SAXSdb — 4jol

▼

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

Protein CBFA2T1

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 338–400 Chain C； UniProt 338–400	Fragment：NHR2 domain of AML1-ETO (unp residues 338-400)	Transcription factor 12 × 2 （Q99081）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 mM Tris, 20% ETHANOL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.91 Å R-free 0.252
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 338–400 Chain D； UniProt 338–400	Fragment：NHR2 domain of AML1-ETO (unp residues 338-400)	Transcription factor 12 × 2 （Q99081）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 mM Tris, 20% ETHANOL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.91 Å R-free 0.252

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 4JOL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WQ6 The tetramer structure of the nervy homolgy two (NHR2) domain of AML1-ETO is critical for AML1-ETO'S activity Deposited 2004-09-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 335–403（69 aa） Fragment：NHR2 domain Chain B 335–403（69 aa） Fragment：NHR2 domain	Non-standard monomer：Yes (specific site not provided by mmCIF) 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, SITTING DROP；pH 5.6；293 K；100mM Na citrate (pH 5.6), 100mM MgCl2, 30% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.270
2DJ8 Solution Structure of zf-MYND Domain of Protein CBFA2TI (Protein MTG8) Deposited 2006-03-31	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 449–450（2 aa） Fragment：zf-MYND	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 0.95mM zf-MYND domain, U-13C, 15N; 20mM d-Tris_HCl (pH 7.0); 100mM NaCl; 1mM d-DTT, 0.02% NaN3; 0.05mM ZnCl2; 1mM IDA; 90% H2O, 10% D20 \| 90% H2O, 10% D20	Resolution not provided
2KNH The Solution structure of the eTAFH domain of AML1-ETO complexed with HEB peptide Deposited 2009-08-25	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 A 119–216（98 aa） Fragment：eTAFH domain (UNP residues 119-216)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 350；Pressure ambient NMR sample composition 25 mM Bis-Tris, 1 mM EDTA, 350 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2KYG Structure of the AML1-ETO Nervy Domain - PKA(RIIa) complex and its contribution to AML1-ETO activity Deposited 2010-05-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 437–467（31 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；303 K；Ionic strength (raw mmCIF value) 0.0；Pressure ambient NMR sample composition 2 mM [U-99% 13C; U-99% 15N] NHR3, 2 mM [U-99% 13C; U-99% 15N] PKA(RIIa), 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2OD1 Solution structure of the MYND domain from human AML1-ETO Deposited 2006-12-21	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 510–559（50 aa） Fragment：MYND domain	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Pressure 1 NMR sample composition 1-2mM protein, 25mM Bis-Tris, 5mM DTT, 50uM ZnCl2, 95% H20, 5% D2O \| 95% H20, 5% D2O	Resolution not provided
2ODD Solution structure of the MYND domain from AML1-ETO complexed with SMRT, a corepressor Deposited 2006-12-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 510–559（50 aa） Fragment：MYND domain (AML1-ETO, residues 658-707)	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 6.8；303 K；Pressure 1 NMR sample composition 2mM SMRT-MYND, 25mM Bis-Tris, pH 6.8, 50uM ZnCl2, 1mM DTT, 95%H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
2PP4 Solution Structure of ETO-TAFH refined in explicit solvent Deposited 2007-04-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 119–225（107 aa） Fragment：TAFH domain, residues 119-225	Mutation：F136Y	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；293 K；Pressure ambient NMR sample composition 1.1 mM protein, 200 mM phosphate buffer, 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	MTG8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–64； UniProt 338–400 Author chain B； PDBConstruct 2–64； UniProt 338–400 Author chain C； PDBConstruct 2–64； UniProt 338–400 Author chain D； PDBConstruct 2–64； UniProt 338–400

Transcription factor 12

Homo sapiens

UniProt Q99081

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 177–200 Chain G； UniProt 177–200	Fragment：A fragment of HEB (unp residues 177-200)	Protein CBFA2T1 × 2 （Q06455）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 mM Tris, 20% ETHANOL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.91 Å R-free 0.252
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 177–200 Chain H； UniProt 177–200	Fragment：A fragment of HEB (unp residues 177-200)	Protein CBFA2T1 × 2 （Q06455）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 mM Tris, 20% ETHANOL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.91 Å R-free 0.252

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 4JOL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KNH The Solution structure of the eTAFH domain of AML1-ETO complexed with HEB peptide Deposited 2009-08-25	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 11–28（18 aa） Fragment：HEB peptide (UNP residues 11-28)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 350；Pressure ambient NMR sample composition 25 mM Bis-Tris, 1 mM EDTA, 350 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HTF4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 2–25； UniProt 177–200 Author chain F； PDBConstruct 2–25； UniProt 177–200 Author chain G； PDBConstruct 2–25； UniProt 177–200 Author chain H； PDBConstruct 2–25； UniProt 177–200

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4jol
Deposition date deposition_date	2013-03-18
Structure title title	Complex structure of AML1-ETO NHR2 domain with HEB fragment
Keywords keywords	leukemia; AML1-ETO; HEB; NHR2 domain, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	27.19 Å
Radius of gyration Rg (electron density) rg_electron	27.28 Å
Forward intensity I(0) i0	22170900.00
Molecular weight molecular_weight	34508.0 kDa
Excluded volume excluded_volume	42506 Å³
Envelope volume envelope_volume	53729 Å³
Hydration-shell volume shell_volume	19085 Å³
Envelope diameter envelope_diameter	114.1 Å
Shell Rg shell_rg	29.53 Å
Envelope Rg envelope_rg	28.41 Å
Shape Rg shape_rg	27.41 Å
Total Rg total_rg	27.11 Å
Total atoms total_atoms	2425
Residues n_residues	285
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

▼

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

Maximum dimension Dmax dmax	109.0 Å
Rg (real space) rg_real	27.88 Å
Rg uncertainty (real space) rg_real_error	1.52 Å
I(0) (real space) i0_real	2.2170e+07
I(0) uncertainty (real space) i0_real_error	4.1300e+05
Rg (reciprocal space) rg_reciprocal	27.66 Å
I(0) (reciprocal space) i0_reciprocal	22170000.0000
Solution quality estimate total_estimate	0.6422
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.7 Å
Skewness Skewness skewness	0.806
Kurtosis Kurtosis kurtosis	0.177
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7741000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.183; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.077; Smooth: 0.720

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Protein CBFA2T1
Molecular weight formula_weight	8036.0 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	2425

SEEMIDHRLTDREWAEEWKHLDHLLNCIMDMVEKTRRSLTVLRRCQEADREELNYWIRRYSDAE

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

Entity 2 Entity 2 polymer

Description description	Transcription factor 12
Molecular weight formula_weight	2622.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

SPLQAKKVRKVPPGLPSSVYAPSPN

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

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4jolA00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	4jolB00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	4jolC00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	4jolD00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	230 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	139.485 Å
Unit-cell length b length_b	139.485 Å
Unit-cell length c length_c	43.169 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.906 Å
Low-resolution limit resolution_low	27.127 Å
R factor r_factor	0.2115
R_work r_work	0.2071
R_free r_free	0.2519

fit	/app/data/saxs_computation/jo/4jol/4jol.fit
pddf	/app/data/pr_computation/jo/4jol/4jol.pr.out
profile	/app/data/saxs_computation/jo/4jol/4jol.dat

Complex structure of AML1-ETO NHR2 domain with HEB fragment

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

Protein CBFA2T1

State in the Current Structure

Other States of the Same Protein in the Database

Transcription factor 12

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)