[English] 日本語
Yorodumi
- PDB-7v8e: Crystal structure of IpaH1.4 LRR domain bound to HOIL-1L UBL domain. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v8e
TitleCrystal structure of IpaH1.4 LRR domain bound to HOIL-1L UBL domain.
Components
  • RING-type E3 ubiquitin transferase
  • RanBP-type and C3HC4-type zinc finger-containing protein 1
KeywordsLIGASE / E3 liagse / ubiquitin / innate immune
Function / homology
Function and homology information


modulation of process of another organism / protein linear polyubiquitination / LUBAC complex / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / negative regulation of NF-kappaB transcription factor activity ...modulation of process of another organism / protein linear polyubiquitination / LUBAC complex / RBR-type E3 ubiquitin transferase / cytoplasmic sequestering of protein / ubiquitin ligase activator activity / negative regulation of necroptotic process / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / negative regulation of NF-kappaB transcription factor activity / protein sequestering activity / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / positive regulation of non-canonical NF-kappaB signal transduction / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / host cell cytoplasm / transcription coactivator activity / protein ubiquitination / defense response to bacterium / extracellular region / identical protein binding / metal ion 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 / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain ...: / : / : / 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 / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Leucine-rich repeats, bacterial type / 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. / Ring finger / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
RING-type E3 ubiquitin transferase / RanBP-type and C3HC4-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesShigella flexneri 5a str. M90T (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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
B: RING-type E3 ubiquitin transferase
C: RanBP-type and C3HC4-type zinc finger-containing protein 1
A: RING-type E3 ubiquitin transferase
D: RanBP-type and C3HC4-type zinc finger-containing protein 1


Theoretical massNumber of molelcules
Total (without water)74,3514
Polymers74,3514
Non-polymers00
Water7,764431
1
B: RING-type E3 ubiquitin transferase
C: RanBP-type and C3HC4-type zinc finger-containing protein 1


Theoretical massNumber of molelcules
Total (without water)37,1752
Polymers37,1752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RING-type E3 ubiquitin transferase
D: RanBP-type and C3HC4-type zinc finger-containing protein 1


Theoretical massNumber of molelcules
Total (without water)37,1752
Polymers37,1752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.809, 142.684, 68.598
Angle α, β, γ (deg.)90.000, 94.035, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 36 through 49 or (resid 50...
d_2ens_1(chain "B" and (resid 36 or (resid 37 and (name...
d_1ens_2(chain "C" and (resid 54 through 55 or (resid 56...
d_2ens_2(chain "D" and (resid 54 through 63 or (resid 67...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYSERC1 - 236
d_21ens_1GLYSERA1 - 236
d_11ens_2ASPLEUB3 - 76
d_21ens_2ASPASPD1 - 10
d_22ens_2HISLEUD14 - 77

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.993261623943, 0.0379218707484, 0.109513826162), (0.0379016551697, -0.999278902674, 0.00226698156266), (0.109520824217, 0.00189904948713, -0.993982687311)5.43914208425, 8.19530428678, -32.358298257
2given(0.999667120983, -0.0255865605408, 0.00331287569647), (-0.025618646526, -0.999621420455, 0.0100349746856), (0.00305486102218, -0.0101165056445, -0.99994416051)-4.77015291414, 8.35848416093, -32.242872517

-
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 5a str. M90T (bacteria)
Strain: M90T / Gene: ipaH1.4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9AFJ5, RING-type E3 ubiquitin transferase
#2: Protein RanBP-type and C3HC4-type zinc finger-containing protein 1 / Heme-oxidized IRP2 ubiquitin ligase 1 / HOIL-1 / RING-type E3 ubiquitin transferase HOIL-1


Mass: 10183.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9BYM8, RBR-type E3 ubiquitin transferase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5
Details: 0.2 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.5), and 25% (w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→49.38 Å / Num. obs: 47800 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 34.14 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.025 / Net I/σ(I): 16.3
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3094 / CC1/2: 0.765 / Rpim(I) all: 0.283 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDS20190606data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DBG

4dbg


Resolution: 1.9→23.78 Å / SU ML: 0.2683 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.1135
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2457 2417 5.06 %
Rwork0.2009 45303 -
obs0.2032 47720 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 0 431 5269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814955
X-RAY DIFFRACTIONf_angle_d0.96976785
X-RAY DIFFRACTIONf_chiral_restr0.0579802
X-RAY DIFFRACTIONf_plane_restr0.0075881
X-RAY DIFFRACTIONf_dihedral_angle_d5.8088653
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS0.55665391425
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.96573419658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.37271420.32992631X-RAY DIFFRACTION99.43
1.94-1.980.34331380.29292711X-RAY DIFFRACTION99.23
1.98-2.030.35681370.26372574X-RAY DIFFRACTION99.12
2.03-2.080.29231620.26042625X-RAY DIFFRACTION99.22
2.08-2.130.28041410.24072703X-RAY DIFFRACTION99.96
2.13-2.20.321290.2432659X-RAY DIFFRACTION99.96
2.2-2.270.30371380.23322701X-RAY DIFFRACTION100
2.27-2.350.29511400.23142630X-RAY DIFFRACTION99.93
2.35-2.440.28651450.23472719X-RAY DIFFRACTION100
2.44-2.550.26641460.23432608X-RAY DIFFRACTION99.71
2.55-2.690.29251290.23462691X-RAY DIFFRACTION99.86
2.69-2.860.28421450.22742681X-RAY DIFFRACTION99.82
2.86-3.080.25891470.22342642X-RAY DIFFRACTION100
3.08-3.380.26951600.21122660X-RAY DIFFRACTION99.96
3.38-3.870.20681330.16692701X-RAY DIFFRACTION99.79
3.87-4.870.17881400.14792677X-RAY DIFFRACTION99.75
4.87-23.780.19651450.17412690X-RAY DIFFRACTION99.2

+
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