SAXSdb — 2aze

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

Transcription factor Dp-1

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 E2F1 × 1 （Q01094） Retinoblastoma-associated protein × 1 （P06400） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Transcription factor E2F1 × 2 （Q01094） Retinoblastoma-associated protein × 2 （P06400） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TDP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–155； UniProt 199–350

Transcription factor E2F1

Homo sapiens

UniProt Q01094

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 Dp-1 × 1 （Q14186） Retinoblastoma-associated protein × 1 （P06400） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Transcription factor Dp-1 × 2 （Q14186） Retinoblastoma-associated protein × 2 （P06400） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E2F1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–106； UniProt 200–301

Retinoblastoma-associated protein

Homo sapiens

UniProt P06400

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 Dp-1 × 1 （Q14186） Transcription factor E2F1 × 1 （Q01094） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Transcription factor Dp-1 × 2 （Q14186） Transcription factor E2F1 × 2 （Q01094） water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RB_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–46； UniProt 829–874

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	2aze
Deposition date deposition_date	2005-09-10
Structure title title	Structure of the Rb C-terminal domain bound to an E2F1-DP1 heterodimer
Keywords keywords	coiled coil, beta sandwich, CELL CYCLE, TRANSCRIPTION; CELL CYCLE, 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.

2aze__assembly_1__model_1

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

Download this curve (.dat)

2aze__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2aze__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.90 Å
Rg (electron density)	23.00 Å
Total Rg	23.72 Å
Atom count	2325
Residues	294
Excluded volume	41267 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2aze__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2aze__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Transcription factor Dp-1
Molecular weight formula_weight	17603.1 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	2456

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

Entity 2 Entity 2 polymer

Description description	Transcription factor E2F1
Molecular weight formula_weight	11898.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSHMGGRLEGLTQDLRQLQESEQQLDHLMNICTTQLRLLSEDTDSQRLAYVTCQDLRSIADPAEQMVMVIKAPPETQLQAVDSSENFQISLKSKQGPIDVFLCPEE

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

Entity 3 Entity 3 polymer

Description description	Retinoblastoma-associated protein
Molecular weight formula_weight	5114.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SRILVSIGESFGTSEKFQKINQMVCNSDRVLKRSAEGSNPPKPLKK

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	131

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2azea1
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.63.1.1 — DP dimerization segment

Domain ID domain_id	d2azea2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2azeb1
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.63.1.2 — E2F dimerization segment

Domain ID domain_id	d2azec1
Class class	j — Peptides
Fold Fold fold	j.119 — Retinoblastoma-associated protein RB1 fragments
Superfamily Superfamily superfamily	j.119.1 — Retinoblastoma-associated protein RB1 fragments
Family Family family	j.119.1.1 — Retinoblastoma-associated protein RB1 fragments

CATH v4.4 (3 domains)

Domain ID domain_id	2azeA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily	80 — Transcription factor DP

Domain ID domain_id	2azeB00
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	540 —

Domain ID domain_id	2azeC00
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	530 —

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Unit-cell length a length_a	146.800 Å
Unit-cell length b length_b	168.600 Å
Unit-cell length c length_c	48.300 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.2210
R_free r_free	0.2620

Structure of the Rb C-terminal domain bound to an E2F1-DP1 heterodimer

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

Transcription factor Dp-1

State in the Current Structure

Other States of the Same Protein in the Database

Transcription factor E2F1

State in the Current Structure

Other States of the Same Protein in the Database

Retinoblastoma-associated protein

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

2aze__assembly_1__model_1

2aze__assembly_1__model_1 | I(q)

2aze__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structure of the Rb C-terminal domain bound to an E2F1-DP1 heterodimer

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

Transcription factor Dp-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

Transcription factor E2F1

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-associated protein

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

2aze__assembly_1__model_1

2aze__assembly_1__model_1 | I(q)

2aze__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)