SAXSdb — 3nyb

▼

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

Poly(A) RNA polymerase protein 2

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	Protein AIR2 × 1 （Q12476） ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAP2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–323； UniProt 161–481

Protein AIR2

Saccharomyces cerevisiae

UniProt Q12476

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Poly(A) RNA polymerase protein 2 × 1 （P53632） ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AIR2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–83； UniProt 118–198

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3nyb
Deposition date deposition_date	2010-07-14
Structure title title	Structure and function of the polymerase core of TRAMP, a RNA surveillance complex
Keywords keywords	;polyA RNA polymerase, zinc knuckle protein, RNA surveillance, Mtr4p binds to Trf4p/Air2p heterodimer, TRANSFERASE-RNA BINDING PROTEIN complex ;; TRANSFERASE/RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3nyb__assembly_1__model_1

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

Download this curve (.dat)

3nyb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nyb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.01 Å
Rg (electron density)	22.84 Å
Total Rg	23.87 Å
Atom count	3081
Residues	387
Excluded volume	54880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nyb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Poly(A) RNA polymerase protein 2
Molecular weight formula_weight	36459.5 kDa
EC 编号 ec_number	2.7.7.-
Mutation mutation	D293A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3139

GSYPWILNHDHSKQKEISDWLTFEIKDFVAYISPSREEIEIRNQTISTIREAVKQLWPDADLHVFGSYSTDLYLPGSDIDCVVTSELGGKESRNNLYSLASHLKKKNLATEVEVVAKARVPIIKFVEPHSGIHIAVSFERTNGIEAAKLIREWLDDTPGLRELVLIVKQFLHARRLNNVHTGGLGGFSIICLVFSFLHMHPRIITNEIDPKDNLGVLLIEFFELYGKNFGYDDVALGSSDGYPVYFPKSTWSAIQPIKNPFSLAIQDPGDESNNISRGSFNIRDIKKAFAGAFDLLTNRCFELHSATFKDRLGKSILGNVIKY

Source Source

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

Entity 2 Entity 2 polymer

Description description	Protein AIR2
Molecular weight formula_weight	9399.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSWKKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKRSSRVPNEDGSAFTGSNL

Source Source

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

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

▼

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3nybA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1410 — Poly(a)-polymerase, middle domain
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3nybA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	3nybB00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	60 — HIV-1 Nucleocapsid Protein
Homologous superfamily homologous superfamily	10 — Zinc finger, CCHC-type

▶

Unit-cell length a length_a	92.720 Å
Unit-cell length b length_b	92.720 Å
Unit-cell length c length_c	103.630 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	6

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	2.701 Å
Low-resolution limit resolution_low	24.656 Å
R factor r_factor	0.1982
R_work r_work	0.1935
R_free r_free	0.2581

Structure and function of the polymerase core of TRAMP, a RNA surveillance complex

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

Poly(A) RNA polymerase protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Protein AIR2

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

3nyb__assembly_1__model_1

3nyb__assembly_1__model_1 | I(q)

3nyb__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Structure and function of the polymerase core of TRAMP, a RNA surveillance complex

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

Poly(A) RNA polymerase protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein AIR2

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

3nyb__assembly_1__model_1

3nyb__assembly_1__model_1 | I(q)

3nyb__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)