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- PDB-7v8g: Crystal structure of HOIP RING1 domain bound to IpaH1.4 LRR domain -

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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 / RBR-type E3 ubiquitin transferase / CD40 signaling pathway / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling ...modulation of process of another organism / protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / RBR-type E3 ubiquitin transferase / CD40 signaling pathway / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / positive regulation of NF-kappaB transcription factor activity / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / T cell receptor signaling pathway / host cell cytoplasm / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / protein ubiquitination / ubiquitin protein ligase binding / extracellular region / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Novel E3 ligase (NEL) domain 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 / : / E3 ubiquitin-protein ligase RNF31, UBA domain / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain ...Novel E3 ligase (NEL) domain 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 / : / E3 ubiquitin-protein ligase RNF31, UBA domain / 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 domain / PUB-like domain superfamily / PUB domain / IBR 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 superfamily / Zinc finger RanBP2-type signature. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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