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- PDB-6jky: Crystal structure of MvcA-UBE2N-Ub complex from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 6jky
TitleCrystal structure of MvcA-UBE2N-Ub complex from Legionella pneumophila
Components
  • MvcA
  • Ub
  • Ubiquitin-conjugating enzyme E2 N
KeywordsSIGNALING PROTEIN / Legionella pneumophila effect factor complex
Function / homology
Function and homology information


UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction ...UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / DNA damage tolerance / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / regulation of DNA repair / negative regulation of TORC1 signaling / antiviral innate immune response / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of DNA repair / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / ubiquitin binding / PINK1-PRKN Mediated Mitophagy / activated TAK1 mediates p38 MAPK activation / Nonhomologous End-Joining (NHEJ) / NOD1/2 Signaling Pathway / positive regulation of NF-kappaB transcription factor activity / TAK1-dependent IKK and NF-kappa-B activation / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / CLEC7A (Dectin-1) signaling / ISG15 antiviral mechanism / FCERI mediated NF-kB activation / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / protein polyubiquitination / Aggrephagy / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / MvcA insertion domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / : ...: / MvcA insertion domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-like domain-containing protein / Ubiquitin-conjugating enzyme E2 N / MvcA insertion domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Homo sapiens (human)
Schistosoma margrebowiei (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.454 Å
AuthorsOuyang, S.Y. / Guan, H.
CitationJournal: Embo J. / Year: 2020
Title: Legionella pneumophila regulates the activity of UBE2N by deamidase-mediated deubiquitination.
Authors: Gan, N. / Guan, H. / Huang, Y. / Yu, T. / Fu, J. / Nakayasu, E.S. / Puvar, K. / Das, C. / Wang, D. / Ouyang, S. / Luo, Z.Q.
History
DepositionMar 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct.title
Revision 1.2Nov 22, 2023Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MvcA
B: Ubiquitin-conjugating enzyme E2 N
C: Ub
D: MvcA
E: Ubiquitin-conjugating enzyme E2 N
F: Ub


Theoretical massNumber of molelcules
Total (without water)139,9316
Polymers139,9316
Non-polymers00
Water1,13563
1
A: MvcA
B: Ubiquitin-conjugating enzyme E2 N
C: Ub


Theoretical massNumber of molelcules
Total (without water)69,9663
Polymers69,9663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-19 kcal/mol
Surface area28740 Å2
MethodPISA
2
D: MvcA
E: Ubiquitin-conjugating enzyme E2 N
F: Ub


Theoretical massNumber of molelcules
Total (without water)69,9663
Polymers69,9663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-21 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.325, 107.605, 263.845
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MvcA


Mass: 44041.871 Da / Num. of mol.: 2 / Mutation: C83A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: lpg2148 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZTL3
#2: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N


Mass: 17099.668 Da / Num. of mol.: 2 / Mutation: K94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N / Production host: Escherichia coli (E. coli)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#3: Protein Ub


Mass: 8824.103 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma margrebowiei (invertebrata)
Gene: SMRZ_LOCUS12712 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A3P7ZMV6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium thiocyanate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97894 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 2.45→65.14 Å / Num. obs: 52753 / % possible obs: 96.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 58.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.071 / Net I/σ(I): 14.9
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.547 / Num. unique obs: 7924 / Rrim(I) all: 0.591

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
autoPROCdata collection
autoPROCdata scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K11 and 1JAT

6k11

1jat


Resolution: 2.454→65.135 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 2639 5.01 %
Rwork0.2087 50044 -
obs0.2111 52683 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.14 Å2 / Biso mean: 79.9412 Å2 / Biso min: 33.06 Å2
Refinement stepCycle: final / Resolution: 2.454→65.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9713 0 0 63 9776
Biso mean---61.67 -
Num. residues----1213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049917
X-RAY DIFFRACTIONf_angle_d0.70413404
X-RAY DIFFRACTIONf_chiral_restr0.0451479
X-RAY DIFFRACTIONf_plane_restr0.0051748
X-RAY DIFFRACTIONf_dihedral_angle_d6.4716108
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4541-2.49870.35961640.29512711100
2.4987-2.54680.34751630.28652647100
2.5468-2.59880.32551620.27912671100
2.5988-2.65530.38841270.3097264598
2.6553-2.71710.4662770.3237120197
2.7171-2.7850.34761450.26452690100
2.785-2.86030.31351250.25992733100
2.8603-2.94450.30781380.2654266199
2.9445-3.03950.33571530.2643266799
3.0395-3.14820.3351300.2622270198
3.1482-3.27420.26421350.24322725100
3.2742-3.42320.33431420.2292711100
3.4232-3.60370.27851260.22732746100
3.6037-3.82940.25681420.2313268799
3.8294-4.12510.26761430.2002275799
4.1251-4.54010.22111300.16962723100
4.5401-5.19680.18861490.16562760100
5.1968-6.54650.22791610.1938269497
6.5465-65.10.20411270.1657291499
Refinement TLS params.Method: refined / Origin x: -42.7003 Å / Origin y: -18.1782 Å / Origin z: -32.783 Å
111213212223313233
T0.4267 Å20.1622 Å20.0237 Å2-0.4543 Å20.0216 Å2--0.4031 Å2
L0.1909 °20.1858 °20.3508 °2--0.018 °2-0.0259 °2--0.2085 °2
S0.0502 Å °-0.0338 Å °0.0169 Å °0.0143 Å °-0.029 Å °-0.028 Å °-0.0048 Å °-0.0229 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA12 - 395
2X-RAY DIFFRACTION1allB2 - 150
3X-RAY DIFFRACTION1allC-1 - 74
4X-RAY DIFFRACTION1allD13 - 393
5X-RAY DIFFRACTION1allE3 - 150
6X-RAY DIFFRACTION1allF0 - 74
7X-RAY DIFFRACTION1allS1 - 64

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