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- PDB-6kfp: Crystal structure of MavC ternary complex -

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Basic information

Entry
Database: PDB / ID: 6kfp
TitleCrystal structure of MavC ternary complex
Components
  • MavC
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-conjugating enzyme E2 N
KeywordsANTITOXIN/TRANSFERASE / deamidase / complex / ANTITOXIN / ANTITOXIN-TRANSFERASE 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 / regulation protein catabolic process at postsynapse / DNA double-strand break processing / postreplication repair / Formation of the ternary complex, and subsequently, the 43S complex / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair ...UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / regulation protein catabolic process at postsynapse / DNA double-strand break processing / postreplication repair / Formation of the ternary complex, and subsequently, the 43S complex / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / Ribosomal scanning and start codon recognition / Translation initiation complex formation / ubiquitin conjugating enzyme activity / SARS-CoV-1 modulates host translation machinery / positive regulation of intracellular signal transduction / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / protein K63-linked ubiquitination / Viral mRNA Translation / protein monoubiquitination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / ubiquitin ligase complex / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of DNA repair / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of TORC1 signaling / Maturation of protein E / Maturation of protein E / cytosolic ribosome / ER Quality Control Compartment (ERQC) / antiviral innate immune response / 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 / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / 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 / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / positive regulation of DNA repair / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / ubiquitin binding / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D
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 / S27a-like superfamily ...: / 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 / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Uncharacterized protein / Ubiquitin-40S ribosomal protein S27a / Ubiquitin-conjugating enzyme E2 N / Ubiquitin-ribosomal protein eS31 fusion protein / MvcA insertion domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsMu, Y. / Wang, Y. / Han, Y. / Li, D. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31822012 China
CitationJournal: Nat Commun / Year: 2020
Title: Structural insights into the mechanism and inhibition of transglutaminase-induced ubiquitination by the Legionella effector MavC.
Authors: Mu, Y. / Wang, Y. / Huang, Y. / Li, D. / Han, Y. / Chang, M. / Fu, J. / Xie, Y. / Ren, J. / Wang, H. / Zhang, Y. / Luo, Z.Q. / Feng, Y.
History
DepositionJul 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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
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: MavC
B: Ubiquitin-conjugating enzyme E2 N
D: Ubiquitin-40S ribosomal protein S27a


Theoretical massNumber of molelcules
Total (without water)68,9933
Polymers68,9933
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-19 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.704, 105.860, 125.391
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein MavC


Mass: 43120.680 Da / Num. of mol.: 1 / Mutation: C74A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_10720 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F4I5, UniProt: Q5ZTL4*PLUS
#2: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17157.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#3: Protein Ubiquitin-40S ribosomal protein S27a / Ub


Mass: 8714.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A / Production host: Escherichia coli (E. coli) / References: UniProt: J3QTR3, UniProt: P62979*PLUS

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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: 2.39 Å3/Da / Density % sol: 48.63 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.92→50 Å / Num. obs: 14312 / % possible obs: 99.42 % / Redundancy: 12 % / Biso Wilson estimate: 49.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Net I/σ(I): 26.6
Reflection shellResolution: 2.92→3.02 Å / Rmerge(I) obs: 0.794 / Num. unique obs: 1390 / CC1/2: 0.882

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Processing

Software
NameVersionClassification
PHASER1.15_3459phasing
PHENIX1.15_3459refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TSC, 1UBQ

5tsc

1ubq


Resolution: 2.92→38.53 Å / SU ML: 0.3455 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 24.9752
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2498 1088 4.95 %
Rwork0.1932 --
obs0.196 14312 80.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.62 Å2
Refinement stepCycle: LAST / Resolution: 2.92→38.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4753 0 0 0 4753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314848
X-RAY DIFFRACTIONf_angle_d0.6066555
X-RAY DIFFRACTIONf_chiral_restr0.0422727
X-RAY DIFFRACTIONf_plane_restr0.0042851
X-RAY DIFFRACTIONf_dihedral_angle_d16.68962975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.92-3.060.4064970.29041649X-RAY DIFFRACTION51.16
3.06-3.220.28341000.25011712X-RAY DIFFRACTION53.59
3.22-3.420.29111110.21922070X-RAY DIFFRACTION63.98
3.42-3.680.261400.19242679X-RAY DIFFRACTION83.21
3.68-4.050.241630.17853164X-RAY DIFFRACTION98.43
4.05-4.640.22261350.15673270X-RAY DIFFRACTION99.94
4.64-5.840.22251500.19653218X-RAY DIFFRACTION99.7
5.84-38.530.24431920.19923146X-RAY DIFFRACTION97.86
Refinement TLS params.Method: refined / Origin x: -16.0035916774 Å / Origin y: -28.3669742342 Å / Origin z: 2.31807943728 Å
111213212223313233
T0.0670735774426 Å2-0.0294188036038 Å20.0840419573436 Å2-0.0923610229113 Å2-0.0619614512505 Å2--0.0284964614979 Å2
L0.136393136346 °20.0443114679594 °2-0.15706682385 °2-0.586109245831 °20.0439275342509 °2--0.248829073116 °2
S0.0930752934195 Å °-0.0554333465342 Å °-0.00118507254158 Å °0.293125954049 Å °-0.246506860809 Å °-0.131527263629 Å °-0.167369864423 Å °0.0637674416562 Å °-0.124249684331 Å °
Refinement TLS groupSelection details: all

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