← Back to search
2mvw

Solution structure of the TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML)

Method: SOLUTION NMR Dmax: 57.6 Å Quality: REASONABLE
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein PML

Homo sapiens

UniProt P29590

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 120–168 Chain B； UniProt 120–168 Fragment：UNP residues 120-168 ZN ZINC ION × 4 SOLUTION NMR NMR measurement conditions：pH 7；298 K；Pressure ambient NMR sample composition：1 mM [U-99% 13C; U-99% 15N] PML B1 box, 25 mM [U-98% 2H] TRIS, 100 mM sodium chloride, 0.2 mM TCEP, 1 mM zinc chloride, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1 mM [U-99% 13C; U-99% 15N] PML B1 box, 25 mM [U-98% 2H] TRIS, 100 mM sodium chloride, 0.2 mM TCEP, 1 mM zinc chloride, 100% D2O | 100% D2O NMR sample composition：0.5 mM [U-99% 13C; U-99% 15N] PML B1 box, 0.5 mM PML B1 box, 25 mM [U-98% 2H] TRIS, 100 mM sodium chloride, 0.2 mM TCEP, 1 mM zinc chloride, 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 2MVW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BOR TRANSCRIPTION FACTOR PML, A PROTO-ONCOPROTEIN, NMR, 1 REPRESENTATIVE STRUCTURE AT PH 7.5, 30 C, IN THE PRESENCE OF ZINC Deposited 1995-09-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 49–104（56 aa） Fragment：RING FINGER DOMAIN, RESIDUES 49 - 104
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.5；303 K
Resolution not provided
2MWX The RING Domain of human Promyelocytic Leukemia Protein (PML) Deposited 2014-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 49–104（56 aa） Fragment：RING Domain, UNP residues 49-104
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Pressure ambient
NMR sample composition 1 mM [U-99% 13C; U-99% 15N] protein_1-1, 25 mM [U-98% 2H] TRIS-2, 100 mM sodium chloride-3, 0.2 mM TCEP-4, 1 mM zinc chloride-5, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-99% 13C; U-99% 15N] _protein1-6, 25 mM [U-98% 2H] TRIS-7, 100 mM sodium chloride-8, 0.2 mM TCEP-9, 1 mM zinc chloride-10, 100% D2O | 100% D2O
Resolution not provided
4WJN Crystal structure of SUMO1 in complex with phosphorylated PML Deposited 2014-10-01 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 547–573（27 aa） Fragment：PML, unp residues 547-573
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM sodium cacodylate, 16% PEG3350, 10mM calcium chloride
Resolution 1.50 Å R-free 0.192
4WJO Crystal Structure of SUMO1 in complex with PML Deposited 2014-10-01 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 547–573（27 aa） Fragment：PML, unp residues 547-573
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM sodium cacodylate pH6.5, 16% PEG3350, 10mM calcium chloride
Resolution 1.46 Å R-free 0.184
5YUF Crystal Structure of PML RING tetramer Deposited 2017-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 49–99（51 aa）
Chain B 49–99（51 aa）
Chain C 49–99（51 aa）
Chain D 49–99（51 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Ammonium Sulfate
Resolution 1.60 Å R-free 0.217
6IMQ Crystal structure of PML B1-box multimers Deposited 2018-10-23 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 120–168（49 aa） Fragment：UNP residues 12-=168
Chain B 120–168（49 aa） Fragment：UNP residues 12-=168
Not recorded ZN ZINC ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG6K
Resolution 2.06 Å R-free 0.227
6IMQ Crystal structure of PML B1-box multimers Deposited 2018-10-23 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 120–168（49 aa） Fragment：UNP residues 12-=168
Chain D 120–168（49 aa） Fragment：UNP residues 12-=168
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG6K
Resolution 2.06 Å R-free 0.227
6UYO Crystal structure of K37-acetylated SUMO1 in complex with PML-SIM Deposited 2019-11-14 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 547–574（28 aa）
Mutation：E574Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE
Resolution 1.64 Å R-free 0.196
6UYO Crystal structure of K37-acetylated SUMO1 in complex with PML-SIM Deposited 2019-11-14 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 547–574（28 aa）
Mutation：E574Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE
Resolution 1.64 Å R-free 0.196
6UYP Crystal structure of K39-acetylated SUMO1 in complex with PML-SIM Deposited 2019-11-14 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 547–574（28 aa）
Mutation：E574Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE
Resolution 1.42 Å R-free 0.172
6UYQ Crystal structure of K45-acetylated SUMO1 in complex with PML-SIM Deposited 2019-11-14 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 547–574（28 aa）
Mutation：E574Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE
Resolution 1.50 Å R-free 0.175
6UYR Crystal structure of K46-acetylated SUMO1 in complex with PML-SIM Deposited 2019-11-14 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 547–574（28 aa）
Mutation：E574Y No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE
Resolution 1.30 Å R-free 0.173
6UYT Crystal structure of K39-acetylated SUMO1 in complex with phosphorylated PML-SIM Deposited 2019-11-14 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 547–574（28 aa）
Mutation：E574Y Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE
Resolution 1.66 Å R-free 0.200
6UYU Crystal structure of K45-acetylated SUMO1 in complex with phosphorylated PML-SIM Deposited 2019-11-14 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 547–574（28 aa）
Mutation：E574Y Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE
Resolution 1.66 Å R-free 0.186
6UYU Crystal structure of K45-acetylated SUMO1 in complex with phosphorylated PML-SIM Deposited 2019-11-14 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 547–574（28 aa）
Mutation：E574Y Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE
Resolution 1.66 Å R-free 0.186
6UYV Crystal structure of K46-acetylated SUMO1 in complex with phosphorylated PML-SIM Deposited 2019-11-14 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 547–574（28 aa）
Mutation：E574Y Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE
Resolution 1.40 Å R-free 0.179
8DJI Ternary complex of SUMO1 with the SIM of PML and zinc Deposited 2022-06-30 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 547–574（28 aa） Fragment：SIM
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM HEPES pH 7.0, 19 to 31 % (w/v) PEG 3350, and 1-5 mM zinc chloride
Resolution 1.97 Å R-free 0.258
8J25 Crystal structure of PML B-box2 mutant Deposited 2023-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–236（54 aa）
Mutation：C213A,A216V ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；22% PEG 3350
Resolution 2.60 Å R-free 0.248
8J2P Crystal structure of PML B-box2 Deposited 2023-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain E 183–236（54 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 3350
Resolution 2.09 Å R-free 0.235
8J2P Crystal structure of PML B-box2 Deposited 2023-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 183–236（54 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% PEG 3350
Resolution 2.09 Å R-free 0.235
8YTC PML-RBCC dimer Deposited 2024-03-25 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 46–256（211 aa）
Chain B 46–256（211 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.30 Å

17 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PML_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–51； UniProt 120–168 Author chain B； PDBConstruct 3–51； UniProt 120–168

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 2mvw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2mvw
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2mvw
Deposition date deposition_date2014-10-17
Structure title titleSolution structure of the TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML)
Keywords keywordsPML, B box, TRIM19, METAL BINDING PROTEIN, E3 ligase; METAL BINDING PROTEIN
Experimental Method methodSOLUTION NMR
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.26 Å
Radius of gyration Rg (electron density) rg_electron15.27 Å
Forward intensity I(0) i0964646000.00
Molecular weight molecular_weight242500.0 kDa
Excluded volume excluded_volume293850 ų
Envelope volume envelope_volume45651 ų
Hydration-shell volume shell_volume19242 ų
Envelope diameter envelope_diameter65.8 Å
Shell Rg shell_rg26.69 Å
Envelope Rg envelope_rg21.22 Å
Shape Rg shape_rg15.32 Å
Total Rg total_rg15.38 Å
Total atoms total_atoms32040
Residues n_residues2040
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax57.6 Å
Rg (real space) rg_real15.38 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real9.6460e+08
I(0) uncertainty (real space) i0_real_error1.2600e+07
Rg (reciprocal space) rg_reciprocal15.37 Å
I(0) (reciprocal space) i0_reciprocal964600000.0000
Solution quality estimate total_estimate0.7218
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.8 Å
Skewness Skewness skewness0.590
Kurtosis Kurtosis kurtosis0.273
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha265200.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.557; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.709; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

9. Files and Curves (10)