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- PDB-6p5b: Crystal Structure of MavC in Complex with Ub-UbE2N -

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Basic information

Entry
Database: PDB / ID: 6p5b
TitleCrystal Structure of MavC in Complex with Ub-UbE2N
Components
  • MavC
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 N
KeywordsTRANSFERASE / ubiquitin / effector / ligase / transglutaminase
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 / postreplication repair / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction / E2 ubiquitin-conjugating enzyme ...: / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / antiviral innate immune response / regulation of DNA repair / ubiquitin ligase complex / 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 / negative regulation of TORC1 signaling / 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 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / positive regulation of DNA repair / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / 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 / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / 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 / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of AXIN
Similarity search - Function
Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain ...Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / 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
Uncharacterized protein / Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 N / Uncharacterized protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.099 Å
AuthorsPuvar, K. / Iyer, S. / Negron Teron, K.I. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM126296-02 United States
CitationJournal: Nat Commun / Year: 2020
Title: Legionella effector MavC targets the Ube2N~Ub conjugate for noncanonical ubiquitination.
Authors: Puvar, K. / Iyer, S. / Fu, J. / Kenny, S. / Negron Teron, K.I. / Luo, Z.Q. / Brzovic, P.S. / Klevit, R.E. / Das, C.
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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
C: Ubiquitin-conjugating enzyme E2 N
E: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)69,9303
Polymers69,9303
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Presence confirmed via SDS-PAGE of protein crystals
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-26 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.844, 147.844, 53.228
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein MavC


Mass: 44194.945 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


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.4 Å3/Da / Density % sol: 48.82 % / Description: Hexagonal rods
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.2 M Na Malonate, 25% PEG 3350, 10 mM NiCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.099→30.359 Å / Num. obs: 38835 / % possible obs: 99.16 % / Redundancy: 35.6 % / Biso Wilson estimate: 32.82 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 22
Reflection shellResolution: 2.099→2.174 Å / Redundancy: 10 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3801 / CC1/2: 0.777 / % possible all: 97.89

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TSC

5tsc


Resolution: 2.099→30.359 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.84
RfactorNum. reflection% reflection
Rfree0.2319 2020 5.2 %
Rwork0.1949 --
obs0.1969 38835 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.93 Å2 / Biso mean: 37.4283 Å2 / Biso min: 16.24 Å2
Refinement stepCycle: final / Resolution: 2.099→30.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 0 196 4890
Biso mean---39.09 -
Num. residues----610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024792
X-RAY DIFFRACTIONf_angle_d0.5426507
X-RAY DIFFRACTIONf_chiral_restr0.04746
X-RAY DIFFRACTIONf_plane_restr0.003840
X-RAY DIFFRACTIONf_dihedral_angle_d3.753592
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.099-2.15150.3291210.251258097
2.1515-2.20960.29651470.23252616100
2.2096-2.27460.27461350.22172661100
2.2746-2.3480.26531380.22112619100
2.348-2.43190.28731280.21822642100
2.4319-2.52930.26071580.21772632100
2.5293-2.64430.25961560.2192635100
2.6443-2.78360.27961330.22262635100
2.7836-2.95790.29961490.21342644100
2.9579-3.1860.24271500.21732624100
3.186-3.50620.22321780.19922636100
3.5062-4.01260.21461470.1742246093
4.0126-5.05170.16741560.1568265199
5.0517-30.3590.21481240.17892780100
Refinement TLS params.

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

IDL11 (°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)
10.01470.5672-0.13470.39830.1967-0.07780.04380.1167-0.1313-0.1360.02710.31520.1019-0.0463-00.269-0.0422-0.04060.30280.0510.449325.0764-14.4763-7.5837
20.4867-0.1948-0.80670.08660.56130.5907-0.0046-0.1097-0.0220.00560.04970.1061-0.07610.06760.00030.2546-0.0167-0.00820.22830.04660.242748.3874-4.1434-13.5049
30.43520.13070.5590.85190.4302-0.0885-0.08790.0055-0.10170.08680.08240.0673-0.0159-0.1249-0.0050.27830.04970.03730.27880.05210.284535.66817.47752.8611
41.5609-0.71280.47151.869-0.14671.0075-0.2134-0.00090.02520.07230.1855-0.2652-0.160.124-0.00010.31640.0569-0.04760.2142-0.0180.277254.285733.69210.287
50.72760.2150.03261.16470.12620.7209-0.0064-0.088-0.17510.19370.04550.1580.0767-0.1556-00.21650.01020.01910.24140.06040.263333.77351.24593.3794
60.4643-0.4058-0.00970.80520.75940.7034-0.17720.2377-0.2583-0.1568-0.03320.15220.03330.0332-0.00070.2855-0.0336-0.02520.2410.01380.212453.441-12.7194-18.9398
70.1527-0.05030.09460.08260.01470.096-0.1886-0.14560.27060.45610.26280.0818-0.22180.03510.00010.3450.026-0.00450.3235-0.00390.252464.342117.669824.5308
80.0634-0.00920.10860.2928-0.07010.1096-0.1501-0.54970.27120.25520.099-0.00530.04930.42970.00020.33850.00930.02560.3919-0.03920.400168.56476.951824.5351
90.8607-0.1647-0.01670.93740.94711.08950.111-0.1627-0.0163-0.145-0.1208-0.2015-0.0155-0.12460.00030.1838-0.01130.00260.20460.04510.133166.77992.349313.0391
100.04010.01130.0482-0.05640.00090.0577-0.15360.3220.1751-0.05220.09530.28630.06610.5106-0.00030.34610.0659-0.06240.38880.03260.340753.398110.93559.9847
110.03770.0150.00830.0241-0.05760.1036-0.0823-0.2280.00880.07490.03330.3085-0.1573-0.19080.00020.2684-0.02280.00970.36820.03060.231858.79412.21917.0318
121.11760.45671.03320.09480.33551.55240.3633-0.08070.622-0.4514-0.6714-0.182-0.4646-0.2323-0.19180.5266-0.01010.11380.3290.05620.518257.6783-6.02690.9706
130.77210.322-0.74610.7849-0.22360.59770.1620.0649-0.171-0.0406-0.1652-0.29850.2369-0.054800.2303-0.0018-0.03450.19580.03070.198765.7982-14.16229.1745
140.5523-0.3920.23880.23340.02910.28310.4537-0.09390.2716-0.4233-0.4669-0.4887-0.1478-0.0204-0.00360.40810.00170.14730.30350.03790.385849.17513.4115-17.5667
150.4602-0.037-0.42740.1917-0.09760.25930.25760.0331-0.0551-0.1142-0.11530.0529-0.16980.0422-0.00010.31250.01530.03630.25860.01850.282246.214412.4095-8.031
160.13330.00540.11890.027-0.04250.10060.55380.0036-0.02640.1875-0.2874-0.0516-0.20490.430.00010.3273-0.01230.02440.3417-0.05570.465858.400213.4117-8.9287
170.9116-0.5611-0.03750.58260.37580.4565-0.11950.0046-0.1588-0.31150.1386-0.5490.01020.1748-0.00690.2701-0.01710.02550.31320.01270.355954.8739.3519-12.8982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 29 )A-3 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 96 )A30 - 96
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 140 )A97 - 140
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 223 )A141 - 223
5X-RAY DIFFRACTION5chain 'A' and (resid 224 through 357 )A224 - 357
6X-RAY DIFFRACTION6chain 'A' and (resid 358 through 384 )A358 - 384
7X-RAY DIFFRACTION7chain 'C' and (resid 3 through 17 )C3 - 17
8X-RAY DIFFRACTION8chain 'C' and (resid 18 through 30 )C18 - 30
9X-RAY DIFFRACTION9chain 'C' and (resid 31 through 86 )C31 - 86
10X-RAY DIFFRACTION10chain 'C' and (resid 87 through 100 )C87 - 100
11X-RAY DIFFRACTION11chain 'C' and (resid 101 through 113 )C101 - 113
12X-RAY DIFFRACTION12chain 'C' and (resid 114 through 123 )C114 - 123
13X-RAY DIFFRACTION13chain 'C' and (resid 124 through 152 )C124 - 152
14X-RAY DIFFRACTION14chain 'E' and (resid 1 through 22 )E1 - 22
15X-RAY DIFFRACTION15chain 'E' and (resid 23 through 44 )E23 - 44
16X-RAY DIFFRACTION16chain 'E' and (resid 45 through 56 )E45 - 56
17X-RAY DIFFRACTION17chain 'E' and (resid 57 through 75 )E57 - 75

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