PDB-9emk: DupA from legionella covalently bound to ubiquitin-based probe

ID or keywords:

Entry

Database: PDB / ID: 9emk

Title

DupA from legionella covalently bound to ubiquitin-based probe

Components

Polyubiquitin-B
Septation initiation protein

Keywords

UNKNOWN FUNCTION / covalent complex / chemical warhead / ubiquitin enzyme / infection

Function / homology

Function and homology information

hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of neuron apoptotic process ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / energy homeostasis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / neuron projection morphogenesis / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Deactivation of the beta-catenin transactivating complex / Regulation of signaling by CBL / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Hh mutants are degraded by ERAD / Degradation of AXIN / Stabilization of p53
Similarity search - Function

Biological species

Legionella pneumophila subsp. pneumophila (bacteria)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.17 Å

Authors

Kim, R.Q. / Kloet, M.S. / van der Heden van Noort, G.

Funding support

Netherlands, European Union, 3items

Organization	Grant number	Country
Netherlands Organisation for Scientific Research (NWO)	VI.Vidi.192.011	Netherlands
European Research Council (ERC)	101087582	European Union
H2020 Marie Curie Actions of the European Commission	H2020-MSCA-ITN-2018	European Union

Citation

Journal: J.Am.Chem.Soc. / Year: 2024
Title: Covalent Probes To Capture Legionella pneumophila Dup Effector Enzymes.
Authors: Kloet, M.S. / Mukhopadhyay, R. / Mukherjee, R. / Misra, M. / Jeong, M. / Talavera Ormeno, C.M.P. / Moutsiopoulou, A. / Tjokrodirijo, R.T.N. / van Veelen, P.A. / Shin, D. / Dikic, I. / ...

History

Deposition	Mar 8, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 16, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9emk.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb9emk.ent.gz		Display	PDB format
PDBx/mmJSON format	9emk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9emk_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9emk_full_validation.pdf.gz	1.4 MB	Display
Data in XML	9emk_validation.xml.gz	54.1 KB	Display
Data in CIF	9emk_validation.cif.gz	69.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/em/9emk ftp://data.pdbj.org/pub/pdb/validation_reports/em/9emk	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (66) #234 - Jun 2019 MDM2 and Cancer similarity (67) #122 - Feb 2010 Enhanceosome similarity (6) #88 - Apr 2007 Clathrin similarity (1) #150 - Jun 2012 Sliding Clamps similarity (5) #172 - Apr 2014 RecA and Rad51 similarity (8) #68 - Aug 2005 Neurotrophins similarity (3) #143 - Nov 2011 Toll-like Receptors similarity (4) #56 - Aug 2004 Caspases similarity (3) #43 - Jul 2003 Src Tyrosine Kinase similarity (2) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (2) #163 - Jul 2013 HIV Capsid similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1)

PDB pages

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Related items in Molecule of the Month

#60 - Dec 2004
Ubiquitin
similarity (66)
#234 - Jun 2019
MDM2 and Cancer
similarity (67)
#122 - Feb 2010
Enhanceosome
similarity (6)
#88 - Apr 2007
Clathrin
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (5)
#172 - Apr 2014
RecA and Rad51
similarity (8)
#68 - Aug 2005
Neurotrophins
similarity (3)
#143 - Nov 2011
Toll-like Receptors
similarity (4)
#56 - Aug 2004
Caspases
similarity (3)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (2)
#126 - Jun 2010
Epidermal Growth Factor
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (2)
#163 - Jul 2013
HIV Capsid
similarity (1)
#195 - Mar 2016
RAF Protein Kinases
similarity (1)
#205 - Jan 2017
Nuclear Pore Complex
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)

Deposited unit

A: Septation initiation protein

B: Polyubiquitin-B

C: Septation initiation protein

D: Polyubiquitin-B

E: Septation initiation protein

F: Polyubiquitin-B

hetero molecules

145 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Septation initiation protein

B: Polyubiquitin-B

hetero molecules

defined by author&software
Evidence: mass spectrometry, 1:1 bound
48.3 kDa, 2 polymers

2

C: Septation initiation protein

D: Polyubiquitin-B

hetero molecules

defined by author&software
48.3 kDa, 2 polymers

3

E: Septation initiation protein

F: Polyubiquitin-B

hetero molecules

defined by author&software
48.3 kDa, 2 polymers

Unit cell

Length a, b, c (Å)	86.808, 86.808, 146.539
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Septation initiation protein Mass: 39498.566 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria) Gene: D1H98_09620 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3A6VNK6
#2: Protein	Polyubiquitin-B Mass: 8504.742 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG47
#3: Chemical	ChemComp-A1H50 / [(2~{R},3~{S},4~{R},5~{S})-5-[(1-ethyl-1,2,3-triazol-4-yl)methoxy]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ethanesulfonate Mass: 323.323 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₇S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.5 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 6000 0.1 M HEPES pH7 0.2 M MgCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 23, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.966 Å / Relative weight: 1
Reflection	Resolution: 2.17→75.3 Å / Num. obs: 65360 / % possible obs: 100 % / Redundancy: 5 % / CC_1/2: 0.998 / R_pim(I) all: 0.043 / Net I/σ(I): 10.7
Reflection shell	Resolution: 2.17→2.22 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4611 / CC_1/2: 0.388 / R_pim(I) all: 0.763 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.17→75.291 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.935 / SU B: 16.388 / SU ML: 0.197 / Cross valid method: FREE R-VALUE / ESU R: 0.258 / ESU R Free: 0.207
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2389	3239	4.96 %
R_work	0.185	62070	-
all	0.188	-	-
obs	-	65309	99.988 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 65.654 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.174 Å²	-0.087 Å²	0 Å²
2-	-	-0.174 Å²	0 Å²
3-	-	-	0.565 Å²

Refinement step

Cycle: LAST / Resolution: 2.17→75.291 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9221	0	69	240	9530

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	9506
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8868
X-RAY DIFFRACTION	r_angle_refined_deg	1.835	1.842	12850
X-RAY DIFFRACTION	r_angle_other_deg	0.653	1.78	20452
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.411	5	1148
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.822	5	71
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.51	10	1635
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.008	10	457
X-RAY DIFFRACTION	r_chiral_restr	0.208	0.2	1395
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	11171
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2182
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	2257
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	8664
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	4674
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	5055
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.187	0.2	339
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.052	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.264	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.261	0.2	71
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.223	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	2.711	3.208	4610
X-RAY DIFFRACTION	r_mcbond_other	2.71	3.208	4610
X-RAY DIFFRACTION	r_mcangle_it	3.952	5.758	5752
X-RAY DIFFRACTION	r_mcangle_other	3.951	5.758	5753
X-RAY DIFFRACTION	r_scbond_it	3.846	3.587	4896
X-RAY DIFFRACTION	r_scbond_other	3.846	3.589	4897
X-RAY DIFFRACTION	r_scangle_it	5.447	6.451	7098
X-RAY DIFFRACTION	r_scangle_other	5.447	6.452	7099
X-RAY DIFFRACTION	r_lrange_it	7.976	39.452	40177
X-RAY DIFFRACTION	r_lrange_other	7.979	39.405	40088

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.17-2.227	0.32	214	0.313	4632	0.314	4846	0.93	0.928	100	0.318
2.227-2.288	0.291	184	0.288	4544	0.288	4728	0.935	0.937	100	0.291
2.288-2.354	0.329	300	0.268	4255	0.272	4556	0.928	0.952	99.9781	0.269
2.354-2.426	0.284	226	0.249	4199	0.251	4426	0.947	0.961	99.9774	0.247
2.426-2.506	0.29	178	0.231	4137	0.233	4315	0.946	0.968	100	0.225
2.506-2.594	0.288	220	0.21	3953	0.214	4174	0.955	0.974	99.976	0.201
2.594-2.691	0.258	201	0.196	3798	0.199	3999	0.963	0.977	100	0.182
2.691-2.801	0.238	236	0.183	3703	0.187	3939	0.965	0.981	100	0.168
2.801-2.925	0.263	206	0.177	3441	0.181	3647	0.959	0.983	100	0.161
2.925-3.068	0.245	150	0.189	3422	0.192	3572	0.967	0.979	100	0.173
3.068-3.234	0.262	164	0.187	3212	0.191	3376	0.957	0.979	100	0.172
3.234-3.429	0.231	186	0.18	2976	0.183	3162	0.969	0.981	100	0.168
3.429-3.666	0.249	142	0.179	2861	0.182	3003	0.968	0.985	100	0.171
3.666-3.959	0.208	129	0.172	2700	0.174	2830	0.976	0.985	99.9647	0.165
3.959-4.335	0.19	112	0.146	2448	0.148	2560	0.98	0.988	100	0.141
4.335-4.845	0.201	78	0.151	2249	0.153	2327	0.974	0.986	100	0.148
4.845-5.591	0.224	108	0.163	1920	0.167	2029	0.973	0.985	99.9507	0.16
5.591-6.838	0.224	98	0.194	1645	0.196	1743	0.974	0.982	100	0.191
6.838-9.63	0.22	69	0.156	1273	0.159	1343	0.973	0.986	99.9255	0.153
9.63-75.291	0.211	38	0.181	702	0.182	742	0.965	0.98	99.7305	0.185

Refinement TLS params.

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

ID	L11 (°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)
1	1.7441	-0.0908	0.1544	2.5488	0.2043	2.0276	-0.0281	0.0075	-0.1224	0.1133	0.0263	-0.2834	0.0673	0.1076	0.0018	0.0854	-0.0562	0.011	0.053	-0.0136	0.0738	5.322	-49.833	18.629
2	5.3475	-0.0826	-0.1213	5.7045	-0.962	5.3617	-0.1236	0.5542	1.1636	0.2385	-0.3397	-1.5676	-1.0561	0.7218	0.4633	0.4999	-0.2318	0.0918	0.6171	0.2419	1.1591	27.978	-41.857	3.364
3	2.1727	1.5915	0.0662	2.4273	0.0864	0.9758	-0.1007	0.2014	-0.064	-0.2134	0.1684	-0.0843	-0.0144	-0.0389	-0.0677	0.1932	-0.1208	0.0416	0.0966	-0.0534	0.1442	21.738	-4.854	2.038
4	4.5526	-4.0595	-2.6487	4.3744	1.0888	4.0242	0.445	0.6839	-1.1053	-0.8531	-0.384	1.5541	0.2132	-0.8913	-0.061	0.9475	-0.3419	-0.4607	0.8688	-0.0924	1.042	6.083	-4.582	-20.321
5	1.2241	0.0496	0.8953	1.7835	1.2009	4.169	0.1362	0.0595	0.1444	-0.1126	-0.2849	0.3262	-0.2601	-1.0138	0.1487	0.0898	0.0643	0.0494	0.3887	-0.0438	0.1983	-24.439	-30.016	-3.408
6	4.401	-0.2076	-2.0908	4.1101	3.5322	6.4278	0.3634	0.3032	0.1726	-0.5298	-0.2892	-0.229	-0.5291	0.2086	-0.0741	0.7033	0.1935	-0.019	0.2889	-0.0313	0.5251	-19.394	-2.351	0.849

Refinement TLS group

Selection: ALL

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