SAXSdb — 1k6o

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

ETS-domain protein ELK-4

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 Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 1–93	Fragment：1-93	5'-D(CPAPCPAPGPGPAPTPGPTPCPCPAPTPAPTPTPAPGPGPAPCPA)-3' × 1 5'-D(TPGPTPCPCPTPAPAPTPAPTPGPGPAPCPAPTPCPCPTPGPTPG)-3' × 1 Serum response factor × 2 （P11831）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP	Resolution 3.19 Å R-free 0.276

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 1K6O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BC7 SERUM RESPONSE FACTOR ACCESSORY PROTEIN 1A (SAP-1)/DNA COMPLEX Deposited 1998-05-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–93（93 aa） Fragment：ETS DOMAIN, RESIDUES 1-93	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；pH 5.8	Resolution 2.01 Å R-free 0.286
1BC8 STRUCTURES OF SAP-1 BOUND TO DNA SEQUENCES FROM THE E74 AND C-FOS PROMOTERS PROVIDE INSIGHTS INTO HOW ETS PROTEINS DISCRIMINATE BETWEEN RELATED DNA TARGETS Deposited 1998-05-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain C 1–93（93 aa） Fragment：ETS DOMAIN, RESIDUES 1-93	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；50 MM NA CACODYLATE (PH 6.0), 5.0% PEG8000, 20 MM ZINC ACETATE	Resolution 1.93 Å R-free 0.277
1HBX Ternary Complex of SAP-1 and SRF with specific SRE DNA Deposited 2001-04-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 2–156（155 aa） Fragment：RESIDUES 2-156	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 1500, NH4NO3, BIS-TRIS BUFFER, DTT, pH 6.50	Resolution 3.15 Å R-free 0.285
1HBX Ternary Complex of SAP-1 and SRF with specific SRE DNA Deposited 2001-04-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain H 2–156（155 aa） Fragment：RESIDUES 2-156	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 1500, NH4NO3, BIS-TRIS BUFFER, DTT, pH 6.50	Resolution 3.15 Å R-free 0.285

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

View Construct and Data Evidence

UniProt name	ELK4_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–93； UniProt 1–93

Serum response factor

Homo sapiens

UniProt P11831

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 Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain B； UniProt 133–235 Chain C； UniProt 133–235	Fragment：133-235	5'-D(CPAPCPAPGPGPAPTPGPTPCPCPAPTPAPTPTPAPGPGPAPCPA)-3' × 1 5'-D(TPGPTPCPCPTPAPAPTPAPTPGPGPAPCPAPTPCPCPTPGPTPG)-3' × 1 ETS-domain protein ELK-4 × 1 （P28324）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP	Resolution 3.19 Å R-free 0.276

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 1K6O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HBX Ternary Complex of SAP-1 and SRF with specific SRE DNA Deposited 2001-04-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 132–223（92 aa） Fragment：CORE RESIDUES 132-223 Chain B 132–223（92 aa） Fragment：CORE RESIDUES 132-223	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 1500, NH4NO3, BIS-TRIS BUFFER, DTT, pH 6.50	Resolution 3.15 Å R-free 0.285
1HBX Ternary Complex of SAP-1 and SRF with specific SRE DNA Deposited 2001-04-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain D 132–223（92 aa） Fragment：CORE RESIDUES 132-223 Chain E 132–223（92 aa） Fragment：CORE RESIDUES 132-223	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 1500, NH4NO3, BIS-TRIS BUFFER, DTT, pH 6.50	Resolution 3.15 Å R-free 0.285
1SRS SERUM RESPONSE FACTOR (SRF) CORE COMPLEXED WITH SPECIFIC SRE DNA Deposited 1995-07-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 87–178（92 aa） Chain B 87–178（92 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K	Resolution 3.20 Å

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SRF_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–103； UniProt 133–235 Author chain C； PDBConstruct 1–103； UniProt 133–235

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	1k6o
Deposition date deposition_date	2001-10-16
Structure title title	Crystal Structure of a Ternary SAP-1/SRF/c-fos SRE DNA Complex
Keywords keywords	;PROTEIN-DNA COMPLEX, TRANSCRIPTION FACTOR, COMBINATORIAL GENE REGULATION, ETS PROTEINS, MADS-BOX PROTEINS, TRANSCRIPTION-DNA COMPLEX ;; TRANSCRIPTION/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	24.55 Å
Radius of gyration Rg (electron density) rg_electron	24.32 Å
Forward intensity I(0) i0	42879100.00
Molecular weight molecular_weight	42863.0 kDa
Excluded volume excluded_volume	50316 Å³
Envelope volume envelope_volume	63995 Å³
Hydration-shell volume shell_volume	22938 Å³
Envelope diameter envelope_diameter	82.2 Å
Shell Rg shell_rg	30.39 Å
Envelope Rg envelope_rg	24.37 Å
Shape Rg shape_rg	24.32 Å
Total Rg total_rg	24.93 Å
Total atoms total_atoms	2957
Residues n_residues	304
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	79.8 Å
Rg (real space) rg_real	24.64 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	4.2880e+07
I(0) uncertainty (real space) i0_real_error	6.1960e+05
Rg (reciprocal space) rg_reciprocal	24.62 Å
I(0) (reciprocal space) i0_reciprocal	42880000.0000
Solution quality estimate total_estimate	0.8894
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.409
Kurtosis Kurtosis kurtosis	-0.368
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5764000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.920; Smooth: 0.920

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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	5'-D(CPAPCPAPGPGPAPTPGPTPCPCPAPTPAPTPTPAPGPGPAPCP*A)-3'
Molecular weight formula_weight	7073.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	2957

CACAGGATGTCCATATTAGGACA

Entity 2 Entity 2 polymer

Description description	5'-D(TPGPTPCPCPTPAPAPTPAPTPGPGPAPCPAPTPCPCPTPGPTP*G)-3'
Molecular weight formula_weight	7046.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

TGTCCTAATATGGACATCCTGTG

Entity 3 Entity 3 polymer

Description description	ETS-domain protein ELK-4
Molecular weight formula_weight	11219.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MDSAITLWQFLLQLLQKPQNKHMICWTSNDGQFKLLQAEEVARLWGIRKNKPNMNYDKLSRALRYYYVKNIIKKVNGQKFVYKFVSYPEILNM

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 polymer

Description description	Serum response factor
Molecular weight formula_weight	11553.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GAKPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASETGHVYTFATRKLQPMITSETGKALIQTCLNSPDSPPRSDPTTDQR

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

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1k6oa_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.21 — ets domain

Domain ID domain_id	d1k6ob_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.88 — SRF-like
Superfamily Superfamily superfamily	d.88.1 — SRF-like
Family Family family	d.88.1.1 — SRF-like

Domain ID domain_id	d1k6oc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.88 — SRF-like
Superfamily Superfamily superfamily	d.88.1 — SRF-like
Family Family family	d.88.1.1 — SRF-like

CATH v4.4 (3 domains)

Domain ID domain_id	1k6oA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	1k6oB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1810 — SRF-like
Homologous superfamily homologous superfamily	10 — Transcription factor, MADS-box

Domain ID domain_id	1k6oC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1810 — SRF-like
Homologous superfamily homologous superfamily	10 — Transcription factor, MADS-box

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8. Citations (1)

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Unit-cell length a length_a	161.784 Å
Unit-cell length b length_b	161.784 Å
Unit-cell length c length_c	41.224 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 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.190 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2700
R_work r_work	0.2204
R_free r_free	0.2757

fit	/app/data/saxs_computation/k6/1k6o/1k6o.fit
pddf	/app/data/pr_computation/k6/1k6o/1k6o.pr.out
profile	/app/data/saxs_computation/k6/1k6o/1k6o.dat

Crystal Structure of a Ternary SAP-1/SRF/c-fos SRE DNA Complex

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

ETS-domain protein ELK-4

State in the Current Structure

Other States of the Same Protein in the Database

Serum response factor

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 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)