2o1p

Structure of yeast Poly(A) Polymerase in a somewhat closed state

Method: X-RAY DIFFRACTION

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

Poly(A) polymerase

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAP_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–538； UniProt 1–538 Author chain B； PDBConstruct 1–538； UniProt 1–538

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	2o1p
Deposition date deposition_date	2006-11-29
Structure title title	Structure of yeast Poly(A) Polymerase in a somewhat closed state
Keywords keywords	poly(A) polymerase, TRANSFERASE; 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.

2o1p__assembly_1__model_1

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

Download this curve (.dat)

2o1p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2o1p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.50 Å
Rg (electron density)	25.23 Å
Total Rg	26.22 Å
Atom count	4164
Residues	523
Excluded volume	74708 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2o1p__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2o1p__assembly_2__model_1`	monomeric （1）	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	Poly(A) polymerase
Molecular weight formula_weight	62623.8 kDa
EC 编号 ec_number	2.7.7.19
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8532

MSSQKVFGITGPVSTVGATAAENKLNDSLIQELKKEGSFETEQETANRVQVLKILQELAQRFVYEVSKKKNMSDGMARDAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVTREDFFTVFDSLLRERKELDEIAPVPDAFVPIIKIKFSGISIDLICARLDQPQVPLSLTLSDKNLLRNLDEKDLRALNGTRVTDEILELVPKPNVFRIALRAIKLWAQRRAVYANIFGFPGGVAWAMLVARICQLYPNACSAVILNRFFIILSEWNWPQPVILKPIEDGPLQVRVWNPKIYAQDRSHRMPVITPAYPSMCATHNITESTKKVILQEFVRGVQITNDIFSNKKSWANLFEKNDFFFRYKFYLEITAYTRGSDEQHLKWSGLVESKVRLLVMKLEVLAGIKIAHPFTKPFESSYCCPTEDDYEMIQDKYGSHKTETALNALKLVTDENKEEESIKDAPKAYLSTMYIGLDFNIENKKEKVDIHIPCTEFVNLCRSFNEDYGDHKVFNLALRFVKGYDLPDEVFDENEKRPSKKSKRKNLLEHHHHHH

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	183

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2o1pa1
Class class	a — All alpha proteins
Fold Fold fold	a.160 — PAP/OAS1 substrate-binding domain
Superfamily Superfamily superfamily	a.160.1 — PAP/OAS1 substrate-binding domain
Family Family family	a.160.1.1 — Poly(A) polymerase, PAP, middle domain

Domain ID domain_id	d2o1pa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.218 — Nucleotidyltransferase
Superfamily Superfamily superfamily	d.218.1 — Nucleotidyltransferase
Family Family family	d.218.1.3 — Poly(A) polymerase, PAP, N-terminal domain

Domain ID domain_id	d2o1pa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.16 — PAP/Archaeal CCA-adding enzyme, C-terminal domain
Family Family family	d.58.16.1 — Poly(A) polymerase, PAP, C-terminal domain

Domain ID domain_id	d2o1pa4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2o1pb1
Class class	a — All alpha proteins
Fold Fold fold	a.160 — PAP/OAS1 substrate-binding domain
Superfamily Superfamily superfamily	a.160.1 — PAP/OAS1 substrate-binding domain
Family Family family	a.160.1.1 — Poly(A) polymerase, PAP, middle domain

Domain ID domain_id	d2o1pb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.218 — Nucleotidyltransferase
Superfamily Superfamily superfamily	d.218.1 — Nucleotidyltransferase
Family Family family	d.218.1.3 — Poly(A) polymerase, PAP, N-terminal domain

Domain ID domain_id	d2o1pb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.16 — PAP/Archaeal CCA-adding enzyme, C-terminal domain
Family Family family	d.58.16.1 — Poly(A) polymerase, PAP, C-terminal domain

Domain ID domain_id	d2o1pb4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	2o1pA01
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	2o1pA02
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	2o1pA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	590 — Poly(A) polymerase predicted RNA binding domain

Domain ID domain_id	2o1pB01
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	2o1pB02
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	2o1pB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	590 — Poly(A) polymerase predicted RNA binding domain

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Unit-cell length a length_a	82.217 Å
Unit-cell length b length_b	108.587 Å
Unit-cell length c length_c	132.718 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	65.510 Å
R factor r_factor	0.1989
R_work r_work	0.1950
R_free r_free	0.2751

Structure of yeast Poly(A) Polymerase in a somewhat closed state

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

Poly(A) polymerase

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

2o1p__assembly_1__model_1

2o1p__assembly_1__model_1 | I(q)

2o1p__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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of yeast Poly(A) Polymerase in a somewhat closed state

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

Poly(A) polymerase

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

2o1p__assembly_1__model_1

2o1p__assembly_1__model_1 | I(q)

2o1p__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 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)