4xr7

Structure of the Saccharomyces cerevisiae PAN2-PAN3 core complex

Method: X-RAY DIFFRACTION

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

PAB-dependent poly(A)-specific ribonuclease subunit PAN2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	PAB-dependent poly(A)-specific ribonuclease subunit PAN3 × 2 （P36102）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	PAB-dependent poly(A)-specific ribonuclease subunit PAN3 × 2 （P36102）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	PAB-dependent poly(A)-specific ribonuclease subunit PAN3 × 2 （P36102）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	PAB-dependent poly(A)-specific ribonuclease subunit PAN3 × 2 （P36102）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAN2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–776； UniProt 340–1115 Author chain D； PDBConstruct 1–776； UniProt 340–1115 Author chain G； PDBConstruct 1–776； UniProt 340–1115 Author chain J； PDBConstruct 1–776； UniProt 340–1115

PAB-dependent poly(A)-specific ribonuclease subunit PAN3

Saccharomyces cerevisiae

UniProt P36102

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	PAB-dependent poly(A)-specific ribonuclease subunit PAN2 × 1 （P53010）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	PAB-dependent poly(A)-specific ribonuclease subunit PAN2 × 1 （P53010）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	PAB-dependent poly(A)-specific ribonuclease subunit PAN2 × 1 （P53010）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	PAB-dependent poly(A)-specific ribonuclease subunit PAN2 × 1 （P53010）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAN3_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–455； UniProt 226–679 Author chain C； PDBConstruct 2–455； UniProt 226–679 Author chain E； PDBConstruct 2–455； UniProt 226–679 Author chain F； PDBConstruct 2–455； UniProt 226–679 Author chain H； PDBConstruct 2–455； UniProt 226–679 Author chain I； PDBConstruct 2–455； UniProt 226–679 Author chain K； PDBConstruct 2–455； UniProt 226–679 Author chain L； PDBConstruct 2–455； UniProt 226–679

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	4xr7
Deposition date deposition_date	2015-01-20
Structure title title	Structure of the Saccharomyces cerevisiae PAN2-PAN3 core complex
Keywords keywords	RNA degradation, Deadenylation, Hydrolase, Pseudokinase; HYDROLASE
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.

4xr7__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4xr7__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4xr7__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	41.70 Å
Rg (electron density)	41.41 Å
Total Rg	41.58 Å
Atom count	11438
Residues	1539
Excluded volume	201830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4xr7__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4xr7__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4xr7__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4xr7__assembly_4__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 (2)

Entity 1 Entity 1 polymer

Description description	PAB-dependent poly(A)-specific ribonuclease subunit PAN2
Molecular weight formula_weight	89263.1 kDa
EC 编号 ec_number	3.1.13.4
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,D,J,A
Atom count atom_count	46467

MLAYPDYFNDITSDGPISVDDETYPLSSVGMPYYLDKLLSAWPPVVFKSEGTIPQLTGKSPLPSSGKLKSNLAVISSQNEKLSTQEFPLLRYDRTKYGMRNAIPDYVCLRDIRKQITSGLETSDIQTYTSINKYEVPPAYSRLPLTSGRFGTDNFDFTPFNNTEYSGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENFETTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTDKRQLENGEPQEHLEEYLESLCIRESIEDFNSSESIKRNMPQKFNRFLLSQLIKEEAQTVNHNITLNQCFGLETEIRTECSCDHYDTTVKLLPSLSISGINKTVIKQLNKKSNGQNILPYIEYAMKNVTQKNSICPTCGKTETITQECTVKNLPSVLSLELSLLDTEFSNIRSSKNWLTSEFYGSIIKNKAVLRSTASELKGTSHIFKYELNGYVAKITDNNNETRLVTYVKKYNPKENCFKWLMFNDYLVVEITEEEALKMTYPWKTPEIIIYCDAEELRKPFFSVDTYSINYDILFRDYFANGIRDTARREYKLLTHDEAPKSGTLVAIDAEFVSLQSELCEIDHQGIRSIIRPKRTALARISIIRGEEGELYGVPFVDDYVVNTNHIEDYLTRYSGILPGDLDPEKSTKRLVRRNVVYRKVWLLMQLGCVFVGHGLNNDFKHININVPRNQIRDTAIYFLQGKRYLSLRYLAYVLLGMNIQEGNHDSIEDAHTALILYKKYLHLKEKAIFEKVLNSVYEEGRAHNFKVPETSKG

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	PAB-dependent poly(A)-specific ribonuclease subunit PAN3
Molecular weight formula_weight	54330.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,K,E,F,H,I,C,B

MHSLLQYHLYAPEQPSSLKSLLKPNERSADQLFIPNNIREDLTKKNLSILQVFPSSGKVIPSIVQDYFNLVPLNFNNNDFLNKTTLFKVFSNYDGKAYVLKRLPNIDKSMNPNKISKIYQIWSKINCTNLIKFRDIFQTTKFGDLSICLVFDYYPNSLSLYDYHFVNFPKFPITNNYLWIYLVQLTNVINSIHSQNLSIGNTLNWRKVLITGDPGRIKLSHCNFMDLLFNDDTDTVVSSGGSTIEGQQQLDYKYLGELLFNLSINIENSNNNTAPKEYRLEEITPQSIDDMRQIDDKFKDVLKYLISDNGDSKKSIHDLTSHFYDKMFMVLESSQTYTEYMESVLSRELENGRLFRLVNKLNCIFGRIESRIDINWSESGTKFPIILFYDYVFHQVDSNGKPIMDLTHVLRCLNKLDAGIQEKLMLVTPDELNCIIISYKELKDLIESTFRSITQHHHHHHHHHH

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	Trichoplusia ni

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6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id	4xr7A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	4xr7B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4xr7B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3700 —

Domain ID domain_id	4xr7C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4xr7C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3700 —

Domain ID domain_id	4xr7D01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	4xr7E01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4xr7E02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3700 —

Domain ID domain_id	4xr7F01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4xr7F02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3700 —

Domain ID domain_id	4xr7G01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	4xr7H01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4xr7H02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3700 —

Domain ID domain_id	4xr7I01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4xr7I02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3700 —

Domain ID domain_id	4xr7J01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	4xr7K01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4xr7K02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3700 —

Domain ID domain_id	4xr7L01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4xr7L02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3700 —

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Unit-cell length a length_a	131.443 Å
Unit-cell length b length_b	205.298 Å
Unit-cell length c length_c	234.410 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.796 Å
Low-resolution limit resolution_low	48.828 Å
R factor r_factor	0.2862
R_work r_work	0.2855
R_free r_free	0.2994

Structure of the Saccharomyces cerevisiae PAN2-PAN3 core complex

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

PAB-dependent poly(A)-specific ribonuclease subunit PAN2

State in the Current Structure

Other States of the Same Protein in the Database

PAB-dependent poly(A)-specific ribonuclease subunit PAN3

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

4xr7__assembly_3__model_1

4xr7__assembly_3__model_1 | I(q)

4xr7__assembly_3__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) 20 domains

CATH v4.4 (20 domains)

7. Citations (1)

Structure of the Saccharomyces cerevisiae PAN2-PAN3 core complex

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

PAB-dependent poly(A)-specific ribonuclease subunit PAN2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PAB-dependent poly(A)-specific ribonuclease subunit PAN3

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

4xr7__assembly_3__model_1

4xr7__assembly_3__model_1 | I(q)

4xr7__assembly_3__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) 20 domains

CATH v4.4 (20 domains)

7. Citations (1)