SAXSdb — 6r9o

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

PAN2-PAN3 deadenylation complex catalytic subunit PAN2

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	AAGGA RNA × 1	Consistent with all polymers

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 18–672； UniProt 461–1115

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	6r9o
Deposition date deposition_date	2019-04-03
Structure title title	Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AAGGA RNA
Keywords keywords	DEDD RNase, deadenylase, pseudoubiquitin hydrolase, HYDROLASE; 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.

6r9o__assembly_1__model_1

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

Download this curve (.dat)

6r9o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6r9o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.67 Å
Rg (electron density)	26.74 Å
Total Rg	27.49 Å
Atom count	4544
Residues	598
Excluded volume	79829 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6r9o__assembly_1__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	PAN2-PAN3 deadenylation complex catalytic subunit PAN2
Molecular weight formula_weight	77776.1 kDa
EC 编号 ec_number	3.1.13.4
Mutation mutation	E912A
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	4544

MHHHHHHHHLEVLFQGPTSDIQTYTSINKYEVPPAYSRLPLTSGRFGTDNFDFTPFNNTEYSGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENFETTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTDKRQLENGEPQEHLEEYLESLCIRESIEDFNSSESIKRNMPQKFNRFLLSQLIKEEAQTVNHNITLNQCFGLETEIRTECSCDHYDTTVKLLPSLSISGINKTVIKQLNKKSNGQNILPYIEYAMKNVTQKNSICPTCGKTETITQECTVKNLPSVLSLELSLLDTEFSNIRSSKNWLTSEFYGSIIKNKAVLRSTASELKGTSHIFKYELNGYVAKITDNNNETRLVTYVKKYNPKENCFKWLMFNDYLVVEITEEEALKMTYPWKTPEIIIYCDAEELRKPFFSVDTYSINYDILFRDYFANGIRDTARREYKLLTHDEAPKSGTLVAIDAAFVSLQSELCEIDHQGIRSIIRPKRTALARISIIRGEEGELYGVPFVDDYVVNTNHIEDYLTRYSGILPGDLDPEKSTKRLVRRNVVYRKVWLLMQLGCVFVGHGLNNDFKHININVPRNQIRDTAIYFLQGKRYLSLRYLAYVLLGMNIQEGNHDSIEDAHTALILYKKYLHLKEKAIFEKVLNSVYEEGRAHNFKVPETSKG

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	AAGGA RNA
Molecular weight formula_weight	1633.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

AAGGA

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6r9oA01
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

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Unit-cell length a length_a	90.761 Å
Unit-cell length b length_b	117.593 Å
Unit-cell length c length_c	256.568 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	3.319 Å
Low-resolution limit resolution_low	85.565 Å
R factor r_factor	0.2574
R_work r_work	0.2545
R_free r_free	0.3092

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AAGGA RNA

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

PAN2-PAN3 deadenylation complex catalytic subunit PAN2

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

6r9o__assembly_1__model_1

6r9o__assembly_1__model_1 | I(q)

6r9o__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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AAGGA RNA

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

PAN2-PAN3 deadenylation complex catalytic 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6r9o__assembly_1__model_1

6r9o__assembly_1__model_1 | I(q)

6r9o__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

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)