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- PDB-5k35: Structure of the Legionella effector, AnkB, in complex with human Skp1 -

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Basic information

Entry
Database: PDB / ID: 5k35
TitleStructure of the Legionella effector, AnkB, in complex with human Skp1
Components
  • Ankyrin-repeat protein B
  • S-phase kinase-associated protein 1
KeywordsPROTEIN BINDING / bacterial effector / host-pathogen interaction / F-box protein / ankyrin repeats / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


F-box domain binding / PcG protein complex / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling ...F-box domain binding / PcG protein complex / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / cullin family protein binding / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / molecular function activator activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Iron uptake and transport / Negative regulation of NOTCH4 signaling / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / beta-catenin binding / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / : / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin remodeling / protein domain specific binding / centrosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A ...F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ankyrin-repeat protein B / S-phase kinase-associated protein 1 / F-box protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsWong, K. / Kozlov, G. / Gehring, K. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)GSP-48370 Canada
CitationJournal: Structure / Year: 2017
Title: Structural Mimicry by a Bacterial F Box Effector Hijacks the Host Ubiquitin-Proteasome System.
Authors: Wong, K. / Perpich, J.D. / Kozlov, G. / Cygler, M. / Abu Kwaik, Y. / Gehring, K.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin-repeat protein B
B: S-phase kinase-associated protein 1


Theoretical massNumber of molelcules
Total (without water)39,9082
Polymers39,9082
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-18 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.576, 57.039, 150.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ankyrin-repeat protein B


Mass: 21228.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: ankB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0A1EKG3, UniProt: Q5ZTL7*PLUS
#2: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


Mass: 18679.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P63208
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M trimethylamine N-oxide, 0.1 M Tris pH 8.5, 20% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 10735 / % possible obs: 100 % / Redundancy: 14.2 % / Rsym value: 0.113 / Net I/σ(I): 48.5
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 6.42 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 36.076 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R: 1.184 / ESU R Free: 0.385
RfactorNum. reflection% reflectionSelection details
Rfree0.27473 541 4.8 %RANDOM
Rwork0.21925 ---
obs0.22203 10735 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 73.448 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2--0.89 Å20 Å2
3----1.82 Å2
Refinement stepCycle: 1 / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 0 5 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192541
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9613427
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.845306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47325.691123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.83215486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9931512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211878
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4033.9191236
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.85.871538
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0754.1081305
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.66832.853951
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 40 -
Rwork0.319 688 -
obs--91.8 %
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)
15.8577-1.49143.27791.39261.59077.6871-0.0887-0.03240.6679-0.10520.0104-0.2831-0.2416-0.07660.07830.49330.05280.02020.4007-0.01620.36116.966122.8002-42.9464
21.35970.4557-0.73741.84380.04289.5305-0.2745-0.22680.0587-0.2291-0.03960.2429-0.9798-0.31570.31410.40550.1138-0.06420.2381-0.04560.11575.765823.5198-30.3851
35.63730.61960.80644.7824-1.46967.16540.35760.09980.1898-0.0649-0.4504-0.1752-0.65940.34040.09280.2638-0.02690.02340.24130.00030.2441-1.162424.3006-5.017
48.69880.1206-3.1994.0325-0.28492.30050.1570.3637-0.427-0.2439-0.3851-0.329-0.18950.22910.22810.25450.0217-0.01560.219-0.00860.2976-6.119216.0446-3.7023
58.34553.9753-1.74383.7286-0.23989.07050.15940.22580.41640.2044-0.08790.6502-0.2731-0.1392-0.07150.17430.04740.00130.2391-0.02020.2804-14.454718.8839-2.3459
66.9337-0.0863-2.22984.4721-1.48021.52370.4345-1.5046-1.21810.5187-0.45460.0191-0.21030.75420.02020.2289-0.1068-0.17360.43040.12890.6588-8.789610.87069.3319
718.7511-0.62823.40112.0616-1.42041.58450.0828-0.75870.65230.0645-0.03070.3718-0.2226-0.0675-0.05220.3572-0.02710.01810.2164-0.01090.3333-20.564216.69445.812
811.0605-2.60146.17672.9241.28896.76610.4430.94330.2759-0.4433-0.56520.058-0.03650.00960.12230.5273-0.0383-0.11980.48280.34390.407-1.156319.6787-71.8102
95.0178-5.43010.076412.29622.45254.41020.17280.3848-0.3904-1.23430.52620.3477-0.203-0.3715-0.6990.4324-0.12840.00270.36220.17780.4289-9.893421.9064-65.0261
101.99210.9961-1.77214.433-0.19612.0525-0.12480.25460.1693-0.54170.10090.0123-0.142-0.20790.02390.33380.03240.02340.20440.05780.20632.127618.5196-64.9225
114.5149-1.921-2.29631.15463.017613.69790.0932-0.4347-0.29860.1612-0.11250.09020.832-1.56080.01930.8142-0.18750.02370.54950.01880.7146-4.987.5328-51.3364
123.06130.98353.45789.1983-1.30764.58310.2899-0.1576-0.16910.2234-0.1429-0.13110.3005-0.075-0.14710.30.05140.07360.33310.02120.27779.29711.0245-53.9109
132.0649-0.83033.04230.9944-2.23479.8605-0.1163-0.14130.25760.2385-0.03430.0422-0.03960.16050.15050.31910.01830.01890.1809-0.01660.26966.241917.9524-48.8299
144.5944-1.00042.45782.91411.90098.4702-0.6092-0.19290.2858-0.0753-0.00120.2024-1.39271.18320.61050.3674-0.1242-0.10750.42230.03450.054317.568425.2648-31.5086
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 24
2X-RAY DIFFRACTION2A25 - 56
3X-RAY DIFFRACTION3A57 - 82
4X-RAY DIFFRACTION4A83 - 110
5X-RAY DIFFRACTION5A111 - 124
6X-RAY DIFFRACTION6A125 - 151
7X-RAY DIFFRACTION7A152 - 165
8X-RAY DIFFRACTION8B2 - 19
9X-RAY DIFFRACTION9B20 - 42
10X-RAY DIFFRACTION10B43 - 65
11X-RAY DIFFRACTION11B66 - 83
12X-RAY DIFFRACTION12B84 - 101
13X-RAY DIFFRACTION13B102 - 133
14X-RAY DIFFRACTION14B134 - 160

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