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- PDB-6k2d: The crystal structure of GBP1 with LRR domain of IpaH9.8 -

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Basic information

Entry
Database: PDB / ID: 6k2d
TitleThe crystal structure of GBP1 with LRR domain of IpaH9.8
Components
  • E3 ubiquitin-protein ligase ipaH9.8
  • Guanylate-binding protein 1
KeywordsHYDROLASE/TRANSFERASE / Complex / HYDROLASE-TRANSFERASE complex
Function / homology
Function and homology information


symbiont-mediated suppression of host inflammatory response / GDP phosphatase activity / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host NF-kappaB cascade / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / protein K27-linked ubiquitination / symbiont cell surface ...symbiont-mediated suppression of host inflammatory response / GDP phosphatase activity / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host NF-kappaB cascade / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / protein K27-linked ubiquitination / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of protein localization to plasma membrane / host cell cytosol / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / spectrin binding / cytokine binding / defense response to protozoan / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / regulation of protein localization to plasma membrane / cellular response to interleukin-1 / protein autoubiquitination / protein K48-linked ubiquitination / regulation of calcium-mediated signaling / G protein activity / lipopolysaccharide binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / RING-type E3 ubiquitin transferase / cytoplasmic vesicle membrane / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / ubiquitin-protein transferase activity / GDP binding / Interferon gamma signaling / ubiquitin protein ligase activity / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / defense response to bacterium / Golgi membrane / innate immune response / GTPase activity / host cell nucleus / GTP binding / Golgi apparatus / enzyme binding / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytoplasm / cytosol
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 / Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain ...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 / Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / 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, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Guanylate-binding protein 1 / E3 ubiquitin-protein ligase ipaH9.8
Similarity search - Component
Biological speciesHomo sapiens (human)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsJi, C.G. / Xiao, J.Y.
CitationJournal: Plos Pathog. / Year: 2019
Title: Structural mechanism for guanylate-binding proteins (GBPs) targeting by the Shigella E3 ligase IpaH9.8.
Authors: Ji, C. / Du, S. / Li, P. / Zhu, Q. / Yang, X. / Long, C. / Yu, J. / Shao, F. / Xiao, J.Y.
History
DepositionMay 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: 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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanylate-binding protein 1
B: E3 ubiquitin-protein ligase ipaH9.8


Theoretical massNumber of molelcules
Total (without water)81,3342
Polymers81,3342
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint1 kcal/mol
Surface area32710 Å2
Unit cell
Length a, b, c (Å)211.736, 211.736, 56.975
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: 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: 54577.098 Da / Num. of mol.: 1
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
#2: Protein E3 ubiquitin-protein ligase ipaH9.8 / Invasion plasmid antigen ipaH9.8 / RING-type E3 ubiquitin transferase ipaH9.8


Mass: 26757.084 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, CP0226, pWR501_0234, SFLP090 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8VSC3, RING-type E3 ubiquitin transferase

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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: 4.53 Å3/Da / Density % sol: 75.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.6M Sodium/potassium phosphate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 17259 / % possible obs: 100 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.068 / Rrim(I) all: 0.208 / Χ2: 0.987 / Net I/σ(I): 7.7 / Num. measured all: 169472
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.6-3.669.42.8958440.7060.9923.0620.988100
3.66-3.739.51.9578420.7240.6692.071.246100
3.73-3.89.81.4568630.9090.4881.5370.976100
3.8-3.88101.5838390.9190.5261.6690.992100
3.88-3.969.71.5388550.8750.5191.6251.438100
3.96-4.0510.20.8668600.9620.2840.9120.976100
4.05-4.16100.858660.9370.2810.8950.991100
4.16-4.27100.6338510.9640.2090.6670.975100
4.27-4.399.80.4698720.9790.1570.4950.97799.9
4.39-4.549.70.3928270.9750.1310.4141.026100
4.54-4.79.20.3538910.9760.1210.3741.003100
4.7-4.898.40.3048460.9720.1090.3241.00999.9
4.89-5.1110.50.2788590.9810.090.2930.938100
5.11-5.3810.70.2688580.980.0860.2820.979100
5.38-5.7110.60.238860.9880.0750.2420.916100
5.71-6.1510.70.2118370.9870.0680.2220.884100
6.15-6.7710.30.1698760.9850.0550.1780.859100
6.77-7.75100.1328860.9910.0440.1390.779100
7.75-9.758.50.1218810.9920.0440.1290.825100
9.75-509.50.1399200.970.050.1481.019100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→48.392 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2872 730 5.04 %RANDOM
Rwork0.2404 ---
obs0.2429 14486 61.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.6→48.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5138 0 0 0 5138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035243
X-RAY DIFFRACTIONf_angle_d0.5427097
X-RAY DIFFRACTIONf_dihedral_angle_d13.3253219
X-RAY DIFFRACTIONf_chiral_restr0.038800
X-RAY DIFFRACTIONf_plane_restr0.005914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5951-3.78450.4355370.2933706X-RAY DIFFRACTION16
3.7845-4.02150.3192790.2711429X-RAY DIFFRACTION32
4.0215-4.33190.27641190.2382246X-RAY DIFFRACTION50
4.3319-4.76740.28691340.21662578X-RAY DIFFRACTION57
4.7674-5.45650.28511980.21583646X-RAY DIFFRACTION81
5.4565-6.87150.32132180.25444521X-RAY DIFFRACTION100
6.8715-48.39660.24712510.24384410X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 79.8906 Å / Origin y: -52.4794 Å / Origin z: 17.4764 Å
111213212223313233
T-0.1022 Å2-0.0073 Å20.3597 Å2--0.17 Å20.3973 Å2---0.333 Å2
L0.1616 °20.4153 °20.0829 °2-0.0484 °2-0.0755 °2--0.2324 °2
S0.1393 Å °0.1386 Å °0.1716 Å °0.1454 Å °0.137 Å °0.5645 Å °-0.1818 Å °-0.3712 Å °0.2583 Å °
Refinement TLS groupSelection details: all

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