[English] 日本語
Yorodumi
- PDB-9jta: Crystal structure of RNF213 RING domain bound to IpaH1.4 LRR domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jta
TitleCrystal structure of RNF213 RING domain bound to IpaH1.4 LRR domain
Components
  • E3 ubiquitin-protein ligase RNF213
  • RING-type E3 ubiquitin transferase
KeywordsCYTOSOLIC PROTEIN / RNF213 / IpaH1.4
Function / homology
Function and homology information


lipid ubiquitination / modulation of process of another organism / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Suppression of apoptosis / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases / regulation of lipid metabolic process / protein K63-linked ubiquitination ...lipid ubiquitination / modulation of process of another organism / negative regulation of non-canonical Wnt signaling pathway / lipid droplet formation / xenophagy / Suppression of apoptosis / sprouting angiogenesis / Transferases; Acyltransferases; Aminoacyltransferases / regulation of lipid metabolic process / protein K63-linked ubiquitination / protein autoubiquitination / immune system process / lipid droplet / RING-type E3 ubiquitin transferase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Signaling by ALK fusions and activated point mutants / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / angiogenesis / host cell cytoplasm / protein ubiquitination / defense response to bacterium / nucleolus / ATP hydrolysis activity / extracellular region / zinc ion binding / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : / Leucine-rich repeats, bacterial type ...E3 ubiquitin-protein ligase RNF213 / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / : / Leucine-rich repeats, bacterial type / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Leucine-rich repeat profile. / Ring finger / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RING-type E3 ubiquitin transferase / E3 ubiquitin-protein ligase RNF213
Similarity search - Component
Biological speciesShigella flexneri 5a str. M90T (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhou, X.D. / Wang, Y.R. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071219 China
CitationJournal: Nat Commun / Year: 2025
Title: Shigella effector IpaH1.4 subverts host E3 ligase RNF213 to evade antibacterial immunity.
Authors: Xindi Zhou / Huijing Zhang / Yaru Wang / Danni Wang / Zhiqiao Lin / Yuchao Zhang / Yubin Tang / Jianping Liu / Yu-Feng Yao / Yixiao Zhang / Lifeng Pan /
Abstract: Ubiquitination plays vital roles in modulating pathogen-host cell interactions. RNF213, a E3 ligase, can catalyze the ubiquitination of lipopolysaccharide (LPS) and is crucial for antibacterial ...Ubiquitination plays vital roles in modulating pathogen-host cell interactions. RNF213, a E3 ligase, can catalyze the ubiquitination of lipopolysaccharide (LPS) and is crucial for antibacterial immunity in mammals. Shigella flexneri, an LPS-containing pathogenic bacterium, has developed mechanisms to evade host antibacterial defenses during infection. However, the precise strategies by which S. flexneri circumvents RNF213-mediated antibacterial immunity remain poorly understood. Here, through comprehensive biochemical, structural and cellular analyses, we reveal that the E3 effector IpaH1.4 of S. flexneri can directly target human RNF213 via a specific interaction between the IpaH1.4 LRR domain and the RING domain of RNF213, and mediate the ubiquitination and proteasomal degradation of RNF213 in cells. Furthermore, we determine the cryo-EM structure of human RNF213 and the crystal structure of the IpaH1.4 LRR/RNF213 RING complex, elucidating the molecular mechanism underlying the specific recognition of RNF213 by IpaH1.4. Finally, our cell based functional assays demonstrate that the targeting of host RNF213 by IpaH1.4 promotes S. flexneri proliferation within infected cells. In summary, our work uncovers an unprecedented strategy employed by S. flexneri to subvert the key host immune factor RNF213, thereby facilitating bacterial proliferation during invasion.
History
DepositionOct 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: RING-type E3 ubiquitin transferase
C: E3 ubiquitin-protein ligase RNF213
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2264
Polymers34,0952
Non-polymers1312
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-6 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.609, 68.609, 147.694
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein RING-type E3 ubiquitin transferase / E3 ubiquitin-protein ligase IpaH1.4


Mass: 26636.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 5a str. M90T (bacteria)
Gene: EKN05_024115 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A4P7TTK5, RING-type E3 ubiquitin transferase
#2: Protein E3 ubiquitin-protein ligase RNF213 / ALK lymphoma oligomerization partner on chromosome 17 / E3 ubiquitin-lipopolysaccharide ligase ...ALK lymphoma oligomerization partner on chromosome 17 / E3 ubiquitin-lipopolysaccharide ligase RNF213 / Mysterin / RING finger protein 213


Mass: 7458.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF213, ALO17, C17orf27, KIAA1554, KIAA1618, MYSTR / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q63HN8, RING-type E3 ubiquitin transferase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Transferases; ...References: UniProt: Q63HN8, RING-type E3 ubiquitin transferase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Transferases; Acyltransferases; Aminoacyltransferases
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M HEPES (pH 7.8), 0.2 M Ammonium acetate, 20% (w/v) polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→62.22 Å / Num. obs: 39533 / % possible obs: 100 % / Redundancy: 25.5 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.6
Reflection shellResolution: 1.702→1.731 Å / Rmerge(I) obs: 1.531 / Num. unique obs: 1927

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V8E

7v8e


Resolution: 1.7→29.38 Å / SU ML: 0.2484 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5554
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2198 1923 4.87 %
Rwork0.1932 37600 -
obs0.1945 39523 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.93 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 2 259 2533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00952328
X-RAY DIFFRACTIONf_angle_d1.11373180
X-RAY DIFFRACTIONf_chiral_restr0.0725367
X-RAY DIFFRACTIONf_plane_restr0.0102420
X-RAY DIFFRACTIONf_dihedral_angle_d14.9746883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.3991560.33922603X-RAY DIFFRACTION100
1.74-1.790.34311270.29572642X-RAY DIFFRACTION100
1.79-1.840.31311360.26752628X-RAY DIFFRACTION100
1.84-1.90.2611340.23172664X-RAY DIFFRACTION100
1.9-1.970.25041480.21322619X-RAY DIFFRACTION100
1.97-2.050.23691090.21022671X-RAY DIFFRACTION100
2.05-2.140.24861380.21362670X-RAY DIFFRACTION100
2.14-2.260.24571400.20252646X-RAY DIFFRACTION100
2.26-2.40.20531400.19652670X-RAY DIFFRACTION100
2.4-2.580.27831280.20622691X-RAY DIFFRACTION100
2.58-2.840.23151260.20712719X-RAY DIFFRACTION100
2.84-3.250.22331400.20772717X-RAY DIFFRACTION100
3.25-4.10.20161420.17062760X-RAY DIFFRACTION100
4.1-29.380.18661590.17012900X-RAY DIFFRACTION99.67

+
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