SAXSdb — 1h9d

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

CORE-BINDING FACTOR ALPHA SUBUNIT1

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 2	CORE-BINDING FACTOR CBF-BETA × 1 （Q13951） ;DNA (5'-(GPTPTPGPCPGPGPTPTPG)-3') ; × 1 ;DNA (5'-(CPAPAPCPCPGPCPAPAPC)-3') ; × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 2 DNA 2	CORE-BINDING FACTOR CBF-BETA × 1 （Q13951） ;DNA (5'-(GPTPTPGPCPGPGPTPTPG)-3') ; × 1 ;DNA (5'-(CPAPAPCPCPGPCPAPAPC)-3') ; × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AML1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–134； UniProt 50–183 Author chain C； PDBConstruct 1–134； UniProt 50–183

CORE-BINDING FACTOR CBF-BETA

HOMO SAPIENS

UniProt Q13951

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 2	CORE-BINDING FACTOR ALPHA SUBUNIT1 × 1 （Q01196） ;DNA (5'-(GPTPTPGPCPGPGPTPTPG)-3') ; × 1 ;DNA (5'-(CPAPAPCPCPGPCPAPAPC)-3') ; × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 2 DNA 2	CORE-BINDING FACTOR ALPHA SUBUNIT1 × 1 （Q01196） ;DNA (5'-(GPTPTPGPCPGPGPTPTPG)-3') ; × 1 ;DNA (5'-(CPAPAPCPCPGPCPAPAPC)-3') ; × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEBB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–134； UniProt 2–135 Author chain D； PDBConstruct 1–134； UniProt 2–135

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	1h9d
Deposition date deposition_date	2001-03-07
Structure title title	Aml1/cbf-beta/dna complex
Keywords keywords	TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR
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.

1h9d__assembly_1__model_1

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

Download this curve (.dat)

1h9d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1h9d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.80 Å
Rg (electron density)	21.24 Å
Total Rg	22.11 Å
Atom count	2395
Residues	270
Excluded volume	41002 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1h9d__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1h9d__assembly_2__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	CORE-BINDING FACTOR ALPHA SUBUNIT1
Molecular weight formula_weight	14909.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4867

SMVEVLADHPGELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRNATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRRHRQKL

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	CORE-BINDING FACTOR CBF-BETA
Molecular weight formula_weight	15815.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

PRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVATGTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLDGMGCLEFDEERAQQE

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	;DNA (5'-(GPTPTPGPCPGPGPTPTPG)-3') ;
Molecular weight formula_weight	3107.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G

GTTGCGGTTG

Entity 4 Entity 4 polymer

Description description	;DNA (5'-(CPAPAPCPCPGPCPAPAPC)-3') ;
Molecular weight formula_weight	2983.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,H

CAACCGCAAC

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	56

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1h9da_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.5 — p53-like transcription factors
Family Family family	b.2.5.6 — RUNT domain

Domain ID domain_id	d1h9db_
Class class	b — All beta proteins
Fold Fold fold	b.54 — Core binding factor beta, CBF
Superfamily Superfamily superfamily	b.54.1 — Core binding factor beta, CBF
Family Family family	b.54.1.1 — Core binding factor beta, CBF

Domain ID domain_id	d1h9dc_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.5 — p53-like transcription factors
Family Family family	b.2.5.6 — RUNT domain

Domain ID domain_id	d1h9dd_
Class class	b — All beta proteins
Fold Fold fold	b.54 — Core binding factor beta, CBF
Superfamily Superfamily superfamily	b.54.1 — Core binding factor beta, CBF
Family Family family	b.54.1.1 — Core binding factor beta, CBF

CATH v4.4 (4 domains)

Domain ID domain_id	1h9dA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	720 —

Domain ID domain_id	1h9dB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	250 — Polyomavirus Enhancer Binding Protein 2; Chain: A;
Homologous superfamily homologous superfamily	10 — Core binding factor, beta subunit

Domain ID domain_id	1h9dC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	720 —

Domain ID domain_id	1h9dD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	250 — Polyomavirus Enhancer Binding Protein 2; Chain: A;
Homologous superfamily homologous superfamily	10 — Core binding factor, beta subunit

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Unit-cell length a length_a	115.033 Å
Unit-cell length b length_b	115.033 Å
Unit-cell length c length_c	133.925 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	48.020 Å
R factor r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2710

Aml1/cbf-beta/dna complex

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

CORE-BINDING FACTOR ALPHA SUBUNIT1

State in the Current Structure

Other States of the Same Protein in the Database

CORE-BINDING FACTOR CBF-BETA

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

1h9d__assembly_1__model_1

1h9d__assembly_1__model_1 | I(q)

1h9d__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 (5)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Aml1/cbf-beta/dna complex

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

CORE-BINDING FACTOR ALPHA SUBUNIT1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CORE-BINDING FACTOR CBF-BETA

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

1h9d__assembly_1__model_1

1h9d__assembly_1__model_1 | I(q)

1h9d__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 (5)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)