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- PDB-8k6f: LnaB-Actin-PRUb ternary complex -

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Basic information

Entry
Database: PDB / ID: 8k6f
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 / protein localization to bicellular tight junction / profilin binding / regulation of transepithelial transport / morphogenesis of a polarized epithelium / regulation of stress fiber assembly / symbiont entry into host cell via disruption of host cell glycocalyx / sarcomere organization / regulation of focal adhesion assembly ...basal body patch / tight junction assembly / protein localization to bicellular tight junction / profilin binding / regulation of transepithelial transport / morphogenesis of a polarized epithelium / regulation of stress fiber assembly / symbiont entry into host cell via disruption of host cell glycocalyx / sarcomere organization / regulation of focal adhesion assembly / apical junction complex / symbiont entry into host cell via disruption of host cell envelope / positive regulation of wound healing / virus tail / filamentous actin / myofibril / regulation of synaptic vesicle endocytosis / phagocytic vesicle / calyx of Held / structural constituent of cytoskeleton / cellular response to type II interferon / Schaffer collateral - CA1 synapse / angiogenesis / positive regulation of cell migration / ubiquitin protein ligase binding / positive regulation of gene expression / extracellular exosome / identical protein binding
Similarity search - Function
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin ...Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Chem-AR6 / ADENOSINE-5'-TRIPHOSPHATE / Actin gamma 1 / Tail fiber
Similarity search - Component
Biological speciesLegionella (bacteria)
Homo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å
AuthorsChen, T.T. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Complex structure of Legionella effector LnaB with host Actin and PR-Ub
Authors: Chen, T.T. / Ouyang, S.
History
DepositionJul 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)183,6519
Polymers182,0776
Non-polymers1,5743
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.690, 214.227, 79.563
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#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
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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 289 K / Method: evaporation / Details: PEG8000, Sodium Choride, Sodium HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.978565 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 3.41→37.29 Å / Num. obs: 24455 / % possible obs: 97 % / Redundancy: 1.9 % / CC1/2: 0.961 / Rmerge(I) obs: 0.1299 / Net I/σ(I): 3.54
Reflection shellResolution: 3.41→3.53 Å / Num. unique obs: 1967 / CC1/2: 0.678

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.41→37.29 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 1967 8.18 %
Rwork0.2218 --
obs0.2236 24054 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.41→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12627 0 76 0 12703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01712955
X-RAY DIFFRACTIONf_angle_d1.88117523
X-RAY DIFFRACTIONf_dihedral_angle_d13.8234901
X-RAY DIFFRACTIONf_chiral_restr0.1171963
X-RAY DIFFRACTIONf_plane_restr0.0082242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.41-3.50.29651370.27711535X-RAY DIFFRACTION96
3.5-3.590.27791370.26241595X-RAY DIFFRACTION97
3.59-3.70.29281430.25471570X-RAY DIFFRACTION96
3.7-3.820.27341390.24491546X-RAY DIFFRACTION97
3.82-3.950.271480.23471597X-RAY DIFFRACTION97
3.96-4.110.23911340.22251569X-RAY DIFFRACTION98
4.11-4.30.26551390.21531578X-RAY DIFFRACTION97
4.3-4.530.22881380.19471600X-RAY DIFFRACTION97
4.53-4.810.2631430.20071562X-RAY DIFFRACTION97
4.81-5.180.19711370.20451568X-RAY DIFFRACTION97
5.18-5.70.261430.24011602X-RAY DIFFRACTION97
5.7-6.520.22721400.24191606X-RAY DIFFRACTION98
6.52-8.20.20191420.22591585X-RAY DIFFRACTION98
8.2-37.290.20081470.17911574X-RAY DIFFRACTION96

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