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- PDB-8dms: Crystal structure of Legionella pneumophila macrodomain MavL in c... -

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Basic information

Entry
Database: PDB / ID: 8dms
TitleCrystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester soaked with ADP-ribose
Components
  • MavL
  • Ubiquitin
KeywordsANTITOXIN / Macrodomain / ADP-ribose / Covalent complex / Glycohydrolase
Function / homology
Function and homology information


ADP-D-ribose binding / 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 ...ADP-D-ribose binding / 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 / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / regulation of mitochondrial membrane potential / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR3 signaling / Degradation of DVL / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53
Similarity search - Function
Macrodomain effector MavL / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. ...Macrodomain effector MavL / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-AR6 / CITRATE ANION / METHYL 4-AMINOBUTANOATE / Polyubiquitin-B / Uncharacterized protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhang, Z. / Das, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01GM126296 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI148103 United States
CitationJournal: Nat Commun / Year: 2024
Title: Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain.
Authors: Zhang, Z. / Fu, J. / Rack, J.G.M. / Li, C. / Voorneveld, J. / Filippov, D.V. / Ahel, I. / Luo, Z.Q. / Das, C.
History
DepositionJul 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MavL
B: MavL
C: Ubiquitin
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6229
Polymers105,4014
Non-polymers1,2215
Water10,953608
1
A: MavL
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0564
Polymers52,7002
Non-polymers3552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MavL
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5665
Polymers52,7002
Non-polymers8663
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.957, 108.957, 209.546
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein MavL


Mass: 44180.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSJ1
#2: Protein Ubiquitin


Mass: 8519.778 Da / Num. of mol.: 2
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 , 5 types, 613 molecules

#3: 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
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-GVE / METHYL 4-AMINOBUTANOATE


Type: peptide-like / Mass: 117.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C5H11NO2
#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.62 Å3/Da / Density % sol: 66.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium citrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→39.1 Å / Num. obs: 78969 / % possible obs: 99.92 % / Redundancy: 2 % / Biso Wilson estimate: 33.17 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.47
Reflection shellResolution: 2.15→2.227 Å / Num. unique obs: 7800 / CC1/2: 0.765

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OMI, 1UBQ

6omi

1ubq


Resolution: 2.15→39.1 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 3804 2.51 %
Rwork0.173 147481 -
obs0.174 78945 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.73 Å2 / Biso mean: 45.1502 Å2 / Biso min: 20.34 Å2
Refinement stepCycle: final / Resolution: 2.15→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6841 0 81 621 7543
Biso mean--79.67 49.52 -
Num. residues----888
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.15-2.180.26291480.271954575605
2.18-2.210.26821450.257754185563
2.21-2.240.26671420.248655015643
2.24-2.270.25141460.253754665612
2.27-2.30.29411480.242753905538
2.3-2.340.2341400.234754845624
2.34-2.380.25721380.230954825620
2.38-2.420.23351420.22754975639
2.42-2.460.2491400.231754255565
2.46-2.510.26861400.224554835623
2.51-2.560.28541400.209354335573
2.56-2.620.26941420.211454535595
2.62-2.680.21951360.208954955631
2.68-2.740.22571420.204154745616
2.74-2.820.22441440.200254345578
2.82-2.90.25011380.197954495587
2.9-2.990.27581420.199655205662
2.99-3.10.21971400.192354905630
3.1-3.220.2561380.174754245562
3.22-3.370.20161420.165854775619
3.37-3.550.18571360.154354245560
3.55-3.770.19741390.145555025641
3.77-4.060.17731400.128154475587
4.06-4.470.13791420.117754555597
4.47-5.120.14971340.116254855619
5.12-6.440.1691340.150754705604
6.44-39.10.1721460.158554465592
Refinement TLS params.Method: refined / Origin x: -23.7557 Å / Origin y: 9.8192 Å / Origin z: 5.3495 Å
111213212223313233
T0.2264 Å20.0519 Å2-0.0337 Å2-0.2837 Å2-0.0425 Å2--0.3307 Å2
L0.7324 °2-0.4031 °20.3862 °2-0.7366 °2-0.576 °2--1.081 °2
S-0.0262 Å °-0.1158 Å °0.2125 Å °0.0215 Å °-0.0754 Å °-0.0642 Å °-0.2226 Å °-0.0893 Å °0.0946 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA41 - 409
2X-RAY DIFFRACTION1allA501
3X-RAY DIFFRACTION1allB41 - 409
4X-RAY DIFFRACTION1allB501
5X-RAY DIFFRACTION1allC1 - 75
6X-RAY DIFFRACTION1allC101
7X-RAY DIFFRACTION1allD1 - 75
8X-RAY DIFFRACTION1allD101 - 201
9X-RAY DIFFRACTION1allS1 - 746

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