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- PDB-1yla: Ubiquitin-conjugating enzyme E2-25 kDa (Huntington interacting pr... -

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Basic information

Entry
Database: PDB / ID: 1yla
TitleUbiquitin-conjugating enzyme E2-25 kDa (Huntington interacting protein 2)
ComponentsUbiquitin-conjugating enzyme E2-25 kDa
KeywordsLIGASE / UBIQUITIN / UBIQUITIN- CONJUGATING ENZYME / Structural Genomics / SGC / Structural Genomics Consortium
Function / homology
Function and homology information


free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / cellular response to interferon-beta ...free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / cellular response to interferon-beta / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of peptidyl-threonine phosphorylation / Negative regulators of DDX58/IFIH1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / UBA-like superfamily / 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 / Helicase, Ruva Protein; domain 3 / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChoe, J. / Avvakumov, G.V. / Newman, E.M. / Mackenzie, F. / Kozieradzki, I. / Bochkarev, A. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Dhe-paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis of E2-25K/UBB+1 interaction leading to proteasome inhibition and neurotoxicity
Authors: Ko, S. / Kang, G.B. / Song, S.M. / Lee, J.-G. / Shin, D.Y. / Yun, J.-H. / Sheng, Y. / Cheong, C. / Jeon, Y.H. / Jung, Y.-K. / Arrowsmith, C.H. / Avvakumov, G.V. / Dhe-Paganon, S. / Yoo, Y.J. ...Authors: Ko, S. / Kang, G.B. / Song, S.M. / Lee, J.-G. / Shin, D.Y. / Yun, J.-H. / Sheng, Y. / Cheong, C. / Jeon, Y.H. / Jung, Y.-K. / Arrowsmith, C.H. / Avvakumov, G.V. / Dhe-Paganon, S. / Yoo, Y.J. / Eom, S.H. / Lee, W.
History
DepositionJan 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 E2-25 kDa
B: Ubiquitin-conjugating enzyme E2-25 kDa


Theoretical massNumber of molelcules
Total (without water)45,1492
Polymers45,1492
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.831, 55.022, 61.762
Angle α, β, γ (deg.)64.19, 74.61, 69.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Ubiquitin-conjugating enzyme E2-25 kDa / Ubiquitin- protein ligase / Ubiquitin carrier protein / E225K / Huntingtin interacting protein 2 / HIP-2


Mass: 22574.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIP2, LIG / Production host: Escherichia coli (E. coli) / References: UniProt: P61086, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.444 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, calcium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 10, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 15647 / % possible obs: 96.1 % / Observed criterion σ(I): -1 / Redundancy: 2.23 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TTE

1tte


Resolution: 2.4→30 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 489316.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.269 772 4.9 %RANDOM
Rwork0.225 ---
obs0.225 15647 96.1 %-
all-15647 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.18 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å21.16 Å2-3.14 Å2
2---2.51 Å2-4.04 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 0 150 3308
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 120 4.7 %
Rwork0.347 2425 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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