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- PDB-4nr3: Crystal Structure of a human Mms2/Ubc13 L121G mutant -

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Basic information

Entry
Database: PDB / ID: 4nr3
TitleCrystal Structure of a human Mms2/Ubc13 L121G mutant
Components
  • Ubiquitin-conjugating enzyme E2 N
  • Ubiquitin-conjugating enzyme E2 variant 2
KeywordsLIGASE / ubc13 / mms2 / E2 / ubiquitin conjugating enzyme
Function / homology
Function and homology information


error-free postreplication DNA repair / : / 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 intracellular signal transduction / positive regulation of double-strand break repair ...error-free postreplication DNA repair / : / 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 intracellular signal transduction / positive regulation of double-strand break repair / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / regulation of DNA repair / ubiquitin ligase complex / antiviral innate immune response / negative regulation of TORC1 signaling / 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 / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / ubiquitin binding / activated TAK1 mediates p38 MAPK activation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / G2/M DNA damage checkpoint / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / Formation of Incision Complex in GG-NER / FCERI mediated NF-kB activation / Aggrephagy / Interleukin-1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / 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 / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 N / Ubiquitin-conjugating enzyme E2 variant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsHodge, C.D. / Edwards, R.A. / Glover, J.N.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Stochastic gate dynamics regulate the catalytic activity of ubiquitination enzymes.
Authors: Rout, M.K. / Hodge, C.D. / Markin, C.J. / Xu, X. / Glover, J.N. / Xiao, W. / Spyracopoulos, L.
History
DepositionNov 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 variant 2
B: Ubiquitin-conjugating enzyme E2 N


Theoretical massNumber of molelcules
Total (without water)34,2042
Polymers34,2042
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-9 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.261, 74.762, 91.761
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 variant 2 / DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation- ...DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation-promoting factor 1 / EDPF-1 / MMS2 homolog / Vitamin D3-inducible protein


Mass: 16676.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMS2, UBE2V2, UEV2 / Plasmid: pHis-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q15819
#2: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / Ubc13 / UbcH13 / Ubiquitin carrier protein N / ...Bendless-like ubiquitin-conjugating enzyme / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17528.064 Da / Num. of mol.: 1 / Mutation: L121G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLU, UBE2N / Plasmid: pHis-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: P61088, ubiquitin-protein ligase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 20% PEG 8000, 0.1 M sodium citrate, pH 6.8, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 4, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 27834 / Num. obs: 27834 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 22.34 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.099 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.833.90.58813290.7193.3
1.83-1.863.90.5413240.785193.7
1.86-1.940.51813231.078194
1.9-1.943.90.47313401.53193.8
1.94-1.9840.36213220.966194.8
1.98-2.0340.27813640.964194.8
2.03-2.083.90.30413551.803195.4
2.08-2.1340.22613751.08195.9
2.13-2.24.10.18613491.071195.2
2.2-2.273.90.21213791.714196.6
2.27-2.354.10.14613661.05195.9
2.35-2.444.10.13513861.052196.9
2.44-2.5540.12114221.021198.3
2.55-2.6940.12314121.157197.5
2.69-2.864.10.10314031.03197.8
2.86-3.0840.08714261.067198.5
3.08-3.3940.07814551.023198.4
3.39-3.8840.07414381.024199
3.88-4.883.90.05815000.98199.5
4.88-503.70.0415660.946198.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1J7D

1j7d


Resolution: 1.802→22.131 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8375 / SU ML: 0.21 / σ(F): 1.36 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 1461 5.26 %random
Rwork0.1877 ---
obs0.1901 27783 96.3 %-
all-27783 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.22 Å2 / Biso mean: 31.4294 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: LAST / Resolution: 1.802→22.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2291 0 0 161 2452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082431
X-RAY DIFFRACTIONf_angle_d1.1273314
X-RAY DIFFRACTIONf_chiral_restr0.078354
X-RAY DIFFRACTIONf_plane_restr0.005442
X-RAY DIFFRACTIONf_dihedral_angle_d13.292946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.802-1.86640.28371510.24392456260792
1.8664-1.94110.31021260.24632529265594
1.9411-2.02940.30071450.22032551269695
2.0294-2.13630.26891270.22132596272396
2.1363-2.270.25191660.20362559272596
2.27-2.44510.26461460.19532622276896
2.4451-2.69080.24721570.19552663282098
2.6908-3.07920.28391570.20782679283698
3.0792-3.87610.22511430.1772749289299
3.8761-22.13220.16021430.148729183061100
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)
11.6824-0.39930.26241.58241.20027.1941-0.1442-0.137-0.18170.4471-0.0501-0.06740.52020.28910.18160.17720.0049-0.03380.16190.01940.163921.807914.243418.9643
22.4383-0.20220.72541.84760.11433.9139-0.15950.02960.11560.20910.062-0.105-0.10860.30050.0550.09650.0013-0.00440.1001-0.01640.126415.679920.180911.148
35.91660.1732-0.96043.0702-3.55167.8429-0.0738-0.03030.43660.1843-0.08330.039-0.3650.25590.10930.07160.00990.00180.0595-0.00010.10568.997523.44295.0652
42.37372.0026-0.46635.0528-2.60727.0268-0.1807-0.19910.33080.21560.17550.6105-0.2546-0.380.01110.09320.04610.00340.1963-0.00190.18312.057919.79739.5467
53.19121.02083.03162.8130.50843.01470.1444-0.0341-0.22140.30070.0680.06310.2314-0.0406-0.19970.11150.00460.02210.110.01390.15929.980810.809513.2977
67.43531.3988-0.11967.2398-0.39777.7861-0.26550.24830.2094-0.30860.28310.1519-0.26060.20680.03240.06710.0377-0.02630.196-0.03830.11435.815919.5816-1.9912
73.95035.1949-3.21039.4262-2.82133.46130.1387-0.23540.66070.3833-0.4947-0.3127-0.19921.07680.38510.5140.0660.02460.47870.18010.472925.166811.360647.8444
82.43453.0241.73283.75612.15221.23350.2969-0.39430.16531.1243-0.34850.3309-0.06560.00260.03890.6361-0.1315-0.00150.36760.0790.328624.502722.076144.2117
95.6345.864-1.4068.9560.10441.58290.3593-0.2226-0.04810.6399-0.108-0.23010.1235-0.0194-0.24750.30710.0296-0.07010.18040.02850.149331.860728.668537.1523
103.49850.6499-0.95365.2202-1.86281.9397-0.3524-0.1763-0.5747-0.5250.3170.24120.83330.0412-0.01160.41470.05410.00060.21080.02660.225829.359817.997332.5187
113.2890.4258-0.0015.449-2.12714.027-0.0704-0.5549-0.83280.3397-0.0203-0.43230.44790.31330.06270.31950.1136-0.04720.31530.07910.352637.41618.93433.512
123.87152.0017-0.15297.87531.32167.43250.21130.5803-0.8397-0.6617-0.0506-0.78350.52760.1154-0.18090.27650.05660.02630.423-0.10390.647746.032527.469722.9244
133.1838-3.2982-2.82623.58942.12178.92440.2147-0.26620.2283-0.01320.2075-0.3854-0.27070.2319-0.41390.22290.00290.01340.1434-0.00420.204538.202639.139528.3549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 35 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 78 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 87 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 107 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 127 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 128 through 145 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 15 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 16 through 33 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 34 through 57 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 58 through 76 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 77 through 113 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 114 through 132 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 133 through 150 )B0

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