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- PDB-2bf8: Crystal structure of SUMO modified ubiquitin conjugating enzyme E... -

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Basic information

Entry
Database: PDB / ID: 2bf8
TitleCrystal structure of SUMO modified ubiquitin conjugating enzyme E2- 25K
Components
  • UBIQUITIN-CONJUGATING ENZYME E2-25 KDA
  • UBIQUITIN-LIKE PROTEIN SMT3C
KeywordsLIGASE / LIGASE-COMPLEX / E2-25K / E2 UBIQUITIN CONJUGATING ENZYME / SUMO / SUMO-TARGET STRUCTURE / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


Synthesis of active ubiquitin: roles of E1 and E2 enzymes / negative regulation of transcription by transcription factor localization / Antigen processing: Ubiquitination & Proteasome degradation / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / negative regulation of transcription by transcription factor localization / Antigen processing: Ubiquitination & Proteasome degradation / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of immune response proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / E2 ubiquitin-conjugating enzyme / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / SUMOylation of ubiquitinylation proteins / roof of mouth development / negative regulation of DNA binding / ubiquitin conjugating enzyme activity / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / potassium channel regulator activity / protein K48-linked ubiquitination / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / protein tag activity / Formation of Incision Complex in GG-NER / protein polyubiquitination / ubiquitin-protein transferase activity / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear membrane / protein stabilization / nuclear body / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / enzyme binding / RNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 K / Small ubiquitin-related modifier 1
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPichler, A. / Knipscheer, P. / Oberhofer, E. / Van Dijk, W.J. / Korner, R. / Velgaard Olsen, J. / Jentsch, S. / Melchior, F. / Sixma, T.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Sumo Imodification of the Ubiquitin Conjugating Enzyme E2-25K
Authors: Pichler, A. / Knipscheer, P. / Oberhofer, E. / Van Dijk, W.J. / Korner, R. / Velgaard Olsen, J. / Jentsch, S. / Melchior, F. / Sixma, T.K.
History
DepositionDec 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2-25 KDA
B: UBIQUITIN-LIKE PROTEIN SMT3C


Theoretical massNumber of molelcules
Total (without water)26,8172
Polymers26,8172
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.391, 58.391, 162.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2-25 KDA / E2-25K / UBIQUITIN-PROTEIN LIGASE / UBIQUITIN CARRIER PROTEIN / E2(25K) / HUNTINGTIN INTERACTING ...E2-25K / UBIQUITIN-PROTEIN LIGASE / UBIQUITIN CARRIER PROTEIN / E2(25K) / HUNTINGTIN INTERACTING PROTEIN 2 / HIP-2


Mass: 17846.412 Da / Num. of mol.: 1 / Fragment: CONSERVED CORE DOMAIN, RESIDUES 1-154
Source method: isolated from a genetically manipulated source
Details: COVALENT ISOPEPTIDE LINK BETWEEN E2-25K LYSINE 14 AND SUMO C-TERMINUS
Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61085, ubiquitin-protein ligase
#2: Protein UBIQUITIN-LIKE PROTEIN SMT3C / SUMO / UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1 / UBIQUITIN-LIKE PROTEIN UBL1 / UBIQUITIN-RELATED ...SUMO / UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1 / UBIQUITIN-LIKE PROTEIN UBL1 / UBIQUITIN-RELATED PROTEIN SUMO-1 / GAP MODIFYING PROTEIN 1 / GMP1 / SENTRIN


Mass: 8970.248 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-97
Source method: isolated from a genetically manipulated source
Details: COVALENT ISOPEPTIDE LINK BETWEEN E2-25K LYSINE 14 AND SUMO C-TERMINUS
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63165
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCOVALENT ISOPEPTIDE BOND BETWEEN E2-25K LYSINE 14 AND SUMO C-TERMINUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 20

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.2 %
Crystal growpH: 8.5
Details: 100 MM TRIS PH 8.5 200 MM MAGNESIUM CHLORIDE 17% PEG 4000 10 % GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC ADSC Q4R / Date: Sep 7, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL, SI(111), SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13257 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 13 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FZY

1fzy


Resolution: 2.3→55.05 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.029 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 651 4.9 %RANDOM
Rwork0.21 ---
obs0.213 12545 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.66 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å20 Å2
2---2.04 Å20 Å2
3---4.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→55.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 0 83 1936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221905
X-RAY DIFFRACTIONr_bond_other_d0.0020.021729
X-RAY DIFFRACTIONr_angle_refined_deg1.641.9482577
X-RAY DIFFRACTIONr_angle_other_deg0.92734052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2765231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69725.05591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64415347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.631510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022095
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
X-RAY DIFFRACTIONr_nbd_refined0.1980.2403
X-RAY DIFFRACTIONr_nbd_other0.190.21782
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2900
X-RAY DIFFRACTIONr_nbtor_other0.0890.21064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0750.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3190.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8131.51512
X-RAY DIFFRACTIONr_mcbond_other0.1731.5467
X-RAY DIFFRACTIONr_mcangle_it0.97921884
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7553866
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4964.5693
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 56 -
Rwork0.293 871 -
obs--98.51 %
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)
13.5484-1.0822-1.95759.48252.94183.35540.0625-0.0756-0.09220.4331-0.1307-0.79760.3162-0.10590.0682-0.1357-0.10810.0391-0.2368-0.0434-0.296140.19517.78369.772
24.7404-4.0568-2.56669.49910.29818.47150.76841.07861.1827-0.7803-0.457-0.425-1.6759-0.7391-0.31140.36630.12060.0810.35770.30020.163817.99152.24774.211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 155
2X-RAY DIFFRACTION2B20 - 97

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