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

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Basic information

Entry
Database: PDB / ID: 8dmq
TitleCrystal structure of Legionella pneumophila macrodomain MavL in complex with ubiquitin vinyl methyl ester
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
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: 2.195 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)107,00515
Polymers105,4014
Non-polymers1,60411
Water7,062392
1
A: MavL
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6989
Polymers52,7002
Non-polymers9987
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MavL
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3076
Polymers52,7002
Non-polymers6074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.719, 108.719, 209.143
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, 403 molecules

#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C6H5O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.6 Å3/Da / Density % sol: 65.85 %
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: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.195→69.71 Å / Num. obs: 73681 / % possible obs: 99.71 % / Redundancy: 10.3 % / Biso Wilson estimate: 39.79 Å2 / CC1/2: 0.978 / Net I/σ(I): 14.95
Reflection shellResolution: 2.195→2.273 Å / Num. unique obs: 7171 / CC1/2: 0.725

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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: 2.195→69.71 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 3615 4.91 %
Rwork0.1777 70032 -
obs0.1792 73645 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.22 Å2 / Biso mean: 46.9195 Å2 / Biso min: 25.84 Å2
Refinement stepCycle: final / Resolution: 2.195→69.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6843 0 109 392 7344
Biso mean--84.76 47.2 -
Num. residues----888
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.195-2.220.30821380.2361256996
2.22-2.250.2591540.23942629100
2.25-2.290.23151420.22812654100
2.29-2.320.28421570.21942666100
2.32-2.360.22771070.22422724100
2.36-2.40.26211350.21472596100
2.4-2.440.25081310.2172709100
2.44-2.480.26491520.22362666100
2.48-2.530.2751170.22472697100
2.53-2.580.25031230.20542707100
2.58-2.640.25731390.21662642100
2.64-2.70.22661400.20232656100
2.7-2.770.24031530.21192675100
2.77-2.840.2421450.20612675100
2.84-2.920.23771310.21352698100
2.92-3.020.22651600.21112694100
3.02-3.130.25091520.2212260898
3.13-3.250.28921500.19682670100
3.25-3.40.24181320.1852733100
3.4-3.580.21021400.1652687100
3.58-3.80.21081490.16072721100
3.8-4.10.16681420.14472720100
4.1-4.510.13981060.12672790100
4.51-5.160.14641190.1282767100
5.16-6.50.16571430.1693275999
6.5-69.710.17281580.16092920100
Refinement TLS params.Method: refined / Origin x: -3.4168 Å / Origin y: 25.5385 Å / Origin z: -29.5408 Å
111213212223313233
T0.3768 Å20.0015 Å2-0.0349 Å2-0.2618 Å2-0.0044 Å2--0.3433 Å2
L0.3667 °20.1877 °2-0.2574 °2-0.8108 °2-0.4838 °2--0.8879 °2
S-0.0738 Å °-0.0377 Å °0.0607 Å °0.0377 Å °0.0238 Å °-0.128 Å °-0.1467 Å °0.0992 Å °0.0469 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA42 - 409
2X-RAY DIFFRACTION1allA501 - 701
3X-RAY DIFFRACTION1allB41 - 410
4X-RAY DIFFRACTION1allB601 - 801
5X-RAY DIFFRACTION1allC1 - 75
6X-RAY DIFFRACTION1allC101 - 301
7X-RAY DIFFRACTION1allD1 - 75
8X-RAY DIFFRACTION1allD101 - 201
9X-RAY DIFFRACTION1allS1 - 515

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