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- PDB-6sku: Legionella effector AnkX in complex with human Rab1b -

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Basic information

Entry
Database: PDB / ID: 6sku
TitleLegionella effector AnkX in complex with human Rab1b
Components
  • Phosphocholine transferase AnkX
  • Ras-related protein Rab-1B
KeywordsSIGNALING PROTEIN / Disease / Post Translational Modification / Crosslink / Small G-protein
Function / homology
Function and homology information


phosphocholine transferase activity / positive regulation of glycoprotein metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic ...phosphocholine transferase activity / positive regulation of glycoprotein metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / regulation of GTPase activity / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / small monomeric GTPase / G protein activity / intracellular protein transport / host cell cytoplasm / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Fido-like domain superfamily / Fido domain / Fic/DOC family / Fido domain profile. / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase ...Fido-like domain superfamily / Fido domain / Fic/DOC family / Fido domain profile. / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Phosphocholine transferase AnkX / Ras-related protein Rab-1B
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsErnst, S. / Ecker, F. / Kaspers, M. / Ochtrop, P. / Hedberg, C. / Groll, M. / Itzen, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchSFB1035 Germany
CitationJournal: Sci Adv / Year: 2020
Title: Legionellaeffector AnkX displaces the switch II region for Rab1b phosphocholination.
Authors: Ernst, S. / Ecker, F. / Kaspers, M.S. / Ochtrop, P. / Hedberg, C. / Groll, M. / Itzen, A.
History
DepositionAug 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphocholine transferase AnkX
B: Ras-related protein Rab-1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8824
Polymers110,4142
Non-polymers4682
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-24 kcal/mol
Surface area44570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.350, 68.470, 137.370
Angle α, β, γ (deg.)90.000, 98.930, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phosphocholine transferase AnkX / PC transferase / Ankyrin repeat-containing protein X


Mass: 90703.148 Da / Num. of mol.: 1 / Mutation: C48S, C84S, G108C, C172S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: ankX, legA8, lpg0695 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5ZXN6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein Ras-related protein Rab-1B


Mass: 19711.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H0U4
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.72 Å3/Da / Density % sol: 66.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 3.5 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 25684 / % possible obs: 97.5 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.9
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2264 / CC1/2: 0.813

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BES, 3NKV

4bes

3nkv


Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 76.522 / SU ML: 0.544 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.532
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2879 1283 5 %RANDOM
Rwork0.2471 ---
obs0.2493 24372 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 230.08 Å2 / Biso mean: 138.743 Å2 / Biso min: 69.28 Å2
Baniso -1Baniso -2Baniso -3
1--3.24 Å2-0 Å2-3.23 Å2
2--13.21 Å20 Å2
3----8.53 Å2
Refinement stepCycle: final / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7528 0 29 0 7557
Biso mean--94.28 --
Num. residues----949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0137699
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177285
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.64510400
X-RAY DIFFRACTIONr_angle_other_deg1.0291.5816976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6925945
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2123.856376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.364151430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1021532
X-RAY DIFFRACTIONr_chiral_restr0.0420.21018
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028451
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021489
X-RAY DIFFRACTIONr_rigid_bond_restr0.154314980
LS refinement shellResolution: 3.2→3.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 95 -
Rwork0.406 1789 -
all-1884 -
obs--98.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.57020.1640.75570.15680.48631.9545-0.1184-0.27740.0224-0.0934-0.04850.1389-0.3429-0.19490.16690.06270.0221-0.05150.1815-0.01080.2837-37.3615-15.126732.053
21.290.0084-0.60631.9408-0.34642.94680.0169-0.40730.06070.057-0.14270.1403-0.1852-0.17270.12580.01730.02-0.0210.2121-0.10240.1662-53.0103-20.764317.8871
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 800
2X-RAY DIFFRACTION2B2 - 202

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