SAXSdb — 5n9g

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

Transcription factor IIIB 50 kDa subunit

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	TATA-box-binding protein × 1 （P20226） ;Transcription factor TFIIIB component B'' homolog ; × 1 （A6H8Y1） DNA/RNA (27-MER) × 1 DNA/RNA (25-MER) × 1 water × 5	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 3 DNA 2	TATA-box-binding protein × 1 （P20226） ;Transcription factor TFIIIB component B'' homolog ; × 1 （A6H8Y1） DNA/RNA (27-MER) × 1 DNA/RNA (25-MER) × 1 SODIUM ION × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BRF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–377； UniProt 62–419 Author chain F； PDBConstruct 20–377； UniProt 62–419

TATA-box-binding protein

Homo sapiens

UniProt P20226

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	Transcription factor IIIB 50 kDa subunit × 1 （Q9HAW0） ;Transcription factor TFIIIB component B'' homolog ; × 1 （A6H8Y1） DNA/RNA (27-MER) × 1 DNA/RNA (25-MER) × 1 water × 5	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 3 DNA 2	Transcription factor IIIB 50 kDa subunit × 1 （Q9HAW0） ;Transcription factor TFIIIB component B'' homolog ; × 1 （A6H8Y1） DNA/RNA (27-MER) × 1 DNA/RNA (25-MER) × 1 SODIUM ION × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBP_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 20–200； UniProt 159–339 Author chain G； PDBConstruct 20–200； UniProt 159–339

;Transcription factor TFIIIB component B'' homolog ;

Homo sapiens

UniProt A6H8Y1

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	Transcription factor IIIB 50 kDa subunit × 1 （Q9HAW0） TATA-box-binding protein × 1 （P20226） DNA/RNA (27-MER) × 1 DNA/RNA (25-MER) × 1 water × 5	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 3 DNA 2	Transcription factor IIIB 50 kDa subunit × 1 （Q9HAW0） TATA-box-binding protein × 1 （P20226） DNA/RNA (27-MER) × 1 DNA/RNA (25-MER) × 1 SODIUM ION × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BDP1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 20–175； UniProt 241–396 Author chain H； PDBConstruct 20–175； UniProt 241–396

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	5n9g
Deposition date deposition_date	2017-02-24
Structure title title	TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1-
Keywords keywords	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.

5n9g__assembly_1__model_1

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

Download this curve (.dat)

5n9g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5n9g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.57 Å
Rg (electron density)	28.14 Å
Total Rg	28.81 Å
Atom count	5722
Residues	634
Excluded volume	99503 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5n9g__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5n9g__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	Transcription factor IIIB 50 kDa subunit
Molecular weight formula_weight	42195.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	11643

MAHHHHHHSSGLEVLFQGPNEQVSRSQQRGLRRVRDLCRVLQLPPTFEDTAVAYYQQAYRHSGIRAARLQKKEVLVGCCVLITCRQHNWPLTMGAICTLLYADLDVFSSTYMQIVKLLGLDVPSLCLAELVKTYCSSFKLFQASPSVPAKYVEDKEKMLSRTMQLVELANETWLVTGRHPLPVITAATFLAWQSLQPADRLSCSLARFCKLANVDLPYPASSRLQELLAVLLRMAEQLAWLRVLRLDKRSVVKHIGDLLQHRQSLVRSAFRDGTAEVETREKEPPGWGQGQGEGEVGNNSLGLPQGKRPASPALLLPPCMLKSPKRICPVPPVSTVTGDENISDSEIEQYLRTPQEVRDFQRAQAARQAATSVPNPP

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	TATA-box-binding protein
Molecular weight formula_weight	22589.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAHHHHHHSSGLEVLFQGPSGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRKTT

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	;Transcription factor TFIIIB component B'' homolog ;
Molecular weight formula_weight	20414.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAHHHHHHSSGLEVLFQGPGPLLVPRVKVAEDGSIILDEESLTVEVLRTKGPCVVEENDPIFERGSTTTYSSFRKNYYSKPWSNKETDMFFLAISMVGTDFSMIGQLFPHRARIEIKNKFKREEKTNGWRIDKAFQEKRPFDFDFFAHLLQKVLAEEEKRKQKSVKNHSLKEKKS

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	DNA/RNA (27-MER)
Molecular weight formula_weight	8363.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide/polyribonucleotide hybrid
Chain IDs strand_id	D,I

GGTCACACCTATTTTAAGCCCTTCAAC

Entity 5 Entity 5 polymer

Description description	DNA/RNA (25-MER)
Molecular weight formula_weight	8026.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide/polyribonucleotide hybrid
Chain IDs strand_id	E,J

TTGAAGGGCTTAAAATAGGTGTGAC

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	298

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5n9gA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	5n9gB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

Domain ID domain_id	5n9gB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

Domain ID domain_id	5n9gF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	5n9gG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

Domain ID domain_id	5n9gG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

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Unit-cell length a length_a	81.190 Å
Unit-cell length b length_b	124.080 Å
Unit-cell length c length_c	88.610 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.51 °
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	2.700 Å
Low-resolution limit resolution_low	49.040 Å
R factor r_factor	0.1960
R_work r_work	0.1940
R_free r_free	0.2340

TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1-

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

Transcription factor IIIB 50 kDa subunit

State in the Current Structure

Other States of the Same Protein in the Database

TATA-box-binding protein

State in the Current Structure

Other States of the Same Protein in the Database

;Transcription factor TFIIIB component B'' homolog ;

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

5n9g__assembly_1__model_1

5n9g__assembly_1__model_1 | I(q)

5n9g__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

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1-

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

Transcription factor IIIB 50 kDa subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TATA-box-binding 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

;Transcription factor TFIIIB component B'' homolog ;

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

5n9g__assembly_1__model_1

5n9g__assembly_1__model_1 | I(q)

5n9g__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

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)