8qu2

NF-YB/C Heterodimer in Complex with a 16-mer NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker

Method: X-RAY DIFFRACTION

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

Nuclear transcription factor Y subunit alpha

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Nuclear transcription factor Y subunit beta × 1 （P25208） Nuclear transcription factor Y subunit gamma × 1 （Q13952） 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 FORMIC ACID × 2 1,2-ETHANEDIOL × 2 water × 3	Consistent with protein count

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 2–17； UniProt 270–285

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 heterocomplex	Heteromer	Protein 3	Nuclear transcription factor Y subunit alpha × 1 （P23511） Nuclear transcription factor Y subunit gamma × 1 （Q13952） 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 FORMIC ACID × 2 1,2-ETHANEDIOL × 2 water × 3	Consistent with protein count

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 3–95； 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 heterocomplex	Heteromer	Protein 3	Nuclear transcription factor Y subunit alpha × 1 （P23511） Nuclear transcription factor Y subunit beta × 1 （P25208） 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 FORMIC ACID × 2 1,2-ETHANEDIOL × 2 water × 3	Consistent with protein count

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 3–96； 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	8qu2
Deposition date deposition_date	2023-10-13
Structure title title	NF-YB/C Heterodimer in Complex with a 16-mer NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker
Keywords keywords	Peptidometic inhibitor, 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.

8qu2__assembly_1__model_1

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

Download this curve (.dat)

8qu2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8qu2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.87 Å
Rg (electron density)	16.52 Å
Total Rg	17.68 Å
Atom count	1504
Residues	180
Excluded volume	27246 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8qu2__assembly_1__model_1`	trimeric （3）	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 (7)

Entity 1 Entity 1 polymer

Description description	Nuclear transcription factor Y subunit alpha
Molecular weight formula_weight	2061.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1765

XKQLHRILKRRQARAKLX

Entity 2 Entity 2 polymer

Description description	Nuclear transcription factor Y subunit beta
Molecular weight formula_weight	10876.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPSFREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQKFRE

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	Nuclear transcription factor Y subunit gamma
Molecular weight formula_weight	11258.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GPMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPR

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 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	139

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Unit-cell length a length_a	45.080 Å
Unit-cell length b length_b	51.460 Å
Unit-cell length c length_c	72.550 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	orthorhombic

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	19.860 Å
R factor r_factor	0.1420
R_work r_work	0.1404
R_free r_free	0.1719

NF-YB/C Heterodimer in Complex with a 16-mer NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker

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

8qu2__assembly_1__model_1

8qu2__assembly_1__model_1 | I(q)

8qu2__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (3)

NF-YB/C Heterodimer in Complex with a 16-mer NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker

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

8qu2__assembly_1__model_1

8qu2__assembly_1__model_1 | I(q)

8qu2__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (3)