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- PDB-8j9b: LnaB-actin binary complex -

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Basic information

Entry
Database: PDB / ID: 8j9b
TitleLnaB-actin binary complex
Components
  • Actin gamma 1
  • Type IV secretion protein Dot
KeywordsTRANSFERASE / Legionella / AMPylation / Actin
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 / regulation of focal adhesion assembly / apical junction complex / sarcomere organization ...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 / regulation of focal adhesion assembly / apical junction complex / sarcomere organization / positive regulation of wound healing / myofibril / regulation of synaptic vesicle endocytosis / filamentous actin / phagocytic vesicle / calyx of Held / Schaffer collateral - CA1 synapse / structural constituent of cytoskeleton / cellular response to type II interferon / angiogenesis / positive regulation of cell migration / ubiquitin protein ligase binding / positive regulation of gene expression / extracellular exosome / identical protein binding
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 / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin gamma 1 / Type IV secretion protein Dot
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 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: Structure of Legionella effector LnaB-actin binary complex
Authors: Chen, T.T. / Ouyang, S.Y.
History
DepositionMay 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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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: Actin gamma 1
D: Actin gamma 1
E: Actin gamma 1
F: Actin gamma 1
H: Type IV secretion protein Dot
I: Type IV secretion protein Dot
J: Type IV secretion protein Dot
K: Type IV secretion protein Dot


Theoretical massNumber of molelcules
Total (without water)455,52310
Polymers455,52310
Non-polymers00
Water00
1
A: Actin gamma 1
B: Actin gamma 1
C: Actin gamma 1
D: Actin gamma 1
E: Actin gamma 1
F: Actin gamma 1
H: Type IV secretion protein Dot
I: Type IV secretion protein Dot
J: Type IV secretion protein Dot
K: Type IV secretion protein Dot

A: Actin gamma 1
B: Actin gamma 1
C: Actin gamma 1
D: Actin gamma 1
E: Actin gamma 1
F: Actin gamma 1
H: Type IV secretion protein Dot
I: Type IV secretion protein Dot
J: Type IV secretion protein Dot
K: Type IV secretion protein Dot


Theoretical massNumber of molelcules
Total (without water)911,04620
Polymers911,04620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area2950 Å2
ΔGint-14 kcal/mol
Surface area30520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.577, 110.577, 407.927
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Actin gamma 1


Mass: 41838.766 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A8C6VAB1
#2: Protein
Type IV secretion protein Dot


Mass: 51122.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_12730 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AA44XJB8

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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: 2.9 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 289 K / Method: evaporation / Details: PEG4000,Sodium HEPES,Ammonnium sulfate

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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: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.42→135 Å / Num. obs: 74997 / % possible obs: 99.6 % / Redundancy: 4.2 % / CC1/2: 0.975 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.111 / Rrim(I) all: 0.23 / Χ2: 0.96 / Net I/σ(I): 7.7
Reflection shellResolution: 3.42→3.61 Å / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.637 / Num. measured all: 45713 / Num. unique obs: 10997 / CC1/2: 0.47 / Rpim(I) all: 0.358 / Rrim(I) all: 0.733 / Χ2: 0.85 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.42→62.1 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.298 3802 -
Rwork0.287 --
obs-74997 100 %
Refinement stepCycle: LAST / Resolution: 3.42→62.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26805 0 0 0 26805

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