SAXSdb — 2ckz

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

DNA-DIRECTED RNA POLYMERASE III 18 KD POLYPEPTIDE

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 III 25 KD POLYPEPTIDE × 1 （P35718）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA-DIRECTED RNA POLYMERASE III 25 KD POLYPEPTIDE × 1 （P35718）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YJB1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–161； UniProt 1–161 Author chain C； PDBConstruct 1–161； UniProt 1–161

DNA-DIRECTED RNA POLYMERASE III 25 KD POLYPEPTIDE

SACCHAROMYCES CEREVISIAE

UniProt P35718

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 III 18 KD POLYPEPTIDE × 1 （P47076）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA-DIRECTED RNA POLYMERASE III 18 KD POLYPEPTIDE × 1 （P47076）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPC25_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–212； UniProt 1–212 Author chain D； PDBConstruct 1–212； UniProt 1–212

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	2ckz
Deposition date deposition_date	2006-04-24
Structure title title	X-ray structure of RNA polymerase III subcomplex C17-C25.
Keywords keywords	;DNA-DIRECTED RNA POLYMERASE, MULTIPROTEIN COMPLEX, NUCLEOTIDYLTRANSFERASE, NUCLEAR PROTEIN, HYPOTHETICAL PROTEIN, EUKARYOTIC NUCLEIC ACID POLYMERASE, CLASS III GENE TRANSCRIPTION, TRANSFERASE, TRANSCRIPTION, TRNA SYNTHESIS ;; 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.

2ckz__assembly_1__model_1

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

Download this curve (.dat)

2ckz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ckz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.16 Å
Rg (electron density)	21.16 Å
Total Rg	21.98 Å
Atom count	1927
Residues	239
Excluded volume	34776 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ckz__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ckz__assembly_2__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 III 18 KD POLYPEPTIDE
Molecular weight formula_weight	18637.2 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4386

MKVLEERNAFLSDYEVLKFLTDLEKKHLWDQKSLAALKKSRSKGKQNRPYNHPELQGITRNVVNYLSINKNFINQEDEGEERESSGAKDAEKSGISKMSDESFAELMTKLNSFKLFKAEKLQIVNQLPANMVHLYSIVEECDARFDEKTIEEMLEIISAYA

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 III 25 KD POLYPEPTIDE
Molecular weight formula_weight	25178.7 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MFILSKIADLVRIPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLKPGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYFDVNEKIRFRIEREVFVDVKPKSPKERELEERAQLENEIEGKNEETPQNEKPPAYALLGSCQTDGMGLVSWWEHHHHHH

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) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2ckzA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	870 —

Domain ID domain_id	2ckzB01
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	2ckzB02
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	2ckzC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	40 — RNA Polymerase II, Rpb4 subunit

Domain ID domain_id	2ckzD01
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	2ckzD02
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

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Unit-cell length a length_a	138.230 Å
Unit-cell length b length_b	138.230 Å
Unit-cell length c length_c	247.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2359
R_work r_work	0.2359
R_free r_free	0.3073

X-ray structure of RNA polymerase III subcomplex C17-C25.

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

DNA-DIRECTED RNA POLYMERASE III 18 KD POLYPEPTIDE

State in the Current Structure

Other States of the Same Protein in the Database

DNA-DIRECTED RNA POLYMERASE III 25 KD POLYPEPTIDE

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

2ckz__assembly_1__model_1

2ckz__assembly_1__model_1 | I(q)

2ckz__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

X-ray structure of RNA polymerase III subcomplex C17-C25.

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

DNA-DIRECTED RNA POLYMERASE III 18 KD POLYPEPTIDE

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 III 25 KD POLYPEPTIDE

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

2ckz__assembly_1__model_1

2ckz__assembly_1__model_1 | I(q)

2ckz__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)