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- PDB-6ulh: Structure of MavC in complex with its substrate in R3 spacegroup -

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Basic information

Entry
Database: PDB / ID: 6ulh
TitleStructure of MavC in complex with its substrate in R3 spacegroup
Components
  • LPG2147 (MavC)
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 N
KeywordsTRANSFERASE / Transglutaminase / ubiquitination / Legionella pneumophila / deamidation
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 / 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 / antiviral innate immune response / 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 / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / positive regulation of DNA repair / Regulation of BACH1 activity / 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 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / ubiquitin binding / 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 / activated TAK1 mediates p38 MAPK activation / 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 / 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 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...: / 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 / 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
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 N / MvcA insertion domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.968 Å
AuthorsIyer, S. / Puvar, K. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R01GM126296 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
DepositionOct 8, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPG2147 (MavC)
C: Ubiquitin-conjugating enzyme E2 N
E: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)69,9763
Polymers69,9763
Non-polymers00
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-24 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.859, 171.859, 58.362
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein LPG2147 (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: lpg2147 / Plasmid: pGEX-6P-1 / Details (production host): Ampicillin resistance / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZTL4
#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 / Plasmid: pET-His-SUMO / Details (production host): Ampicillin resistance / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#3: Protein Ubiquitin


Mass: 8622.922 Da / Num. of mol.: 1 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pRSET / Details (production host): ampicillin resistance / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 48.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Sodium Acetate: HCl, pH 4.6 3.5 M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo data collection / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.968→25.903 Å / Num. obs: 45560 / % possible obs: 99.91 % / Redundancy: 5.8 % / Biso Wilson estimate: 31.44 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.046 / Rrim(I) all: 0.108 / Net I/σ(I): 10.5
Reflection shellResolution: 1.968→2.039 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4570 / CC1/2: 0.72 / % possible all: 99.74

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
TRUNCATEdata reduction
HKL-2000data scaling
PHENIXv1.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TSC, 2GMI, 1UBQ

5tsc

2gmi

1ubq


Resolution: 1.968→25.903 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2007 4.41 %random selection
Rwork0.1829 43548 --
obs0.1848 45555 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.41 Å2 / Biso mean: 39.8601 Å2 / Biso min: 15.39 Å2
Refinement stepCycle: final / Resolution: 1.968→25.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 0 272 4902
Biso mean---40.28 -
Num. residues----596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514733
X-RAY DIFFRACTIONf_angle_d0.7196423
X-RAY DIFFRACTIONf_chiral_restr0.0464724
X-RAY DIFFRACTIONf_plane_restr0.0044838
X-RAY DIFFRACTIONf_dihedral_angle_d2.8623566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9682-2.01740.28371390.2493134
2.0174-2.07190.32491390.24243092
2.0719-2.13290.30041410.23063121
2.1329-2.20170.25361430.21253088
2.2017-2.28030.27021470.20973115
2.2803-2.37160.24551420.20093122
2.3716-2.47940.21811460.19533125
2.4794-2.610.24231420.20593089
2.61-2.77340.23211450.21033112
2.7734-2.98720.28461440.2183103
2.9872-3.28730.27261450.20153114
3.2873-3.76170.19551410.16433123
3.7617-4.73460.17591460.13733097
4.7346-25.9030.1961470.15943113
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)
12.1996-0.5272-0.45611.1986-0.44395.4901-0.1542-0.08040.0519-0.02250.0063-0.0681-0.27730.2140.13910.21110.0419-0.01590.3554-0.03660.236712.231533.4935-8.7733
21.7808-0.437-0.92380.70660.35231.4843-0.4252-0.2396-0.65150.20230.10350.27660.58150.27350.18410.40510.1010.11390.27110.10490.3848-1.83822.765710.8638
32.7659-1.6219-0.91574.49630.43755.0420.01490.2888-0.214-0.0137-0.15050.03160.2364-0.05620.14320.1555-0.0038-0.01810.2394-0.01080.2962-26.856639.996212.928
43.5332-1.2517-1.84361.30591.18792.1351-0.2629-0.3542-0.29030.24760.05660.10790.38740.32650.12760.26440.05650.02190.24960.10710.234-8.911233.820620.508
51.5735-0.3138-1.21920.80350.8052.2657-0.2244-0.5367-0.26030.12810.0847-0.05280.40230.81310.08980.25760.16740.00860.46340.10010.25511.200928.182111.7303
65.7522-1.1112.03481.9812-0.21675.32630.06710.47510.2259-0.1868-0.1353-0.1149-0.34820.25970.07720.23880.07310.04390.4102-0.00460.191314.215736.27-18.891
72.39870.350.32114.743-1.01745.38690.1859-0.651-0.06380.40960.13690.3977-0.1519-0.3664-0.30470.2997-0.04690.04060.30980.03790.3023-8.192759.438823.3723
87.33140.2045-0.51341.93110.84483.19020.1716-0.15280.2665-0.04260.08120.0449-0.3470.3617-0.24090.3064-0.10830.00130.21330.01090.22053.790962.296516.7755
98.14380.5573-0.92742.3643-1.02443.1659-0.16470.47140.1878-0.4360.29270.2209-0.3913-0.0148-0.1320.283-0.1125-0.03220.30360.02270.2581-1.286359.27710.5973
103.1519-2.8367-1.5953.2934-0.23174.48390.13550.82930.2756-1.38240.2275-0.1497-0.2653-0.2536-0.34030.457-0.1706-0.02050.4868-0.03380.32137.167755.95744.2664
113.66853.4707-3.43543.2801-3.27577.3096-0.85520.8367-0.5872-0.64940.91960.58380.77-0.56970.17850.5243-0.0853-0.02790.4816-0.00650.6406-6.312248.09813.2875
121.2661-0.5959-0.73244.60141.46583.03660.0285-0.0280.0912-0.64220.2742-0.4867-0.0460.6588-0.33460.3211-0.07640.01260.3907-0.03130.280710.414349.11938.8802
132.84162.14280.13957.82630.80123.4107-0.1207-0.15360.2685-0.41180.7004-0.9671-0.62030.9606-0.41190.3824-0.26510.08040.6835-0.12770.407219.795460.682710.1791
142.10333.0461-0.83374.6223-0.41873.8305-0.51071.0548-1.3268-0.31780.23140.00040.787-0.65710.41060.3343-0.06340.02420.5337-0.1550.4107-5.516924.442-10.3539
153.1554-1.93853.52474.7152-1.46868.96140.17780.1237-0.4875-0.1964-0.27460.43750.4675-1.03110.03270.2558-0.03350.00040.448-0.06490.3924-11.225126.8159-1.3784
166.8735-0.84423.59692.8935-2.33279.7077-0.4117-0.33610.0790.0401-0.01830.3385-0.6954-0.42560.3720.2320.0566-0.00330.2662-0.05980.2908-2.254231.79720.7869
179.67223.1647-7.02477.2497-3.34435.28940.1925-0.42960.78640.95820.42170.7003-0.8866-0.2521-0.87470.40780.18690.03290.5718-0.01390.3712-10.315838.153-5.3972
185.7036-1.1480.90151.9583-2.23954.7418-0.27660.9250.2395-0.29730.05140.3834-0.4475-0.55710.2850.28650.1215-0.02620.4952-0.03050.3122-5.358735.0216-7.9689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 73 )A9 - 73
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 140 )A74 - 140
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 193 )A141 - 193
4X-RAY DIFFRACTION4chain 'A' and (resid 194 through 248 )A194 - 248
5X-RAY DIFFRACTION5chain 'A' and (resid 249 through 357 )A249 - 357
6X-RAY DIFFRACTION6chain 'A' and (resid 358 through 384 )A358 - 384
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 27 )C2 - 27
8X-RAY DIFFRACTION8chain 'C' and (resid 28 through 50 )C28 - 50
9X-RAY DIFFRACTION9chain 'C' and (resid 51 through 76 )C51 - 76
10X-RAY DIFFRACTION10chain 'C' and (resid 77 through 86 )C77 - 86
11X-RAY DIFFRACTION11chain 'C' and (resid 87 through 100 )C87 - 100
12X-RAY DIFFRACTION12chain 'C' and (resid 101 through 132 )C101 - 132
13X-RAY DIFFRACTION13chain 'C' and (resid 133 through 152 )C133 - 152
14X-RAY DIFFRACTION14chain 'E' and (resid 1 through 16 )E1 - 16
15X-RAY DIFFRACTION15chain 'E' and (resid 17 through 34 )E17 - 34
16X-RAY DIFFRACTION16chain 'E' and (resid 35 through 44 )E35 - 44
17X-RAY DIFFRACTION17chain 'E' and (resid 45 through 56 )E45 - 56
18X-RAY DIFFRACTION18chain 'E' and (resid 57 through 76 )E57 - 76

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