SAXSdb — 6r5k

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

PAN2-PAN3 deadenylation complex catalytic subunit PAN2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 1	Polyadenylate-binding protein, cytoplasmic and nuclear × 3 （P04147） poly(A) RNA × 1 PAN2-PAN3 deadenylation complex subunit PAN3 × 1 （P36102） PAN2-PAN3 deadenylation complex subunit PAN3 × 1 （P36102） MAGNESIUM ION × 2	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 1–1115； UniProt 1–1115

Polyadenylate-binding protein, cytoplasmic and nuclear

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P04147

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 1	PAN2-PAN3 deadenylation complex catalytic subunit PAN2 × 1 （P53010） poly(A) RNA × 1 PAN2-PAN3 deadenylation complex subunit PAN3 × 1 （P36102） PAN2-PAN3 deadenylation complex subunit PAN3 × 1 （P36102） MAGNESIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PABP_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 5–581； UniProt 1–577 Author chain F； PDBConstruct 5–581； UniProt 1–577 Author chain H； PDBConstruct 5–581； UniProt 1–577

PAN2-PAN3 deadenylation complex subunit PAN3

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P36102

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 1	PAN2-PAN3 deadenylation complex catalytic subunit PAN2 × 1 （P53010） Polyadenylate-binding protein, cytoplasmic and nuclear × 3 （P04147） poly(A) RNA × 1 MAGNESIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAN3_YEAST
Isoform	—
PDB entities	4, 5
Chains and sequence ranges	Author chain N； PDBConstruct 2–457； UniProt 226–679 Author chain O； PDBConstruct 1–679； UniProt 1–679

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	6r5k
Deposition date deposition_date	2019-03-25
Structure title title	Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase
Keywords keywords	poly(A)-tail, mRNA, RNP, PABP, Pab1, Pan2-Pan3, Ccr4-Not, deadenylase, RRM, cryoEM, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

6r5k__assembly_1__model_1

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

Download this curve (.dat)

6r5k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6r5k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.71 Å
Rg (electron density)	52.39 Å
Total Rg	52.50 Å
Atom count	23508
Residues	2932
Excluded volume	409850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6r5k__assembly_1__model_1`	heptameric （7）	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 (6)

Entity 1 Entity 1 polymer

Description description	PAN2-PAN3 deadenylation complex catalytic subunit PAN2
Molecular weight formula_weight	127186.6 kDa
EC 编号 ec_number	3.1.13.4
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	23508

MNNWQHFFNNPVDLSEHLKKPYFRFDNRDKEITAISFDEKANLIWSGDSYGCISSYDPTFQLYTRYRGHIGGNSVKDILSHRDGILSISEDSLHFANRRGVTKLNLTSIDIAAFSELNTMCYSPHSLKNNIYCGGDNTNWGIASIDLNRGCLDSLLNYSSKVKLMCSNNKVLSIGRQTGTVDLLDPTSNRTIKSFNAHSASISAMDLRDNTLVTVGKSKRFYNLYADPFVNVYDLRTMRQLPPVSFSKGTTMGSGGADFVQLHPLLPTVMIVASSSGSFDFIDLSNPTLRTQYVHPCQSIKKLCLSPNGDVLGILEADNHLDTWRRSSNNMGMFTNTPEMLAYPDYFNDITSDGPISVDDETYPLSSVGMPYYLDKLLSAWPPVVFKSEGTIPQLTGKSPLPSSGKLKSNLAVISSQNEKLSTQEFPLLRYDRTKYGMRNAIPDYVCLRDIRKQITSGLETSDIQTYTSINKYEVPPAYSRLPLTSGRFGTDNFDFTPFNNTEYSGLDPDVDNHYTNAIIQLYRFIPEMFNFVVGCLKDENFETTLLTDLGYLFDMMERSHGKICSSSNFQASLKSLTDKRQLENGEPQEHLEEYLESLCIRESIEDFNSSESIKRNMPQKFNRFLLSQLIKEEAQTVNHNITLNQCFGLETEIRTECSCDHYDTTVKLLPSLSISGINKTVIKQLNKKSNGQNILPYIEYAMKNVTQKNSICPTCGKTETITQECTVKNLPSVLSLELSLLDTEFSNIRSSKNWLTSEFYGSIIKNKAVLRSTASELKGTSHIFKYELNGYVAKITDNNNETRLVTYVKKYNPKENCFKWLMFNDYLVVEITEEEALKMTYPWKTPEIIIYCDAEELRKPFFSVDTYSINYDILFRDYFANGIRDTARREYKLLTHDEAPKSGTLVAIDAEFVSLQSELCEIDHQGIRSIIRPKRTALARISIIRGEEGELYGVPFVDDYVVNTNHIEDYLTRYSGILPGDLDPEKSTKRLVRRNVVYRKVWLLMQLGCVFVGHGLNNDFKHININVPRNQIRDTAIYFLQGKRYLSLRYLAYVLLGMNIQEGNHDSIEDAHTALILYKKYLHLKEKAIFEKVLNSVYEEGRAHNFKVPETSKG

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Polyadenylate-binding protein, cytoplasmic and nuclear
Molecular weight formula_weight	64778.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,H

GPDSMADITDKTAEQLENLNIQDDQKQAATGSESQSVENSSASLYVGDLEPSVSEAHLYDIFSPIGSVSSIRVCRDAITKTSLGYAYVNFNDHEAGRKAIEQLNYTPIKGRLCRIMWSQRDPSLRKKGSGNIFIKNLHPDIDNKALYDTFSVFGDILSSKIATDENGKSKGFGFVHFEEEGAAKEAIDALNGMLLNGQEIYVAPHLSRKERDSQLEETKAHYTNLYVKNINSETTDEQFQELFAKFGPIVSASLEKDADGKLKGFGFVNYEKHEDAVKAVEALNDSELNGEKLYVGRAQKKNERMHVLKKQYEAYRLEKMAKYQGVNLFVKNLDDSVDDEKLEEEFAPYGTITSAKVMRTENGKSKGFGFVCFSTPEEATKAITEKNQQIVAGKPLYVAIAQRKDVRRSQLAQQIQARNQMRYQQATAAAAAAAAGMPGQFMPPMFYGVMPPRGVPFNGPNPQQMNPMGGMPKNGMPPQFRNGPVYGVPPQGGFPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLESDELFEQHYKEASAAYESFKKEQEQQTEQA

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	poly(A) RNA
Molecular weight formula_weight	29583.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Entity 4 Entity 4 polymer

Description description	PAN2-PAN3 deadenylation complex subunit PAN3
Molecular weight formula_weight	53218.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MHSLLQYHISLYAPEQPSSLKSLLKPNERSADQLFIPNNIREDLTKKNLSILQVFPSSGKVIPSIVQDYFNLVPLNFNNNDFLNKTTLFKVFSNYDGKAYVLKRLPNIDKSMNPNKISKIYQIWSKINCTNLIKFRDIFQTTKFGNLSICLVFDYYPNSLSLYDYHFVNFPKFPITNNYLWIYLVQLTNVINSIHSQNLSIGNTLNWRKVLITGDPGRIKLSHCNFMDLLFNDDTDTVVSSGGSTIEGQQQLDYKYLGELLFNLSINIENSNNNTAPKEYRLEEITPQSIDDMRQIDDKFKDVLKYLISDNGDSKKSIHDLTSHFYDKMFMVLESSQTYTEYMESVLSRELENGRLFRLVNKLNCIFGRIESRIDINWSESGTKFPIILFYDYVFHQVDSNGKPIMDLTHVLRCLNKLDAGIQEKLMLVTPDELNCIIISYKQLKDLIESTFRSITQA

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 5 Entity 5 polymer

Description description	PAN2-PAN3 deadenylation complex subunit PAN3
Molecular weight formula_weight	77906.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O

MDKINPDWAKDIPCRNITIYGYCKKEKEGCPFKHSDNTTATTINDVPPPIDVGEATTPTMTSVPKFNAKVSASFTPMTVGSDSLTTVTNTTSAATNATGNIAMAATSATASTVNPMINPIVNSSLVNNNNNNSNISISIPTTASSSNYDPFNAPIFTPSSTSSIHTNANAHSFPFPSIANSGGININATDDNSNNMSMANNVPPPMQPPPIESSNLKYPRIYPPPHSLLQYHLYAPEQPSSLKSLLKPNERSADQLFIPNNIREDLTKKNLSILQVFPSSGKVIPSIVQDYFNLVPLNFNNNDFLNKTTLFKVFSNYDGKAYVLKRLPNIDKSMNPNKISKIYQIWSKINCTNLIKFRDIFQTTKFGDLSICLVFDYYPNSLSLYDYHFVNFPKFPITNNYLWIYLVQLTNVINSIHSQNLSIGNTLNWRKVLITGDPGRIKLSHCNFMDLLFNDDTDTVVSSGGSTIEGQQQLDYKYLGELLFNLSINIENSNNNTAPKEYRLEEITPQSIDDMRQIDDKFKDVLKYLISDNGDSKKSIHDLTSHFYDKMFMVLESSQTYTEYMESVLSRELENGRLFRLVNKLNCIFGRIESRIDINWSESGTKFPIILFYDYVFHQVDSNGKPIMDLTHVLRCLNKLDAGIQEKLMLVTPDELNCIIISYKELKDLIESTFRSITQHHHHHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Trichoplusia ni

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	4.800 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	4.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	29165

Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase

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

Polyadenylate-binding protein, cytoplasmic and nuclear

State in the Current Structure

Other States of the Same Protein in the Database

PAN2-PAN3 deadenylation complex 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

6r5k__assembly_1__model_1

6r5k__assembly_1__model_1 | I(q)

6r5k__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

7. Citations (1)

Cryo-EM structure of a poly(A) RNP bound to the Pan2-Pan3 deadenylase

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

Polyadenylate-binding protein, cytoplasmic and nuclear

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PAN2-PAN3 deadenylation complex 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

6r5k__assembly_1__model_1

6r5k__assembly_1__model_1 | I(q)

6r5k__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

7. Citations (1)