel complex / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / EPHB-mediated forward signaling / substantia nigra development / RAC1 GTPase cycle / adenylate cyclase activator activity / regulation of cell migration
Similarity search - Function
: / C-terminal repeat from RTX toxins / : / : / Pasteurella multocida toxin, C2 domain / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain ...: / C-terminal repeat from RTX toxins / : / : / Pasteurella multocida toxin, C2 domain / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serralysin-like metalloprotease, C-terminal / Small GTPase Rho / small GTPase Rho family profile. / : / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / EF-hand domain pair / Rab subfamily of small GTPases / 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 / Small GTP-binding protein domain / Alpha/Beta hydrolase fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Multifunctional-autoprocessing repeats-in-toxin / Calmodulin-2 / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.32 Å
AuthorsLee Y / Choi S / Jang SY / Hwang J / Kim MH
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
Other governmentthe Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM1382312) Korea, Republic Of
Other governmentthe Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM2112335) Korea, Republic Of
CitationJournal: Nat Commun / Year: 2024
Title: Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet.
Authors: Sanghyeon Choi / Youngjin Lee / Shinhye Park / Song Yee Jang / Jongbin Park / Do Won Oh / Su-Man Kim / Tae-Hwan Kim / Ga Seul Lee / Changyi Cho / Byoung Sik Kim / Donghan Lee / Eun-Hee Kim / ...Authors: Sanghyeon Choi / Youngjin Lee / Shinhye Park / Song Yee Jang / Jongbin Park / Do Won Oh / Su-Man Kim / Tae-Hwan Kim / Ga Seul Lee / Changyi Cho / Byoung Sik Kim / Donghan Lee / Eun-Hee Kim / Hae-Kap Cheong / Jeong Hee Moon / Ji-Joon Song / Jungwon Hwang / Myung Hee Kim /
Abstract: Multiple bacterial genera take advantage of the multifunctional autoprocessing repeats-in-toxin (MARTX) toxin to invade host cells. Secretion of the MARTX toxin by Vibrio vulnificus, a deadly ...Multiple bacterial genera take advantage of the multifunctional autoprocessing repeats-in-toxin (MARTX) toxin to invade host cells. Secretion of the MARTX toxin by Vibrio vulnificus, a deadly opportunistic pathogen that causes primary septicemia, the precursor of sepsis, is a major driver of infection; however, the molecular mechanism via which the toxin contributes to septicemia remains unclear. Here, we report the crystal and cryo-electron microscopy (EM) structures of a toxin effector duet comprising the domain of unknown function in the first position (DUF1)/Rho inactivation domain (RID) complexed with human targets. These structures reveal how the duet is used by bacteria as a potent weapon. The data show that DUF1 acts as a RID-dependent transforming NADase domain (RDTND) that disrupts NAD homeostasis by hijacking calmodulin. The cryo-EM structure of the RDTND-RID duet complexed with calmodulin and Rac1, together with immunological analyses in vitro and in mice, provide mechanistic insight into how V. vulnificus uses the duet to suppress ROS generation by depleting NAD(P) and modifying Rac1 in a mutually-reinforcing manner that ultimately paralyzes first line immune responses, promotes dissemination of invaders, and induces sepsis. These data may allow development of tools or strategies to combat MARTX toxin-related human diseases.
History
DepositionSep 26, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37593.png

Downloads & links

-
Map

FileDownload / File: emd_37593.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpixel size: 0.66extraction box size: 500 pixel (500 x 0.66 = 330 A)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 500 pix.
= 330. Å		0.66 Å/pix.
x 500 pix.
= 330. Å		0.66 Å/pix.
x 500 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.0868115 - 1.77167
Average (Standard dev.)-0.00012427119 (±0.019421889)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: pixel size: 0.66extraction box size: 500 pixel (500 x 0.66 = 330 A)

Fileemd_37593_half_map_1.map
Annotationpixel size: 0.66extraction box size: 500 pixel (500 x 0.66 = 330 A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: pixel size: 0.66extraction box size: 500 pixel (500 x 0.66 = 330 A)

Fileemd_37593_half_map_2.map
Annotationpixel size: 0.66extraction box size: 500 pixel (500 x 0.66 = 330 A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RDTND-RID effector duet complexed with Ca2+CaM and Rac1Q61L

EntireName: RDTND-RID effector duet complexed with Ca2+CaM and Rac1Q61L
Components
  • Complex: RDTND-RID effector duet complexed with Ca2+CaM and Rac1Q61L
    • Complex: RDTND-RID
      • Protein or peptide: RDTND-RID
    • Complex: Calmodulin
      • Protein or peptide: Calmodulin
    • Complex: Rac1
      • Protein or peptide: Rac1

-
Supramolecule #1: RDTND-RID effector duet complexed with Ca2+CaM and Rac1Q61L

SupramoleculeName: RDTND-RID effector duet complexed with Ca2+CaM and Rac1Q61L
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: RDTND-RID

SupramoleculeName: RDTND-RID / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: single mutation, C2838A
Source (natural)Organism: Vibrio vulnificus (bacteria)

-
Supramolecule #3: Calmodulin

SupramoleculeName: Calmodulin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: Sequence conflict, Q124E
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #4: Rac1

SupramoleculeName: Rac1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 / Details: single muatation, Q61L
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: RDTND-RID

MacromoleculeName: RDTND-RID / type: protein_or_peptide / ID: 1 / Details: single mutant C2838A / Enantiomer: LEVO
Source (natural)Organism: Vibrio vulnificus (bacteria)
SequenceString: MGEASHDSAE SLVAARAEKV ANLYRWLDTD NDVATDKYVP VPGFERVDVD VSDEVKQRMI QSMSGYIEHT DNQVPKDQAE ALATLFVEST LDYDWDKRVE FLTKLESYGY SFEAPHAEKS IVSFWSGKNF KQYRDILDNA QTDGKKVVYD IDVKGNAFAI DLNKHLMRWG ...String:
MGEASHDSAE SLVAARAEKV ANLYRWLDTD NDVATDKYVP VPGFERVDVD VSDEVKQRMI QSMSGYIEHT DNQVPKDQAE ALATLFVEST LDYDWDKRVE FLTKLESYGY SFEAPHAEKS IVSFWSGKNF KQYRDILDNA QTDGKKVVYD IDVKGNAFAI DLNKHLMRWG GLFLDPDNAE QNQLKSSIDA ATFSNTGFWS SVYATGAQND VYVIAEGGVR LGNYFWNVEL PALRQLQREG LVGEIRLLDK PVSEYKDLPA DQIGRRLTDA GVAVKVRFDA LSHERQAELL ADNPDGYKAD TLVELDVKLS AIDSMLRESL PFYSLRTERN LLVQEGEEGF EVRSWPGIDG KSKTILLDNP EDAAQQKSIE RFILANFDNF EQMPDELFLV DNKVLSHHDG RTRIIAQKED GAWTYNTNVE LMSVTELLDA AHVNGKVRGD SYQQVIDALT EYHASTVEHA DYELESVEKL LNLRKQIEGY VLGHPDSGRV EAMNSLLNQV NSRLEEVSVL AVSEQSIKAH DSFSRLYDQL DNANLKESKH LYLDGNGDFV TKGKGNLATI DQLGGSDAVL EKVKAAVTHE YGQVVADTIF ARLSANDLAK DGKGIDIAGL NKVHQAIEQH MSPVSATMYI WKPSDHSTLG HAALQIGQGR TQLEGQAAAD FNKQNYVSWW PLGSKSSNIR NIFNVATEDQ PDLKLRWSDF SQPAHQNDTL EHDMASEEND GFGLKDGETK LKRFIEKLNA AKGIDASYKD ASEGYASVLL GNPDMLASTG IPAHVFQPFV DQWNDTSYDM MDVANRFAEE LQKQAQASGD PALVEKRIDN VVRLFAERAL EEIEAFKASQ ADEGRVFRIN LEGLDVAAMQ AEWKRLSNDP DARYQLLTKN ASSTVAKVLK AGGADKLIGH TWRPKFGVWT PTELFNFGQA LQEAQLEIAA KKQSHQVTDV LDAL

UniProtKB: Multifunctional-autoprocessing repeats-in-toxin

-
Macromolecule #2: Calmodulin

MacromoleculeName: Calmodulin / type: protein_or_peptide / ID: 2 / Details: Q124E, "sequence conflict" / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GAMADQLTEE QIAEFKEAFS LFDKDGDGTI TTKELGTVMR SLGQNPTEAE LQDMINEVDA DGNGTIDFPE FLTMMARKMK DTDSEEEIRE AFRVFDKDGN GYISAAELRH VMTNLGEKLT DEEVDQMIRE ADIDGDGQVN YEEFVQMMTA K

UniProtKB: Calmodulin-2

-
Macromolecule #3: Rac1

MacromoleculeName: Rac1 / type: protein_or_peptide / ID: 3 / Details: single mutation, Q61L / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GHMQAIKCVV VGDGAVGKTC LLISYTTNAF PGEYIPTVFD NYSANVMVDG KPVNLGLWDT AGLEDYDRLR PLSYPQTDVF LICFSLVSPA SFENVRAKWY PEVRHHCPNT PIILVGTKLD LRDDKDTIEK LKEKKLTPIT YPQGLAMAKE IGAVKYLECS ALTQRGLKTV FDEAIRAVL

UniProtKB: Ras-related C3 botulinum toxin substrate 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPESHydroxyethyl piperazine Ethane Sulfonicacid
150.0 mMNaClsodium chloride
1.0 %glycerolglycerol

Details: 50 mM HEPES-NaOH (pH 7.5), 150 mM NaCl, and 1% (v/v) glycerol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 2.2 µm / Nominal defocus min: 1.4000000000000001 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 247635
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

8k9z

source_name: PDB, initial_model_type: experimental model

5xn7

source_name: PDB, initial_model_type: experimental model

3th5

source_name: PDB, initial_model_type: experimental model

+
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