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2mp2

Solution structure of SUMO dimer in complex with SIM2-3 from RNF4

Method: SOLUTION NMR Dmax: 72.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Small ubiquitin-related modifier 3

Homo sapiens

UniProt P55854

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 12–92 Chain B； UniProt 2–90 Fragment：UNP residues 12-92 Fragment：UNP residues 2-90 E3 ubiquitin-protein ligase RNF4 × 1 （Q9QZS2） SOLUTION NMR NMR measurement conditions：pH 7；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition：0.3 mM [U-99% 13C; U-99% 15N] SUMO 1, 0.3 mM SUMO 2, 1.0 mM RNF4, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.3 mM SUMO 1, 0.3 mM [U-99% 13C; U-99% 15N] SUMO 2, 1.0 mM RNF4, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.3 mM [U-99% 13C; U-99% 15N] SUMO 1, 0.3 mM SUMO 2, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.3 mM SUMO 1, 0.3 mM [U-99% 13C; U-99% 15N] SUMO 2, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2MP2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1U4A Solution structure of human SUMO-3 C47S Deposited 2004-07-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 14–92（79 aa） Fragment：ubiquitin-like domain
Mutation：C47S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.25；298 K；Ionic strength (raw mmCIF value) 25mM phosphate buffer, 75mM Nacl；Pressure 1
NMR sample composition 0.8mM 15N-labeled protein | 25mM phosphate buffer, 75mM Nacl 90% H2O, 10% D2O
NMR sample composition 0.6mM 13C,15N-labeled protein | 25mM phosphate buffer, 75mM Nacl 90% H2O, 10% D2O
Resolution not provided
2IO1 Crystal structure of human Senp2 in complex with preSUMO-3 Deposited 2006-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 14–103（90 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；7% PEG 4000, 0.1M Sodium acetate, 0.2M Magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.230
2IO1 Crystal structure of human Senp2 in complex with preSUMO-3 Deposited 2006-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 14–103（90 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；7% PEG 4000, 0.1M Sodium acetate, 0.2M Magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.230
2IO1 Crystal structure of human Senp2 in complex with preSUMO-3 Deposited 2006-10-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 14–103（90 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；7% PEG 4000, 0.1M Sodium acetate, 0.2M Magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.60 Å R-free 0.230
6K5R Complex of SUMO2 with Phosphorylated viral SIM IE2 Deposited 2019-05-30 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 15–91（77 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 162.7；Pressure 1
NMR sample composition 0.3 mM [U-15N] SUMO2, 3 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-13C; U-15N] SUMO2, 1.5 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6NNQ Non-covalent structure of SENP1 in complex with SUMO2 Deposited 2019-01-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 15–92（78 aa） Fragment：residues 15-92
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；20% PEG 6000, 0.1M HEPES, pH 7.5
Resolution 2.62 Å R-free 0.277
7R2E Structure of human Senp7 with SUMO2 Deposited 2022-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 16–91（76 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Sodium HEPES 7.0, 15 % w/v PEG 20,000
Resolution 1.74 Å R-free 0.230
7R2E Structure of human Senp7 with SUMO2 Deposited 2022-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 16–91（76 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Sodium HEPES 7.0, 15 % w/v PEG 20,000
Resolution 1.74 Å R-free 0.230
7ZJU Structure of human USPL1 in covalent complex with SUMO3-2Br probe Deposited 2022-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–91（90 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 1 OXU 2-bromanylethanamine × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；100 mM Tris pH 8.8, 19% PEG6000, 200 mM CaCl2
Resolution 2.17 Å R-free 0.238
7ZJU Structure of human USPL1 in covalent complex with SUMO3-2Br probe Deposited 2022-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–91（90 aa）
Not recorded ZN ZINC ION × 1 GOL GLYCEROL × 2 OXU 2-bromanylethanamine × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293 K；100 mM Tris pH 8.8, 19% PEG6000, 200 mM CaCl2
Resolution 2.17 Å R-free 0.238
9GNN Structure of SENP5 in complex with SUMO2 Deposited 2024-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 14–91（78 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, Phosphate/citrate 4.2, 20 % w/v PEG 8000
Resolution 2.36 Å R-free 0.283
9GNN Structure of SENP5 in complex with SUMO2 Deposited 2024-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 14–91（78 aa）
Not recorded AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, Phosphate/citrate 4.2, 20 % w/v PEG 8000
Resolution 2.36 Å R-free 0.283

7 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SUMO3_HUMAN
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 2–82； UniProt 12–92 Author chain B； PDBConstruct 2–90； UniProt 2–90

E3 ubiquitin-protein ligase RNF4

OrganismNot specified

UniProt Q9QZS2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 45–69 Fragment：UNP residues 45-69 Small ubiquitin-related modifier 3 × 1 （P55854） Small ubiquitin-related modifier 3 × 1 （P55854） SOLUTION NMR NMR measurement conditions：pH 7；303 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition：0.3 mM [U-99% 13C; U-99% 15N] SUMO 1, 0.3 mM SUMO 2, 1.0 mM RNF4, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.3 mM SUMO 1, 0.3 mM [U-99% 13C; U-99% 15N] SUMO 2, 1.0 mM RNF4, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.3 mM [U-99% 13C; U-99% 15N] SUMO 1, 0.3 mM SUMO 2, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.3 mM SUMO 1, 0.3 mM [U-99% 13C; U-99% 15N] SUMO 2, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name RNF4_MOUSE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–25； UniProt 45–69

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2mp2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2mp2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2mp2
Deposition date deposition_date2014-05-09
Structure title titleSolution structure of SUMO dimer in complex with SIM2-3 from RNF4
Keywords keywordsSUMO, dimer, SIM, RNF4, Complex, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.05 Å
Radius of gyration Rg (electron density) rg_electron19.83 Å
Forward intensity I(0) i0786888000.00
Molecular weight molecular_weight223580.0 kDa
Excluded volume excluded_volume274700 ų
Envelope volume envelope_volume48678 ų
Hydration-shell volume shell_volume20099 ų
Envelope diameter envelope_diameter76.1 Å
Shell Rg shell_rg27.08 Å
Envelope Rg envelope_rg21.50 Å
Shape Rg shape_rg19.83 Å
Total Rg total_rg19.99 Å
Total atoms total_atoms30970
Residues n_residues1970
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax72.9 Å
Rg (real space) rg_real20.22 Å
Rg uncertainty (real space) rg_real_error0.55 Å
I(0) (real space) i0_real7.8690e+08
I(0) uncertainty (real space) i0_real_error1.0440e+07
Rg (reciprocal space) rg_reciprocal20.19 Å
I(0) (reciprocal space) i0_reciprocal786900000.0000
Solution quality estimate total_estimate0.7866
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.7 Å
Skewness Skewness skewness0.528
Kurtosis Kurtosis kurtosis-0.373
Angular range angular_range— – 0.3950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3831000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.552; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.567; Smooth: 1.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2mp2A00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2mp2B00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)