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- PDB-6loj: The complex structure of IpaH9.8-LRR and hGBP1 -

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Basic information

Entry
Database: PDB / ID: 6loj
TitleThe complex structure of IpaH9.8-LRR and hGBP1
Components
  • Guanylate-binding protein 1
  • Invasion plasmid antigen
KeywordsLIGASE/HYDROLASE / IpaH9.8 / hGBP1 / LRR / TRANSFERASE / LIGASE-HYDROLASE complex
Function / homology
Function and homology information


modulation of process of another organism / GDP phosphatase activity / non-canonical inflammasome complex assembly / negative regulation of substrate adhesion-dependent cell spreading / protein localization to vacuole / symbiont cell surface / protein K27-linked ubiquitination / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane ...modulation of process of another organism / GDP phosphatase activity / non-canonical inflammasome complex assembly / negative regulation of substrate adhesion-dependent cell spreading / protein localization to vacuole / symbiont cell surface / protein K27-linked ubiquitination / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / host cell cytosol / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / spectrin binding / defense response to protozoan / ligase activity / cytokine binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cellular response to interleukin-1 / negative regulation of protein localization to plasma membrane / protein K48-linked ubiquitination / regulation of protein localization to plasma membrane / regulation of calcium-mediated signaling / cytoplasmic vesicle membrane / lipopolysaccharide binding / Hsp90 protein binding / negative regulation of ERK1 and ERK2 cascade / RING-type E3 ubiquitin transferase / cellular response to type II interferon / Interferon gamma signaling / ubiquitin-protein transferase activity / GDP binding / ubiquitin protein ligase activity / cellular response to tumor necrosis factor / actin cytoskeleton / actin binding / G protein activity / cytoplasmic vesicle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response to virus / host cell cytoplasm / protein ubiquitination / defense response to bacterium / symbiont-mediated suppression of host innate immune response / Golgi membrane / innate immune response / GTPase activity / GTP binding / host cell nucleus / enzyme binding / Golgi apparatus / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / Guanylate-binding protein, C-terminal / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / : / Guanylate-binding protein, C-terminal domain superfamily ...Novel E3 ligase (NEL) domain profile. / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / Guanylate-binding protein, C-terminal / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / : / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / Leucine-rich repeats, bacterial type / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / RING-type E3 ubiquitin transferase / E3 ubiquitin-protein ligase ipaH9.8 / Guanylate-binding protein 1
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.72 Å
AuthorsYe, Y. / Huang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21907006 China
CitationJournal: Commun Biol / Year: 2020
Title: Substrate-binding destabilizes the hydrophobic cluster to relieve the autoinhibition of bacterial ubiquitin ligase IpaH9.8.
Authors: Ye, Y. / Xiong, Y. / Huang, H.
History
DepositionJan 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Invasion plasmid antigen
B: Guanylate-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4393
Polymers93,9962
Non-polymers4431
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-5 kcal/mol
Surface area41260 Å2
Unit cell
Length a, b, c (Å)122.490, 122.490, 582.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Invasion plasmid antigen


Mass: 25620.730 Da / Num. of mol.: 1 / Fragment: LRR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaH9.8, NCTC9783_05321 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A380D7J9, UniProt: D2AJU0*PLUS, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Guanylate-binding protein 1 / GTP-binding protein 1 / HuGBP-1 / Guanine nucleotide-binding protein 1 / Interferon-induced ...GTP-binding protein 1 / HuGBP-1 / Guanine nucleotide-binding protein 1 / Interferon-induced guanylate-binding protein 1


Mass: 68375.047 Da / Num. of mol.: 1 / Mutation: Q507H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBP1 / Production host: Escherichia coli (E. coli)
References: UniProt: P32455, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
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: 6.39 Å3/Da / Density % sol: 80.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2.5M NaCl, 0.1M K/Na phosphate buffer, pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.72→60.91 Å / Num. obs: 28447 / % possible obs: 99.65 % / Redundancy: 37.3 % / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 12.52
Reflection shellResolution: 3.72→3.853 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 2.59 / Num. unique obs: 2754 / CC1/2: 0.775 / % possible all: 99.38

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F5N

1f5n


Resolution: 3.72→60.91 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 2.59 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 1416 4.99 %RANDOM
Rwork0.2272 26956 --
obs0.2287 28371 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 412.45 Å2 / Biso mean: 192.1398 Å2 / Biso min: 91.02 Å2
Refinement stepCycle: final / Resolution: 3.72→60.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6101 0 28 0 6129
Biso mean--181.13 --
Num. residues----793
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.72-3.850.36441360.3404260599
3.85-4.010.34971370.30522605100
4.01-4.190.28071350.2528261899
4.19-4.410.2751400.213264699
4.41-4.690.22831390.18052647100
4.69-5.050.21741400.17242655100
5.05-5.560.25941420.21272693100
5.56-6.360.28781430.26692711100
6.36-8.010.30431460.27852774100
8.01-60.910.21811580.20723002100
Refinement TLS params.Method: refined / Origin x: -45.3127 Å / Origin y: 28.1399 Å / Origin z: 5.9112 Å
111213212223313233
T1.7485 Å20.0241 Å20.2423 Å2-0.8474 Å2-0.0121 Å2--1.1455 Å2
L0.8174 °2-0.8232 °2-0.734 °2-1.1102 °21.329 °2--2.212 °2
S-0.2669 Å °-0.1897 Å °0.0902 Å °0.3663 Å °0.4451 Å °0.0352 Å °0.1583 Å °-0.0485 Å °-0.1103 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA19 - 240
2X-RAY DIFFRACTION1allB3 - 585
3X-RAY DIFFRACTION1allB601

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