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- PDB-3tgd: Crystal structure of the human ubiquitin-conjugating enzyme (E2) ... -

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Basic information

Entry
Database: PDB / ID: 3tgd
TitleCrystal structure of the human ubiquitin-conjugating enzyme (E2) UbcH5b
ComponentsUbiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / UBC-like / ubiqutin-conjugating enzyme / ubiquitin binding
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol
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 D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPage, R.C. / Amick, J. / Misra, S.
CitationJournal: To be Published
Title: Crystal structure of the human ubiquitin-conjugating enzyme (E2) UbcH5b
Authors: Page, R.C. / Amick, J. / Misra, S.
History
DepositionAug 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 D2


Theoretical massNumber of molelcules
Total (without water)17,1591
Polymers17,1591
Non-polymers00
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.342, 50.277, 64.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating ...Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2


Mass: 17158.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2 / Plasmid: pGST-Parallel2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P62837, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M potassium phosphate, 0.8M sodium phosphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 15, 2011 / Details: mirrors
RadiationMonochromator: VariMax confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30.887 Å / Num. all: 15004 / Num. obs: 15004 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.04 % / Biso Wilson estimate: 15.38 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 30.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.55 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1511 / % possible all: 80.1

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIX1.7_743model building
PHENIX(phenix.refine: 1.7.1_743)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIX1.7_743phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ESK

2esk


Resolution: 1.8→30.887 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.28 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 1518 10.13 %RANDOM
Rwork0.1788 ---
obs0.1812 14979 97.46 %-
all-15004 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.45 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.443 Å2-0 Å2-0 Å2
2---0.2372 Å20 Å2
3----0.2058 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 0 232 1437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011266
X-RAY DIFFRACTIONf_angle_d1.1921733
X-RAY DIFFRACTIONf_dihedral_angle_d13.843482
X-RAY DIFFRACTIONf_chiral_restr0.1186
X-RAY DIFFRACTIONf_plane_restr0.007227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85810.28791100.2411965X-RAY DIFFRACTION78
1.8581-1.92450.25481340.19651162X-RAY DIFFRACTION96
1.9245-2.00150.21571290.19021233X-RAY DIFFRACTION99
2.0015-2.09260.22511390.18241236X-RAY DIFFRACTION100
2.0926-2.20290.1871470.17041230X-RAY DIFFRACTION100
2.2029-2.34090.2091340.17891247X-RAY DIFFRACTION100
2.3409-2.52150.20271420.17641248X-RAY DIFFRACTION100
2.5215-2.77510.18761410.18281253X-RAY DIFFRACTION100
2.7751-3.17640.2011390.1771258X-RAY DIFFRACTION100
3.1764-4.00050.18181480.1661281X-RAY DIFFRACTION100
4.0005-30.89140.20111550.17631348X-RAY DIFFRACTION100
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)
10.34610.09410.08910.030.00830.0806-0.0960.06770.0881-0.01750.14740.1069-0.0159-0.0110.00530.07030.01170.00210.05210.01190.09467.697-16.9091-24.2213
20.3440.18860.10.3380.26120.22390.0081-0.0331-0.027-0.01620.0053-0.08180.01370.01250.00830.03450.0058-0.0060.03690.00680.034613.2011-7.5787-13.0441
30.00290.0013-0.00490.31790.10260.0430.0192-0.04980.01410.1563-0.06880.160.091-0.0540.00850.0672-0.00820.01410.1089-0.00290.08961.3766-12.7623-9.1449
40.11130.0325-0.09370.14910.06270.14580.0301-0.04490.03740.0571-0.12120.09220.0087-0.1594-0.00640.0793-0.0044-0.00720.08210.00230.06435.56211.3987-5.9204
50.51010.1964-0.39290.0756-0.15210.38470.14070.05640.1043-0.0258-0.01210.0817-0.22030.08390.08660.1024-0.0169-0.00690.08480.0030.082115.178911.0954-8.0845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -4:25)
2X-RAY DIFFRACTION2chain 'A' and (resseq 26:84)
3X-RAY DIFFRACTION3chain 'A' and (resseq 85:98)
4X-RAY DIFFRACTION4chain 'A' and (resseq 99:130)
5X-RAY DIFFRACTION5chain 'A' and (resseq 131:147)

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