1tf6

CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION

Method: X-RAY DIFFRACTION

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

PROTEIN (TRANSCRIPTION FACTOR IIIA)

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(APCPGPGPGPCPCPTPGPGPTPTPAPGPTPAPC PCPTPGPGPAP* TPGPGPGPAPGPAPCPC)-3') ; × 1 ;DNA (5'-D(TPGPGPTPCPTPCPCPCPAPTPCPCPAPGPGPT PAPCPTPAPAP* CPCPAPGPGPCPCPCPG)-3') ; × 1 ZINC ION × 6	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	;DNA (5'-D(APCPGPGPGPCPCPTPGPGPTPTPAPGPTPAPC PCPTPGPGPAP* TPGPGPGPAPGPAPCPC)-3') ; × 1 ;DNA (5'-D(TPGPGPTPCPTPCPCPCPAPTPCPCPAPGPGPT PAPCPTPAPAP* CPCPAPGPGPCPCPCPG)-3') ; × 1 ZINC ION × 6	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TF3A_XENLA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–190； UniProt 23–212 Author chain D； PDBConstruct 1–190； UniProt 23–212

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	1tf6
Deposition date deposition_date	1998-03-02
Structure title title	CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION
Keywords keywords	;COMPLEX (TRANSCRIPTION REGULATION-DNA), RNA POLYMERASE III, TRANSCRIPTION INITIATION, ZINC FINGER PROTEIN, TRANSCRIPTION-DNA COMPLEX ;; 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.

1tf6__assembly_1__model_1

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

Download this curve (.dat)

1tf6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tf6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.61 Å
Rg (electron density)	31.23 Å
Total Rg	31.40 Å
Atom count	2737
Residues	241
Excluded volume	44391 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tf6__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1tf6__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(APCPGPGPGPCPCPTPGPGPTPTPAPGPTPAPC PCPTPGPGPAP* TPGPGPGPAPGPAPCPC)-3') ;
Molecular weight formula_weight	9634.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,E
Atom count atom_count	5495

ACGGGCCTGGTTAGTACCTGGATGGGAGACC

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPGPGPTPCPTPCPCPCPAPTPCPCPAPGPGPT PAPCPTPAPAP* CPCPAPGPGPCPCPCPG)-3') ;
Molecular weight formula_weight	9434.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,F

TGGTCTCCCATCCAGGTACTAACCAGGCCCG

Entity 3 Entity 3 polymer

Description description	PROTEIN (TRANSCRIPTION FACTOR IIIA)
Molecular weight formula_weight	22126.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGEKALPVVYKRYICSFADCGAAYNKNWKLQAHLCKHTGEKPFPCKEEGCEKGFTSLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKANMKKHFNRFHNIKICVYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1tf6a1
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1tf6a2
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1tf6a3
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1tf6a4
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1tf6a5
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1tf6a6
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1tf6d1
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1tf6d2
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1tf6d3
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1tf6d4
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1tf6d5
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

Domain ID domain_id	d1tf6d6
Class class	g — Small proteins
Fold Fold fold	g.37 — beta-beta-alpha zinc fingers
Superfamily Superfamily superfamily	g.37.1 — beta-beta-alpha zinc fingers
Family Family family	g.37.1.1 — Classic zinc finger, C2H2

CATH v4.4 (12 domains)

Domain ID domain_id	1tf6A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1tf6A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1tf6A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1tf6A04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1tf6A05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1tf6A06
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1tf6D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1tf6D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1tf6D03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1tf6D04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1tf6D05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

Domain ID domain_id	1tf6D06
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	60 — Classic Zinc Finger

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Unit-cell length a length_a	64.180 Å
Unit-cell length b length_b	64.712 Å
Unit-cell length c length_c	78.035 Å
Unit-cell angle α angle_alpha	90.07 °
Unit-cell angle β angle_beta	92.98 °
Unit-cell angle γ angle_gamma	102.95 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.3080
R_work r_work	0.3080
R_free r_free	0.3630

CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION

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

PROTEIN (TRANSCRIPTION FACTOR IIIA)

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

1tf6__assembly_1__model_1

1tf6__assembly_1__model_1 | I(q)

1tf6__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION

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

PROTEIN (TRANSCRIPTION FACTOR IIIA)

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

1tf6__assembly_1__model_1

1tf6__assembly_1__model_1 | I(q)

1tf6__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)