SAXSdb — 5yuf

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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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 49–99 Chain B； UniProt 49–99 Chain C； UniProt 49–99 Chain D； UniProt 49–99	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

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 5YUF	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 mutation/modification Different oligomeric state 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 ligand/ion 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 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
6IMQ Crystal structure of PML B1-box multimers Deposited 2018-10-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 1–51； UniProt 49–99 Author chain B； PDBConstruct 1–51； UniProt 49–99 Author chain C； PDBConstruct 1–51； UniProt 49–99 Author chain D； PDBConstruct 1–51； UniProt 49–99

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	5yuf
Deposition date deposition_date	2017-11-22
Structure title title	Crystal Structure of PML RING tetramer
Keywords keywords	PML nuclear body biogenesis, sumoylation, RING tetramerization, PML-RARA, targeted therapy, ONCOPROTEIN; ONCOPROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	18.06 Å
Radius of gyration Rg (electron density) rg_electron	17.06 Å
Forward intensity I(0) i0	8970040.00
Molecular weight molecular_weight	20941.0 kDa
Excluded volume excluded_volume	25561 Å³
Envelope volume envelope_volume	30924 Å³
Hydration-shell volume shell_volume	15230 Å³
Envelope diameter envelope_diameter	55.4 Å
Shell Rg shell_rg	22.99 Å
Envelope Rg envelope_rg	16.97 Å
Shape Rg shape_rg	17.07 Å
Total Rg total_rg	17.95 Å
Total atoms total_atoms	2772
Residues n_residues	186
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	55.5 Å
Rg (real space) rg_real	17.90 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	8.9700e+06
I(0) uncertainty (real space) i0_real_error	1.1430e+05
Rg (reciprocal space) rg_reciprocal	17.92 Å
I(0) (reciprocal space) i0_reciprocal	8970000.0000
Solution quality estimate total_estimate	0.8993
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	-0.024
Kurtosis Kurtosis kurtosis	-0.533
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	775800.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein PML
Molecular weight formula_weight	5615.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2996

EEEFQFLRCQQCQAEAKCPKLLPCLHTLCSGCLEASGMQCPICQAPWPLGA

来源 Source

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5yufa_
Class class	g — Small proteins
Fold Fold fold	g.44 — RING/U-box
Superfamily Superfamily superfamily	g.44.1 — RING/U-box
Family Family family	g.44.1.1 — RING finger domain, C3HC4

Domain ID domain_id	d5yufb_
Class class	g — Small proteins
Fold Fold fold	g.44 — RING/U-box
Superfamily Superfamily superfamily	g.44.1 — RING/U-box
Family Family family	g.44.1.1 — RING finger domain, C3HC4

Domain ID domain_id	d5yufc_
Class class	g — Small proteins
Fold Fold fold	g.44 — RING/U-box
Superfamily Superfamily superfamily	g.44.1 — RING/U-box
Family Family family	g.44.1.1 — RING finger domain, C3HC4

Domain ID domain_id	d5yufd_
Class class	g — Small proteins
Fold Fold fold	g.44 — RING/U-box
Superfamily Superfamily superfamily	g.44.1 — RING/U-box
Family Family family	g.44.1.1 — RING finger domain, C3HC4

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8. Citations (1)

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Unit-cell length a length_a	38.510 Å
Unit-cell length b length_b	84.690 Å
Unit-cell length c length_c	86.110 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	26.825 Å
R factor r_factor	0.2035
R_work r_work	0.2028
R_free r_free	0.2168

fit	/app/data/saxs_computation/yu/5yuf/5yuf.fit
pddf	/app/data/pr_computation/yu/5yuf/5yuf.pr.out
profile	/app/data/saxs_computation/yu/5yuf/5yuf.dat

Crystal Structure of PML RING tetramer

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

Refinement Refinement

Diffraction experiment Diffraction