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- PDB-8k6i: LnaB-Actin-PRUb ternary complex -

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Basic information

Entry
Database: PDB / ID: 8k6i
TitleLnaB-Actin-PRUb ternary complex
Components
  • Actin gamma 1
  • Legionella effector LnaB
  • ubiquitin
KeywordsTOXIN / AMPylation / Legionella effector
Function / homology
Function and homology information


basal body patch / tight junction assembly / profilin binding / regulation of transepithelial transport / morphogenesis of a polarized epithelium / protein localization to bicellular tight junction / regulation of stress fiber assembly / sarcomere organization / regulation of focal adhesion assembly / apical junction complex ...basal body patch / tight junction assembly / profilin binding / regulation of transepithelial transport / morphogenesis of a polarized epithelium / protein localization to bicellular tight junction / regulation of stress fiber assembly / sarcomere organization / regulation of focal adhesion assembly / apical junction complex / positive regulation of wound healing / myofibril / filamentous actin / regulation of synaptic vesicle endocytosis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / phagocytic vesicle / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / APC/C:Cdc20 mediated degradation of Securin / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / SCF-beta-TrCP mediated degradation of Emi1 / calyx of Held / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR3 signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR2 signaling / Degradation of DVL / Peroxisomal protein import / Negative regulation of FGFR4 signaling / Stabilization of p53 / Dectin-1 mediated noncanonical NF-kB signaling
Similarity search - Function
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / : / Ubiquitin domain ...Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / : / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin conserved site / ATPase, nucleotide binding domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-AR6 / PHOSPHATE ION / Actin gamma 1 / Polyubiquitin-C
Similarity search - Component
Biological speciesLegionella (bacteria)
Homo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsChen, T.T. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Structure and mechanism of an actin-dependent bacterial phosphoryl AMPylase.
Authors: Chen, T.T. / Lu, Q. / Zheng, S.R. / Fu, J. / Chen, J. / Kang, L. / Wu, J. / Luo, J. / Tong, J. / Li, S. / Li, X. / Li, S. / Li, J. / Wang, S. / Feng, Y. / Luo, Z.Q. / Ouyang, S.
History
DepositionJul 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin gamma 1
B: Actin gamma 1
C: Legionella effector LnaB
D: Legionella effector LnaB
E: ubiquitin
F: ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,0208
Polymers182,3656
Non-polymers6542
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.377, 165.308, 224.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 3 types, 6 molecules ABCDEF

#1: Protein Actin gamma 1


Mass: 41838.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A8C6VAB1
#2: Protein Legionella effector LnaB


Mass: 40622.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella (bacteria) / Production host: Escherichia coli (E. coli)
#3: Protein ubiquitin


Mass: 8720.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48

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Non-polymers , 3 types, 37 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 289 K / Method: evaporation / Details: Sodium Chloride, PEG8000, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.19→41.33 Å / Num. obs: 36304 / % possible obs: 91 % / Redundancy: 2 % / CC1/2: 0.75 / Net I/σ(I): 5.56
Reflection shellResolution: 3.19→3.3 Å / Num. unique obs: 1662 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.19→41.33 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.47 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3148 1662 4.99 %
Rwork0.2922 --
obs0.2933 33338 91.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.19→41.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12449 0 19 35 12503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02312708
X-RAY DIFFRACTIONf_angle_d2.44317175
X-RAY DIFFRACTIONf_dihedral_angle_d17.9894810
X-RAY DIFFRACTIONf_chiral_restr0.1681934
X-RAY DIFFRACTIONf_plane_restr0.012203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.280.3481220.33972522X-RAY DIFFRACTION90
3.28-3.390.34741230.33012591X-RAY DIFFRACTION90
3.39-3.510.29881410.28922705X-RAY DIFFRACTION95
3.51-3.650.37531470.30072654X-RAY DIFFRACTION93
3.65-3.820.32771470.29052663X-RAY DIFFRACTION93
3.82-4.020.33051460.28562585X-RAY DIFFRACTION91
4.02-4.270.3171170.29232583X-RAY DIFFRACTION90
4.27-4.60.28961630.26972606X-RAY DIFFRACTION90
4.6-5.060.27361350.2742616X-RAY DIFFRACTION90
5.06-5.790.3191440.31232650X-RAY DIFFRACTION90
5.79-7.290.31461280.30552651X-RAY DIFFRACTION89
7.29-41.330.27811490.2592850X-RAY DIFFRACTION92

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