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- PDB-2vrr: Structure of SUMO modified Ubc9 -

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Basic information

Entry
Database: PDB / ID: 2vrr
TitleStructure of SUMO modified Ubc9
Components
  • SMALL UBIQUITIN-RELATED MODIFIER 1
  • SUMO-CONJUGATING ENZYME UBC9
KeywordsCELL CYCLE/LIGASE / E2 / UBC9 / SUMO / LIGASE / NUCLEUS / MITOSIS / MEMBRANE / PHOSPHOPROTEIN / ISOPEPTIDE BOND / CHROMOSOME PARTITION / POSTTRANSLATIONAL MODIFICATION / UBL CONJUGATION PATHWAY / UBIQUITIN LIKE MOLECULE / DEVELOPMENTAL PROTEIN / HOST-VIRUS INTERACTION / CYTOPLASM / CELL CYCLE / MODIFICATION / CELL DIVISION / CELL CYCLE-LIGASE complex
Function / homology
Function and homology information


positive regulation of intracellular steroid hormone receptor signaling pathway / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMOylation of nuclear envelope proteins / Vitamin D (calciferol) metabolism / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of transcription factors ...positive regulation of intracellular steroid hormone receptor signaling pathway / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMOylation of nuclear envelope proteins / Vitamin D (calciferol) metabolism / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / SUMOylation of RNA binding proteins / SUMOylation of DNA methylation proteins / SUMOylation of DNA damage response and repair proteins / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / SUMOylation of immune response proteins / regulation of signaling receptor activity / SUMO ligase complex / SUMO conjugating enzyme activity / transferase complex / Formation of Incision Complex in GG-NER / Transcriptional and post-translational regulation of MITF-M expression and activity / Processing of DNA double-strand break ends / bHLH transcription factor binding / RING-like zinc finger domain binding / SUMOylation of nuclear envelope proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HLH domain binding / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / negative regulation of action potential / negative regulation of transcription initiation by RNA polymerase II / import into nucleus / small protein activating enzyme binding / regulation of calcium ion transmembrane transport / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / SUMOylation of DNA methylation proteins / negative regulation of protein import into nucleus / Maturation of nucleoprotein / nuclear export / XY body / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cardiac muscle cell contraction / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / roof of mouth development / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / ubiquitin-specific protease binding / cellular response to cadmium ion / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / ubiquitin-like protein ligase binding / nuclear pore / protein sumoylation / potassium channel regulator activity / Regulation of IFNG signaling / transporter activator activity / postsynaptic cytosol / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / ionotropic glutamate receptor binding / protein modification process / transcription coregulator binding / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / Maturation of DENV proteins / chromosome segregation / regulation of protein stability / positive regulation of protein-containing complex assembly / PML body / PKR-mediated signaling / fibrillar center / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / Formation of Incision Complex in GG-NER / protein tag activity / ubiquitin-protein transferase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nuclear envelope / cellular response to heat / nuclear membrane / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / positive regulation of canonical NF-kappaB signal transduction / nuclear speck / protein stabilization / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding
Similarity search - Function
Small ubiquitin-related modifier 1, Ubl domain / : / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme ...Small ubiquitin-related modifier 1, Ubl domain / : / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Small ubiquitin-related modifier 1 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKnipscheer, P. / Flotho, A. / Klug, H. / Olsen, J.V. / van Dijk, W.J. / Fish, A. / Johnson, E.S. / Mann, M. / Sixma, T.K. / Pichler, A.
CitationJournal: Mol. Cell / Year: 2008
Title: Ubc9 sumoylation regulates SUMO target discrimination.
Authors: Knipscheer, P. / Flotho, A. / Klug, H. / Olsen, J.V. / van Dijk, W.J. / Fish, A. / Johnson, E.S. / Mann, M. / Sixma, T.K. / Pichler, A.
History
DepositionApr 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Jul 31, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.6Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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

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Assembly

Deposited unit
A: SUMO-CONJUGATING ENZYME UBC9
B: SMALL UBIQUITIN-RELATED MODIFIER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4687
Polymers27,2612
Non-polymers2075
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-5.4 kcal/mol
Surface area16110 Å2
MethodPQS
Unit cell
Length a, b, c (Å)27.520, 66.610, 122.579
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 SUMO-CONJUGATING ENZYME UBC9 / UBC9 / SUMO-PROTEIN LIGASE / UBIQUITIN-CONJUGATING ENZYME E2 I / UBIQUITIN-PROTEIN LIGASE I / ...UBC9 / SUMO-PROTEIN LIGASE / UBIQUITIN-CONJUGATING ENZYME E2 I / UBIQUITIN-PROTEIN LIGASE I / UBIQUITIN CARRIER PROTEIN I / UBIQUITIN CARRIER PROTEIN 9 / MUBC9


Mass: 18030.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63280, ubiquitin-protein ligase
#2: Protein SMALL UBIQUITIN-RELATED MODIFIER 1 / SUMO1 / SUMO-1 / SENTRIN / UBIQUITIN-LIKE PROTEIN SMT3C / SMT3 HOMOLOG 3 / UBIQUITIN-HOMOLOGY ...SUMO1 / SUMO-1 / SENTRIN / UBIQUITIN-LIKE PROTEIN SMT3C / SMT3 HOMOLOG 3 / UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1 / UBIQUITIN-LIKE PROTEIN UBL1 / GAP-MODIFYING PROTEIN 1 / GMP1


Mass: 9230.559 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63165
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 20-97 OF SUMO1 PRECEDED BY A START METHIONINE

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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: 2.08 Å3/Da / Density % sol: 40.9 % / Description: NONE
Crystal growpH: 6.5
Details: 24% (W/V) PEG3350, 200 MM SODIUM FORMATE, 100 MM BIS-TRIS PROPANE PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2005 / Details: HELIOS MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.22→60 Å / Num. obs: 11764 / % possible obs: 97.3 % / Observed criterion σ(I): 1.8 / Redundancy: 12.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.2
Reflection shellResolution: 2.21→2.32 Å / Redundancy: 10 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 81.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1U9B, 2BF8

1u9b

2bf8


Resolution: 2.22→61.31 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.874 / SU B: 11.002 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS RESIDUES B94-B96 ARE DISORDERED AND HAVE BEEN GIVEN AN OCCUPANCY OF 0. THERE IS A COVALENT ISOPEPTIDE LINKAGE BETWEEN LYSINE A14 AND GLYCINE B97
RfactorNum. reflection% reflectionSelection details
Rfree0.256 547 4.7 %RANDOM
Rwork0.171 ---
obs0.175 11169 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.14 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.22→61.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 13 192 2109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222012
X-RAY DIFFRACTIONr_bond_other_d0.0020.021437
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9752717
X-RAY DIFFRACTIONr_angle_other_deg0.96133520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03624.84295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37315375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4041511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022236
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02387
X-RAY DIFFRACTIONr_nbd_refined0.2020.2393
X-RAY DIFFRACTIONr_nbd_other0.1980.21460
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2925
X-RAY DIFFRACTIONr_nbtor_other0.0870.21045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2156
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6361.51220
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09221973
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9863818
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1184.5743
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: 2.22→2.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 35
Rwork0.189 761
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)
11.6245-0.4178-0.10722.1545-0.41351.3649-0.0237-0.0749-0.16190.0542-0.0274-0.00020.1660.05620.0511-0.1433-0.0117-0.0032-0.06950.0233-0.1907-6.3926.71810.116
25.2598-1.210.78427.23422.21243.5148-0.06240.13120.2994-0.1458-0.0046-0.0757-0.2776-0.05820.0669-0.0685-0.01030.0236-0.02250.0095-0.156-14.62939.36725.341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 158
2X-RAY DIFFRACTION2B20 - 97

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