SAXSdb — 4awl

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

NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 3 DNA 2	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA × 1 （P25208） NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA × 1 （Q13952） HSP70 PROMOTER FRAGMENT × 1 HSP70 PROMOTER FRAGMENT × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NFYA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–72； UniProt 233–303

NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA

HOMO SAPIENS

UniProt P25208

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 3 DNA 2	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA × 1 （P23511） NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA × 1 （Q13952） HSP70 PROMOTER FRAGMENT × 1 HSP70 PROMOTER FRAGMENT × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NFYB_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–94； UniProt 51–143

NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA

HOMO SAPIENS

UniProt Q13952

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 3 DNA 2	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA × 1 （P23511） NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA × 1 （P25208） HSP70 PROMOTER FRAGMENT × 1 HSP70 PROMOTER FRAGMENT × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NFYC_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–94； UniProt 27–120

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	4awl
Deposition date deposition_date	2012-06-04
Structure title title	The NF-Y transcription factor is structurally and functionally a sequence specific histone
Keywords keywords	TRANSCRIPTION-DNA COMPLEX, NF-Y, DNA-BINDING; TRANSCRIPTION/DNA
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.

4awl__assembly_1__model_1

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

Download this curve (.dat)

4awl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4awl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.74 Å
Rg (electron density)	22.35 Å
Total Rg	23.18 Å
Atom count	2947
Residues	284
Excluded volume	49466 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4awl__assembly_1__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA
Molecular weight formula_weight	9329.8 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	2949

MEEPLYVNAKQYHRILKRRQARAKLEAEGKIPKERRKYLHESRHRHAMARKRGEGGRFFSPKEKDSPHMQDPGSLVPR

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	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA
Molecular weight formula_weight	10853.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSFREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQKFRE

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	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA
Molecular weight formula_weight	11104.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPR

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 polymer

Description description	HSP70 PROMOTER FRAGMENT
Molecular weight formula_weight	7618.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TTCTGAGCCAATCACCGAGCTCGAT

Entity 5 Entity 5 polymer

Description description	HSP70 PROMOTER FRAGMENT
Molecular weight formula_weight	7739.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

ATCGAGCTCGGTGATTGGCTCAGAA

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4awlA00
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	2430 —

Domain ID domain_id	4awlB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	4awlC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

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Unit-cell length a length_a	54.700 Å
Unit-cell length b length_b	62.560 Å
Unit-cell length c length_c	139.680 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.080 Å
Low-resolution limit resolution_low	35.460 Å
R factor r_factor	0.1942
R_work r_work	0.1913
R_free r_free	0.2497

The NF-Y transcription factor is structurally and functionally a sequence specific histone

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

NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA

State in the Current Structure

Other States of the Same Protein in the Database

NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA

State in the Current Structure

Other States of the Same Protein in the Database

NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA

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

4awl__assembly_1__model_1

4awl__assembly_1__model_1 | I(q)

4awl__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 (6)

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 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

The NF-Y transcription factor is structurally and functionally a sequence specific histone

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

NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT 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

NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA

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

4awl__assembly_1__model_1

4awl__assembly_1__model_1 | I(q)

4awl__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 (6)

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 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)