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- PDB-7wjq: Crystal structure of GSDMB in complex with Ipah7.8 -

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Basic information

Entry
Database: PDB / ID: 7wjq
TitleCrystal structure of GSDMB in complex with Ipah7.8
Components
  • Isoform 2 of Gasdermin-B
  • Probable E3 ubiquitin-protein ligase ipaH7.8
KeywordsANTIVIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host programmed cell death / cytotoxic T cell pyroptotic cell death / effector-mediated activation of programmed cell death in host / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / phosphatidylinositol-4,5-bisphosphate binding ...symbiont-mediated suppression of host programmed cell death / cytotoxic T cell pyroptotic cell death / effector-mediated activation of programmed cell death in host / wide pore channel activity / killing by host of symbiont cells / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / phosphatidylinositol-4,5-bisphosphate binding / RING-type E3 ubiquitin transferase / phospholipid binding / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / killing of cells of another organism / defense response to Gram-negative bacterium / host cell cytoplasm / protein ubiquitination / defense response to bacterium / extracellular region / plasma membrane / 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 / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Leucine-rich repeats, bacterial type / Leucine-rich repeat 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 / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Leucine-rich repeats, bacterial type / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase ipaH7.8 / Gasdermin-B
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, X. / Zhang, H. / Yin, H.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Nat Commun / Year: 2023
Title: Insights into the GSDMB-mediated cellular lysis and its targeting by IpaH7.8
Authors: Yin, H. / Zheng, J. / He, Q. / Zhang, X. / Li, X. / Ma, Y. / Liang, X. / Gao, J. / Kocsis, B.L. / Li, Z. / Liu, X. / Alto, N.M. / Li, L. / Zhang, H.
History
DepositionJan 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
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: Probable E3 ubiquitin-protein ligase ipaH7.8
B: Isoform 2 of Gasdermin-B


Theoretical massNumber of molelcules
Total (without water)72,3782
Polymers72,3782
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint4 kcal/mol
Surface area28560 Å2
Unit cell
Length a, b, c (Å)70.471, 87.584, 102.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Probable E3 ubiquitin-protein ligase ipaH7.8 / Probable RING-type E3 ubiquitin transferase ipaH7.8


Mass: 27895.385 Da / Num. of mol.: 1 / Mutation: M262D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P18014, RING-type E3 ubiquitin transferase
#2: Protein Isoform 2 of Gasdermin-B / Gasdermin-like protein


Mass: 44482.590 Da / Num. of mol.: 1 / Mutation: R221S, K222A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSDMB, GSDML, PP4052, PRO2521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TAX9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion
Details: NaCl, HEPES sodium, PEG 8000, ammonium sulfate, 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→66.67 Å / Num. obs: 17543 / % possible obs: 97 % / Redundancy: 10.7 % / Biso Wilson estimate: 47.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.6
Reflection shellResolution: 2.7→2.83 Å / Num. unique obs: 2254 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TJ4

5tj4


Resolution: 2.7→48.43 Å / SU ML: 0.2498 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2522 864 4.94 %
Rwork0.2102 16621 -
obs0.2123 17485 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.35 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 0 0 21 4555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264600
X-RAY DIFFRACTIONf_angle_d0.5426219
X-RAY DIFFRACTIONf_chiral_restr0.0379732
X-RAY DIFFRACTIONf_plane_restr0.005803
X-RAY DIFFRACTIONf_dihedral_angle_d4.271605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.870.30271400.25222737X-RAY DIFFRACTION97.39
2.87-3.090.30551370.2782803X-RAY DIFFRACTION99.9
3.09-3.40.30961440.24682823X-RAY DIFFRACTION99.97
3.4-3.840.27151270.2162576X-RAY DIFFRACTION99.63
3.92-4.910.2261440.17092717X-RAY DIFFRACTION98.66
4.91-48.430.21191720.19262965X-RAY DIFFRACTION99.49
Refinement TLS params.Method: refined / Origin x: -26.7751240815 Å / Origin y: 5.07059930869 Å / Origin z: 12.2707426571 Å
111213212223313233
T0.312999175299 Å20.00315807305084 Å20.0298832482729 Å2-0.233052161562 Å20.0393003458233 Å2--0.208836038515 Å2
L1.71395090539 °2-0.571914583919 °2-0.599069481318 °2-0.864517506396 °20.55425983462 °2--0.890128622495 °2
S0.191002324365 Å °0.242519002104 Å °0.0761870586289 Å °-0.128874693433 Å °-0.122412075256 Å °-0.0583201579421 Å °-0.146630403701 Å °-0.115184697655 Å °-0.0637512599141 Å °
Refinement TLS groupSelection details: all

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