SAXSdb — 3u5v

▼

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

Protein max, Transcription factor E2-alpha chimera

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	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 560–610	Fragment：SEE REMARK 999	NO3 NITRATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% glycerol, 3.2-3.5 M sodium nitrate, 0.1 M sodium acetate anhydrous, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.235

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 3U5V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MH0 Solution NMR structure of the p300 Taz2:ETAD1 complex Deposited 2013-11-12	Different construct 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 1–37（37 aa） Fragment：Activation domain 1 (ETAD1), E2A residues 1-37	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；288 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1.4 mM [U-99% 13C; U-99% 15N] ETAD1, 2 mM Taz2, 20 mM MES, 1 mM sodium azide, 5 mM beta-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3078 uM ETAD1, 1038 uM [U-99% 13C; U-99% 15N] Taz2, 20 mM MES, 1 mM sodium azide, 5 mM beta-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2YPA Structure of the SCL:E47:LMO2:LDB1 complex bound to DNA Deposited 2012-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 535–613（79 aa） Fragment：RESIDUES 535-613	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE	Resolution 2.80 Å R-free 0.269
2YPB Structure of the SCL:E47 complex bound to DNA Deposited 2012-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 535–613（79 aa） Fragment：RESIDUES 535-613	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；5 % (V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 40 MM MAGNESIUM CHLORIDE, 50 MM SODIUM CACODYLATE PH 6.0 AND 2MM GLUTATHIONE	Resolution 2.87 Å R-free 0.288
6MGN mouse Id1 (51-104) - human hE47 (348-399) complex Deposited 2018-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 558–609（52 aa） Fragment：unp residues 558-609	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.1 M potassium phosphate (pH 6.0), 0.25 M NaCl, 22.5% PEG8000.	Resolution 1.90 Å R-free 0.217

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TFE2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–68； UniProt 560–610

Protein max, Transcription factor E2-alpha chimera

Homo sapiens

UniProt P28574

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 22–36	Fragment：SEE REMARK 999	NO3 NITRATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；5% glycerol, 3.2-3.5 M sodium nitrate, 0.1 M sodium acetate anhydrous, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.235

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 3U5V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A93 NMR SOLUTION STRUCTURE OF THE C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1998-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 74–102（29 aa） Fragment：HETERODIMERIC LEUCINE ZIPPER	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.8；298 K；Ionic strength (raw mmCIF value) 10mM；Pressure 1 NMR sample composition WATER	Resolution not provided
2A93 NMR SOLUTION STRUCTURE OF THE C-MYC-MAX HETERODIMERIC LEUCINE ZIPPER, 40 STRUCTURES Deposited 1998-06-09	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 74–102（29 aa） Fragment：LEUCINE ZIPPER	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.8；298 K；Ionic strength (raw mmCIF value) 100 mM；Pressure 1 NMR sample composition WATER	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MAX_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–17； UniProt 22–36

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	3u5v
Deposition date deposition_date	2011-10-11
Structure title title	Crystal structure of Max-E47
Keywords keywords	basic helix-loop-helix (bHLH), transcription factor, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.28 Å
Radius of gyration Rg (electron density) rg_electron	16.48 Å
Forward intensity I(0) i0	1386200.00
Molecular weight molecular_weight	7364.0 kDa
Excluded volume excluded_volume	9022 Å³
Envelope volume envelope_volume	12419 Å³
Hydration-shell volume shell_volume	7688 Å³
Envelope diameter envelope_diameter	66.2 Å
Shell Rg shell_rg	19.51 Å
Envelope Rg envelope_rg	17.55 Å
Shape Rg shape_rg	16.51 Å
Total Rg total_rg	17.10 Å
Total atoms total_atoms	514
Residues n_residues	62
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	67.1 Å
Rg (real space) rg_real	17.62 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	1.3860e+06
I(0) uncertainty (real space) i0_real_error	2.0260e+04
Rg (reciprocal space) rg_reciprocal	17.58 Å
I(0) (reciprocal space) i0_reciprocal	1386000.0000
Solution quality estimate total_estimate	0.7483
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.1 Å
Skewness Skewness skewness	0.658
Kurtosis Kurtosis kurtosis	0.061
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	130500.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.536; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.140; Smooth: 0.976

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein max, Transcription factor E2-alpha chimera
Molecular weight formula_weight	9075.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	548

MGADKRAHHNALERKRRRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERNLNPLNHHHHHH

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3u5vA01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	37.480 Å
Unit-cell length b length_b	49.466 Å
Unit-cell length c length_c	74.100 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	8

Space group space_group	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	23.256 Å
R factor r_factor	0.2082
R_work r_work	0.2070
R_free r_free	0.2350

fit	/app/data/saxs_computation/u5/3u5v/3u5v.fit
pddf	/app/data/pr_computation/u5/3u5v/3u5v.pr.out
profile	/app/data/saxs_computation/u5/3u5v/3u5v.dat

Crystal structure of Max-E47

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

Protein max, Transcription factor E2-alpha chimera

State in the Current Structure

Other States of the Same Protein in the Database

Protein max, Transcription factor E2-alpha chimera

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)