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- PDB-3a4s: The crystal structure of the SLD2:Ubc9 complex -

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Basic information

Entry
Database: PDB / ID: 3a4s
TitleThe crystal structure of the SLD2:Ubc9 complex
Components
  • NFATC2-interacting protein
  • SUMO-conjugating enzyme UBC9
KeywordsLIGASE/TRNASCRIPTION / ubiquitin fold / SUMO / Coiled coil / Cytoplasm / Methylation / Nucleus / ATP-binding / Cell cycle / Cell division / Chromosome partition / Host-virus interaction / Isopeptide bond / Ligase / Mitosis / Nucleotide-binding / Ubl conjugation / Ubl conjugation pathway / LIGASE-TRNASCRIPTION COMPLEX
Function / homology
Function and homology information


SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / transferase complex / SUMOylation of nuclear envelope proteins / HLH domain binding / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly ...SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / transferase complex / SUMOylation of nuclear envelope proteins / HLH domain binding / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / mitotic nuclear membrane reassembly / synaptonemal complex / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / nuclear export / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / SUMOylation of ubiquitinylation proteins / transcription factor binding / SUMOylation of transcription factors / SUMOylation of DNA replication proteins / protein sumoylation / postsynaptic cytosol / nuclear pore / SUMOylation of DNA damage response and repair proteins / presynaptic cytosol / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / Meiotic synapsis / SUMOylation of chromatin organization proteins / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / chromosome segregation / SUMOylation of intracellular receptors / PML body / PKR-mediated signaling / modulation of chemical synaptic transmission / protein modification process / Schaffer collateral - CA1 synapse / Formation of Incision Complex in GG-NER / nuclear envelope / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / 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 ...: / 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
NFATC2-interacting protein / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSekiyama, N. / Arita, K. / Ikeda, Y. / Ariyoshi, M. / Tochio, H. / Saitoh, H. / Shirakawa, M.
CitationJournal: Proteins / Year: 2009
Title: Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45
Authors: Sekiyama, N. / Arita, K. / Ikeda, Y. / Hashiguchi, K. / Ariyoshi, M. / Tochio, H. / Saitoh, H. / Shirakawa, M.
History
DepositionJul 14, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: SUMO-conjugating enzyme UBC9
B: SUMO-conjugating enzyme UBC9
C: NFATC2-interacting protein
D: NFATC2-interacting protein


Theoretical massNumber of molelcules
Total (without water)54,2404
Polymers54,2404
Non-polymers00
Water00
1
A: SUMO-conjugating enzyme UBC9


Theoretical massNumber of molelcules
Total (without water)18,4421
Polymers18,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SUMO-conjugating enzyme UBC9


Theoretical massNumber of molelcules
Total (without water)18,4421
Polymers18,4421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NFATC2-interacting protein


Theoretical massNumber of molelcules
Total (without water)8,6781
Polymers8,6781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NFATC2-interacting protein


Theoretical massNumber of molelcules
Total (without water)8,6781
Polymers8,6781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.250, 49.420, 90.295
Angle α, β, γ (deg.)103.20, 92.10, 101.13
Int Tables number1
Space group name H-MP1

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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 / p18


Mass: 18442.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Ubc9 / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63279, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein NFATC2-interacting protein / Nip45 / Nuclear factor of activated T-cells / cytoplasmic 2-interacting protein / 45 kDa NF-AT- ...Nip45 / Nuclear factor of activated T-cells / cytoplasmic 2-interacting protein / 45 kDa NF-AT-interacting protein / 45 kDa NFAT-interacting protein


Mass: 8677.913 Da / Num. of mol.: 2 / Fragment: SLD2, Ubiquitin-like domain, residues 339-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nip45 / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O09130
Sequence detailsTHIS COORDINATES IN ALL CHAINS USE NON-SEQUENTIAL RESIDUE NUMBERING TO CLARIFY THE EXPRESSION TAGS.

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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: 2.49 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% polyethylene glycol 1500, 0.1M SPG buffer : SPG buffer was prepared by mixing succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7, pH 6.0, VAPOR DIFFUSION, ...Details: 25% polyethylene glycol 1500, 0.1M SPG buffer : SPG buffer was prepared by mixing succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→46.4 Å / Num. obs: 13920 / % possible obs: 93.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.93 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.2 / Num. measured all: 645440
Reflection shellResolution: 2.58→2.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.196 / % possible all: 73.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries; 1A3S and 3A4R

1a3s

3a4r


Resolution: 2.7→46.366 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.776 / SU ML: 0.41 / σ(F): 1.98 / Phase error: 29.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 1255 9.9 %
Rwork0.2217 11418 -
obs0.2265 12673 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.944 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 98.02 Å2 / Biso mean: 42.69 Å2 / Biso min: 11.66 Å2
Baniso -1Baniso -2Baniso -3
1-14.023 Å20.885 Å2-7.712 Å2
2---11.316 Å2-2.774 Å2
3----2.707 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 0 0 3563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033652
X-RAY DIFFRACTIONf_angle_d0.7044925
X-RAY DIFFRACTIONf_dihedral_angle_d14.351388
X-RAY DIFFRACTIONf_chiral_restr0.046520
X-RAY DIFFRACTIONf_plane_restr0.003632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.80820.32671180.24731135X-RAY DIFFRACTION87
2.8082-2.93590.33541400.26941254X-RAY DIFFRACTION92
2.9359-3.09070.35591330.26021294X-RAY DIFFRACTION97
3.0907-3.28430.31531500.26251305X-RAY DIFFRACTION98
3.2843-3.53780.28131410.24341247X-RAY DIFFRACTION97
3.5378-3.89370.26491420.20381302X-RAY DIFFRACTION99
3.8937-4.45670.21691470.18911286X-RAY DIFFRACTION98
4.4567-5.61340.23421450.17861315X-RAY DIFFRACTION99
5.6134-46.37230.21021390.20071280X-RAY DIFFRACTION97

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