SAXSdb — 5tuv

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

Transcription factor DP1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Transcription factor E2F5 × 1 （Q15329） Retinoblastoma-like protein 1 × 1 （P28749）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Transcription factor E2F5 × 1 （Q15329） Retinoblastoma-like protein 1 × 1 （P28749）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Transcription factor E2F5 × 2 （Q15329） Retinoblastoma-like protein 1 × 2 （P28749）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TFDP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–155； UniProt 199–350 Author chain D； PDBConstruct 4–155； UniProt 199–350

Transcription factor E2F5

Homo sapiens

UniProt Q15329

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Transcription factor DP1 × 1 （Q14186） Retinoblastoma-like protein 1 × 1 （P28749）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Transcription factor DP1 × 1 （Q14186） Retinoblastoma-like protein 1 × 1 （P28749）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Transcription factor DP1 × 2 （Q14186） Retinoblastoma-like protein 1 × 2 （P28749）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E2F5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–112； UniProt 124–232 Author chain E； PDBConstruct 4–112； UniProt 124–232

Retinoblastoma-like protein 1

Homo sapiens

UniProt P28749

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Transcription factor DP1 × 1 （Q14186） Transcription factor E2F5 × 1 （Q15329）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Transcription factor DP1 × 1 （Q14186） Transcription factor E2F5 × 1 （Q15329）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Transcription factor DP1 × 2 （Q14186） Transcription factor E2F5 × 2 （Q15329）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBL1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–41； UniProt 994–1031 Author chain F； PDBConstruct 4–41； UniProt 994–1031

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	5tuv
Deposition date deposition_date	2016-11-07
Structure title title	Crystal structure of the E2F5-DP1-p107 ternary complex
Keywords keywords	Transcription factor, cell-cycle regulation, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5tuv__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5tuv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5tuv__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	22.98 Å
Rg (electron density)	22.30 Å
Total Rg	23.02 Å
Atom count	1863
Residues	240
Excluded volume	33003 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5tuv__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5tuv__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5tuv__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Transcription factor DP1
Molecular weight formula_weight	17603.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	3532

GEFAQECQNLEVERQRRLERIKQKQSQLQELILQQIAFKNLVQRNRHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSISNDKFEYLFNFDNTFEIHDDIEVLKRMGMACGLESGSCSAEDLKMARSLVPKALEPYVTEMAQGTVGGVFITTA

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Transcription factor E2F5
Molecular weight formula_weight	12962.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GHMKEVIDRLRYLKAEIEDLELKERELDQQKLWLQQSIKNVMDDSINNRFSYVTHEDICNCFNGDTLLAIQAPSGTQLEVPIPEMGQNGQKKYQINLKSHSGPIHVLLINKE

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Retinoblastoma-like protein 1
Molecular weight formula_weight	4663.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GEFSGLTPRSALLYKFNGSPSKSLKDINNMIRQGEQRTKKR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5tuvb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.63 — E2F-DP heterodimerization region
Superfamily Superfamily superfamily	e.63.1 — E2F-DP heterodimerization region
Family Family family	e.63.1.0 — automated matches

Domain ID domain_id	d5tuve_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.63 — E2F-DP heterodimerization region
Superfamily Superfamily superfamily	e.63.1 — E2F-DP heterodimerization region
Family Family family	e.63.1.0 — automated matches

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Unit-cell length a length_a	60.980 Å
Unit-cell length b length_b	57.340 Å
Unit-cell length c length_c	99.198 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.64 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	49.266 Å
R factor r_factor	0.2147
R_work r_work	0.2122
R_free r_free	0.2601

Crystal structure of the E2F5-DP1-p107 ternary complex

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

Transcription factor DP1

State in the Current Structure

Other States of the Same Protein in the Database

Transcription factor E2F5

State in the Current Structure

Other States of the Same Protein in the Database

Retinoblastoma-like protein 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5tuv__assembly_1__model_1

5tuv__assembly_1__model_1 | I(q)

5tuv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Crystal structure of the E2F5-DP1-p107 ternary complex

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

Transcription factor DP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcription factor E2F5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Retinoblastoma-like protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5tuv__assembly_1__model_1

5tuv__assembly_1__model_1 | I(q)

5tuv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)