SAXSdb — 5t01

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

Transcription factor AP-1

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 254–315 Chain B； UniProt 254–315	Fragment：DNA binding domain (UNP residues 254-315) Mutation：C269S	;DNA (5'-D(PCPTPCPCPTPAPTPGPAPCPTPCPGPTPCPCPAPT)-3') ; × 1 ;DNA (5'-D(APAPTPGPGPAP(5CM)PGPAPGPTPCPAPTPAPGPGPAP*G)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；0.05 M Citric acid 0.05 M Bis-Tris propane 16% PEG3350	Resolution 1.89 Å R-free 0.227

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 5T01	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A02 STRUCTURE OF THE DNA BINDING DOMAINS OF NFAT, FOS AND JUN BOUND TO DNA Deposited 1997-12-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain J 253–308（56 aa） Fragment：JUN	Mutation：C279S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；THE COMPLEX WAS CRYSTALLIZED IN 300-400 MM AMMONIUM ACETATE SALT, PH 7.5 (10 MM)., VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.303
1JNM Crystal Structure of the Jun/CRE Complex Deposited 2001-07-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 254–315（62 aa） Fragment：bZIP domain Chain B 254–315（62 aa） Fragment：bZIP domain	Mutation：C269S Mutation：C269S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 4000, Cacodylate, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.286
1JUN NMR STUDY OF C-JUN HOMODIMER Deposited 1995-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–44（43 aa） Fragment：LEUCINE ZIPPER DOMAIN, RESIDUES 272 - 315 Chain B 2–44（43 aa） Fragment：LEUCINE ZIPPER DOMAIN, RESIDUES 272 - 315	Mutation：INS(272-275), INS(315) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：INS(272-275), INS(315) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.6；310 K	Resolution not provided
1S9K Crystal Structure of Human NFAT1 and Fos-Jun on the IL-2 ARRE1 Site Deposited 2004-02-04	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain E 257–308（52 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；300-400 mM Ammonium Acetate Salt, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.10 Å R-free 0.275
1T2K Structure Of The DNA Binding Domains Of IRF3, ATF-2 and Jun Bound To DNA Deposited 2004-04-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 254–314（61 aa） Fragment：bZip domain	Mutation：C269S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；100 mM NaCacodylate, pH 6.5, 12.5% (w/v) PEG 6000, 400 mM NH4OAc, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.00 Å R-free 0.296

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	JUN_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 3–64； UniProt 254–315 Author chain B； PDBConstruct 3–64； UniProt 254–315

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	5t01
Deposition date deposition_date	2016-08-15
Structure title title	Human c-Jun DNA binding domain homodimer in complex with methylated DNA
Keywords keywords	;Zta, Zebra, BZLF-1, AP-1, Epstein-Barr virus, EBV, 5-methylcytosine, 5mC, DNA methylation, transcription factor, basic leucine-zipper, bZIP, TRANSCRIPTION REGULATOR-DNA complex ;; TRANSCRIPTION REGULATOR/DNA
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	26.24 Å
Radius of gyration Rg (electron density) rg_electron	27.66 Å
Forward intensity I(0) i0	19778200.00
Molecular weight molecular_weight	25993.0 kDa
Excluded volume excluded_volume	29213 Å³
Envelope volume envelope_volume	43648 Å³
Hydration-shell volume shell_volume	15772 Å³
Envelope diameter envelope_diameter	96.8 Å
Shell Rg shell_rg	29.09 Å
Envelope Rg envelope_rg	28.33 Å
Shape Rg shape_rg	27.62 Å
Total Rg total_rg	27.89 Å
Total atoms total_atoms	1769
Residues n_residues	160
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	94.5 Å
Rg (real space) rg_real	26.78 Å
Rg uncertainty (real space) rg_real_error	1.14 Å
I(0) (real space) i0_real	1.9780e+07
I(0) uncertainty (real space) i0_real_error	3.4900e+05
Rg (reciprocal space) rg_reciprocal	26.61 Å
I(0) (reciprocal space) i0_reciprocal	19780000.0000
Solution quality estimate total_estimate	0.7222
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.682
Kurtosis Kurtosis kurtosis	-0.251
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1347000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.472; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.145; Smooth: 0.824

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(PCPTPCPCPTPAPTPGPAPCPTPCPGPTPCPCPAPT)-3') ;
Molecular weight formula_weight	5706.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	1889

TCTCCTATGACTCGTCCAT

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APAPTPGPGPAP(5CM)PGPAPGPTPCPAPTPAPGPGPAP*G)-3') ;
Molecular weight formula_weight	5956.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

AATGGACGAGTCATAGGAG

Entity 3 Entity 3 polymer

Description description	Transcription factor AP-1
Molecular weight formula_weight	7591.0 kDa
Mutation mutation	C269S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

HMKAERKRMRNRIAASKSRKRKLERIARLEEKVKTLKAQNSELASTANMLREQVAQLKQKVMNH

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 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5t01A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	5t01B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

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8. Citations (1)

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Unit-cell length a length_a	158.871 Å
Unit-cell length b length_b	42.490 Å
Unit-cell length c length_c	45.167 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.890 Å
Low-resolution limit resolution_low	27.750 Å
R factor r_factor	0.1949
R_work r_work	0.1931
R_free r_free	0.2271

fit	/app/data/saxs_computation/t0/5t01/5t01.fit
pddf	/app/data/pr_computation/t0/5t01/5t01.pr.out
profile	/app/data/saxs_computation/t0/5t01/5t01.dat

Human c-Jun DNA binding domain homodimer in complex with methylated DNA

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

Transcription factor AP-1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)