SAXSdb — 8ytc

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

Protein PML

Homo sapiens

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 46–256 Chain B； UniProt 46–256	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 5.30 Å

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 8YTC	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 method Different experimental conditions Different structure-quality metrics	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
2MVW Solution structure of the TRIM19 B-box1 (B1) of human promyelocytic leukemia (PML) Deposited 2014-10-17	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 120-168 Chain B 120–168（49 aa） Fragment：UNP residues 120-168	Not recorded	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
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 method Different experimental conditions Different structure-quality metrics	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 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 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 ligand/ion 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 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 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 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 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 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 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 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 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 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

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 1–211； UniProt 46–256 Author chain B； PDBConstruct 1–211； UniProt 46–256

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8ytc
Deposition date deposition_date	2024-03-25
Structure title title	PML-RBCC dimer
Keywords keywords	PML nuclear body, RBCC dimer, NUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	22.06 Å
Radius of gyration Rg (electron density) rg_electron	21.54 Å
Forward intensity I(0) i0	26662100.00
Molecular weight molecular_weight	37489.0 kDa
Excluded volume excluded_volume	46111 Å³
Envelope volume envelope_volume	57584 Å³
Hydration-shell volume shell_volume	22730 Å³
Envelope diameter envelope_diameter	78.1 Å
Shell Rg shell_rg	27.90 Å
Envelope Rg envelope_rg	21.35 Å
Shape Rg shape_rg	21.53 Å
Total Rg total_rg	22.38 Å
Total atoms total_atoms	2604
Residues n_residues	332
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	74.2 Å
Rg (real space) rg_real	22.03 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	2.6660e+07
I(0) uncertainty (real space) i0_real_error	3.6720e+05
Rg (reciprocal space) rg_reciprocal	22.03 Å
I(0) (reciprocal space) i0_reciprocal	26660000.0000
Solution quality estimate total_estimate	0.7996
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.7 Å
Skewness Skewness skewness	0.334
Kurtosis Kurtosis kurtosis	-0.284
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7509000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	5.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	307216

Description description	Protein PML
Molecular weight formula_weight	23824.1 kDa
EC 编号 ec_number	2.3.2.-
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2604

PML-RBCC dimer

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

Protein PML

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/yt/8ytc/8ytc.fit
pddf	/app/data/pr_computation/yt/8ytc/8ytc.pr.out
profile	/app/data/saxs_computation/yt/8ytc/8ytc.dat