2rf4

Crystal structure of the RNA Polymerase I subcomplex A14/43

Method: X-RAY DIFFRACTION

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

DNA-directed RNA polymerase I subunit RPA4

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase I subunit RPA4 × 1 （P50106）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase I subunit RPA4 × 1 （P50106）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase I subunit RPA4 × 1 （P50106）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPA43_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–172； UniProt 2–172 Author chain A； PDBConstruct 173–214； UniProt 210–251 Author chain C； PDBConstruct 2–172； UniProt 2–172 Author chain C； PDBConstruct 173–214； UniProt 210–251 Author chain E； PDBConstruct 2–172； UniProt 2–172 Author chain E； PDBConstruct 173–214； UniProt 210–251

DNA-directed RNA polymerase I subunit RPA4

Saccharomyces cerevisiae

UniProt P50106

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase I subunit RPA4 × 1 （P46669）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase I subunit RPA4 × 1 （P46669）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase I subunit RPA4 × 1 （P46669）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPA14_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–52； UniProt 1–52 Author chain B； PDBConstruct 53–87； UniProt 78–112 Author chain D； PDBConstruct 1–52； UniProt 1–52 Author chain D； PDBConstruct 53–87； UniProt 78–112 Author chain F； PDBConstruct 1–52； UniProt 1–52 Author chain F； PDBConstruct 53–87； UniProt 78–112

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	2rf4
Deposition date deposition_date	2007-09-28
Structure title title	Crystal structure of the RNA Polymerase I subcomplex A14/43
Keywords keywords	;Transferase DNA/RNA, DNA-binding, Phosphorylation, RNA Polymerase I, Pol I, PolI, RPolI, Nuclear Protein, Nucleolar Protein, Transcription, Transferase, DDRP, Rpb4/7, Ribosome biogenesis, DNA-directed RNA polymerase, Nucleus ;; TRANSFERASE
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.

2rf4__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2rf4__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rf4__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.90 Å
Rg (electron density)	20.08 Å
Total Rg	20.87 Å
Atom count	1826
Residues	229
Excluded volume	32662 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rf4__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2rf4__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2rf4__assembly_3__model_1`	dimeric （2）	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 (2)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase I subunit RPA4
Molecular weight formula_weight	24223.1 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	5530

MSQVKRANENRETARFIKKHKKQVTNPIDEKNGTSNCIVRVPIALYVSLAPMYLENPLQGVMKQHLNPLVMKYNNKVGGVVLGYEGLKILDADPLSKEDTSEKLIKITPDTPFGFTWCHVNLYVWQPQVGDVLEGYIFIQSASHIGLLIHDAFNASIKKNNIPVDWTFVHNDGNRSLGHWVDSNGEPIDGKLRFTVRNVHTTGRVVSVDGTLIS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase I subunit RPA4
Molecular weight formula_weight	9675.9 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MMKGSRRTGNNTATTLNTPVVIHATQLPQHVSTDEVLQFLESFIDEKENIIDIDTNLSSSISQLKRIQRDFKGLPPAQDFSAAPIQV

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2rf4a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
Family Family family	d.230.1.2 — RNA polymerase I subunit A43, N-terminal domain

Domain ID domain_id	d2rf4a2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d2rf4b_
Class class	g — Small proteins
Fold Fold fold	g.98 — RNA polymerase I subunit A14-like
Superfamily Superfamily superfamily	g.98.1 — RNA polymerase I subunit A14-like
Family Family family	g.98.1.1 — RNA polymerase I subunit A14

Domain ID domain_id	d2rf4c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
Family Family family	d.230.1.2 — RNA polymerase I subunit A43, N-terminal domain

Domain ID domain_id	d2rf4c2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d2rf4d_
Class class	g — Small proteins
Fold Fold fold	g.98 — RNA polymerase I subunit A14-like
Superfamily Superfamily superfamily	g.98.1 — RNA polymerase I subunit A14-like
Family Family family	g.98.1.1 — RNA polymerase I subunit A14

Domain ID domain_id	d2rf4e1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
Family Family family	d.230.1.2 — RNA polymerase I subunit A43, N-terminal domain

Domain ID domain_id	d2rf4e2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d2rf4f_
Class class	g — Small proteins
Fold Fold fold	g.98 — RNA polymerase I subunit A14-like
Superfamily Superfamily superfamily	g.98.1 — RNA polymerase I subunit A14-like
Family Family family	g.98.1.1 — RNA polymerase I subunit A14

CATH v4.4 (9 domains)

Domain ID domain_id	2rf4A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

Domain ID domain_id	2rf4A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2rf4B01
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	3390 —

Domain ID domain_id	2rf4C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

Domain ID domain_id	2rf4C02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2rf4D01
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	3390 —

Domain ID domain_id	2rf4E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

Domain ID domain_id	2rf4E02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2rf4F01
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	3390 —

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Unit-cell length a length_a	229.857 Å
Unit-cell length b length_b	63.942 Å
Unit-cell length c length_c	65.395 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	12

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2524
R_free r_free	0.2854

Crystal structure of the RNA Polymerase I subcomplex A14/43

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

DNA-directed RNA polymerase I subunit RPA4

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase I subunit RPA4

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

2rf4__assembly_2__model_1

2rf4__assembly_2__model_1 | I(q)

2rf4__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structure of the RNA Polymerase I subcomplex A14/43

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

DNA-directed RNA polymerase I subunit RPA4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerase I subunit RPA4

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

2rf4__assembly_2__model_1

2rf4__assembly_2__model_1 | I(q)

2rf4__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)