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- PDB-8k6v: LnaB-Actin-PRUb ternary complex -

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Basic information

Entry
Database: PDB / ID: 8k6v
TitleLnaB-Actin-PRUb ternary complex
Components
  • Actin gamma 1
  • 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 / symbiont entry into host cell via disruption of host cell glycocalyx / sarcomere organization / regulation of focal adhesion assembly ...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 / 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 / myofibril / filamentous actin / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-AR6 / Actin gamma 1 / Tail fiber
Similarity search - Component
Biological speciesLegionella (bacteria)
Homo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: LnaB
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1045
Polymers91,0393
Non-polymers1,0662
Water2,270126
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)215.964, 55.044, 79.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Actin gamma 1


Mass: 41838.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A8C6VAB1
#2: Protein LnaB


Mass: 40622.980 Da / Num. of mol.: 1
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.: 1
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

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Non-polymers , 3 types, 128 molecules

#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 289 K / Method: evaporation / Details: Magnesium acetate, MOPS, PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979191 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: 0.979191 Å / Relative weight: 1
ReflectionResolution: 2.6→79.75 Å / Num. obs: 30202 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.915 / Net I/σ(I): 4.7
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 2918 / CC1/2: 0.693

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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: 2.6→79.75 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3069 1511 5.02 %
Rwork0.2527 --
obs0.2555 30085 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→79.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6252 0 67 126 6445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166447
X-RAY DIFFRACTIONf_angle_d1.5988728
X-RAY DIFFRACTIONf_dihedral_angle_d18.3092445
X-RAY DIFFRACTIONf_chiral_restr0.115979
X-RAY DIFFRACTIONf_plane_restr0.0091111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.41591370.38082520X-RAY DIFFRACTION99
2.68-2.780.35371360.30962550X-RAY DIFFRACTION100
2.78-2.890.34241420.27252565X-RAY DIFFRACTION100
2.89-3.020.35221190.30562559X-RAY DIFFRACTION100
3.02-3.180.37691370.28842569X-RAY DIFFRACTION100
3.18-3.380.30531250.27372586X-RAY DIFFRACTION100
3.38-3.640.37131260.28492584X-RAY DIFFRACTION100
3.64-4.010.34571360.25932603X-RAY DIFFRACTION100
4.01-4.590.26561460.19922624X-RAY DIFFRACTION100
4.59-5.780.25631460.21472631X-RAY DIFFRACTION100
5.78-79.750.23151610.20162783X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 28.536 Å / Origin y: 11.9357 Å / Origin z: 38.7402 Å
111213212223313233
T0.2436 Å20.015 Å20.0422 Å2-0.1994 Å2-0.0179 Å2--0.2456 Å2
L0.2426 °20.0215 °2-0.0591 °2-0.0366 °2-0.1443 °2--0.5604 °2
S0.0264 Å °-0.0143 Å °0.0164 Å °0.011 Å °-0.0023 Å °0.0148 Å °0.0149 Å °-0.0376 Å °-0.0312 Å °
Refinement TLS groupSelection details: all

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