[English] 日本語
Yorodumi
- PDB-7v8g: Crystal structure of HOIP RING1 domain bound to IpaH1.4 LRR domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v8g
TitleCrystal structure of HOIP RING1 domain bound to IpaH1.4 LRR domain
Components
  • E3 ubiquitin-protein ligase RNF31
  • RING-type E3 ubiquitin transferase
KeywordsLIGASE / E3 ligase / ubiquitin / innate immune
Function / homology
Function and homology information


modulation of process of another organism / protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / K48-linked polyubiquitin modification-dependent protein binding ...modulation of process of another organism / protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / K48-linked polyubiquitin modification-dependent protein binding / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / host cell cytoplasm / protein ubiquitination / defense response to bacterium / ubiquitin protein ligase binding / zinc ion binding / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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 / : / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like ...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 / : / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / PUB-like domain superfamily / PUB domain / PUB domain / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Leucine-rich repeats, bacterial type / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF31 / RING-type E3 ubiquitin transferase
Similarity search - Component
Biological speciesShigella flexneri serotype 5a
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLiu, J. / Wang, Y. / Pan, L.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071297 China
National Natural Science Foundation of China (NSFC)21822705 China
National Natural Science Foundation of China (NSFC)91753113 China
National Natural Science Foundation of China (NSFC)21621002 China
National Natural Science Foundation of China (NSFC)32071219 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Mechanistic insights into the subversion of the linear ubiquitin chain assembly complex by the E3 ligase IpaH1.4 of Shigella flexneri.
Authors: Liu, J. / Wang, Y. / Wang, D. / Wang, Y. / Xu, X. / Zhang, Y. / Li, Y. / Zhang, M. / Gong, X. / Tang, Y. / Shen, L. / Li, M. / Pan, L.
History
DepositionAug 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RING-type E3 ubiquitin transferase
B: RING-type E3 ubiquitin transferase
D: E3 ubiquitin-protein ligase RNF31
C: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5208
Polymers77,2594
Non-polymers2624
Water0
1
A: RING-type E3 ubiquitin transferase
C: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7604
Polymers38,6292
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RING-type E3 ubiquitin transferase
D: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7604
Polymers38,6292
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.896, 35.141, 145.871
Angle α, β, γ (deg.)90.000, 93.687, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 38 through 41 or (resid 42...
d_2ens_1(chain "B" and ((resid 38 through 40 and (name N...
d_1ens_2(chain "C" and (resid 698 through 709 or (resid 710...
d_2ens_2(chain "D" and (resid 698 through 737 or (resid 738...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNMETA1 - 235
d_21ens_1ASNMETB1 - 235
d_11ens_2GLUGLUF4 - 93
d_12ens_2ZNZNG
d_21ens_2GLUGLUC1 - 90
d_22ens_2ZNZND

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.884705442802, -0.466139519923, 0.00319803728883), (-0.466149455628, -0.884668205264, 0.00817628358751), (-0.000982086997558, -0.00872436593302, -0.999961459729)23.1123205341, -18.14406048, 72.9340927344
2given(0.884243430136, -0.466702981804, -0.0173747816474), (-0.466759938387, -0.884383631536, 0.000867287269621), (-0.0157707380453, 0.00734295894102, -0.999848670938)23.0581201569, -17.6876849939, 73.3559168907

-
Components

#1: Protein RING-type E3 ubiquitin transferase


Mass: 26991.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri serotype 5a (strain M90T) (bacteria)
Strain: M90T / Gene: ipaH1.4, S0283, pWR501_0283 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9AFJ5, RING-type E3 ubiquitin transferase
#2: Protein E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP


Mass: 11637.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96EP0, RBR-type E3 ubiquitin transferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8
Details: 2%(v/v) 1,4-dioxane, 0.1 M Tris-HCl (pH 8.0), 15%(v/v) PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.75→72.78 Å / Num. obs: 18572 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 53.84 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.05 / Net I/σ(I): 11
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 5.1 / Num. unique obs: 2667 / CC1/2: 0.963 / Rpim(I) all: 0.168 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDS20190606data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EDV

5edv


Resolution: 2.75→60.36 Å / SU ML: 0.3307 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2661
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2781 972 5.24 %
Rwork0.2201 17577 -
obs0.2233 18549 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.64 Å2
Refinement stepCycle: LAST / Resolution: 2.75→60.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 4 0 4800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01374908
X-RAY DIFFRACTIONf_angle_d1.99536734
X-RAY DIFFRACTIONf_chiral_restr0.1221815
X-RAY DIFFRACTIONf_plane_restr0.0143879
X-RAY DIFFRACTIONf_dihedral_angle_d9.0969674
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS0.683834204686
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS1.46056418511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.90.34461410.26392461X-RAY DIFFRACTION99.43
2.9-3.080.33821370.25752473X-RAY DIFFRACTION100
3.08-3.320.34541350.26322484X-RAY DIFFRACTION100
3.32-3.650.31141300.22952475X-RAY DIFFRACTION99.88
3.65-4.180.25251490.19572506X-RAY DIFFRACTION99.89
4.18-5.270.24011390.18882539X-RAY DIFFRACTION99.93
5.27-60.360.26121410.22562639X-RAY DIFFRACTION99.5

+
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