Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6R5K

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

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
A	0000289	biological_process	nuclear-transcribed mRNA poly(A) tail shortening
A	0000932	cellular_component	P-body
A	0003676	molecular_function	nucleic acid binding
A	0004527	molecular_function	exonuclease activity
A	0004535	molecular_function	poly(A)-specific ribonuclease activity
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0006301	biological_process	postreplication repair
A	0006397	biological_process	mRNA processing
A	0008270	molecular_function	zinc ion binding
A	0031251	cellular_component	PAN complex
A	0046872	molecular_function	metal ion binding
D	0003676	molecular_function	nucleic acid binding
D	0003723	molecular_function	RNA binding
D	0003729	molecular_function	mRNA binding
D	0003730	molecular_function	mRNA 3'-UTR binding
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0005840	cellular_component	ribosome
D	0006397	biological_process	mRNA processing
D	0006417	biological_process	regulation of translation
D	0006446	biological_process	regulation of translational initiation
D	0008143	molecular_function	poly(A) binding
D	0008266	molecular_function	poly(U) RNA binding
D	0008428	molecular_function	ribonuclease inhibitor activity
D	0010494	cellular_component	cytoplasmic stress granule
D	0031124	biological_process	mRNA 3'-end processing
D	0043232	cellular_component	intracellular non-membrane-bounded organelle
D	0051028	biological_process	mRNA transport
D	0060211	biological_process	regulation of nuclear-transcribed mRNA poly(A) tail shortening
D	0140693	molecular_function	molecular condensate scaffold activity
D	1990841	molecular_function	promoter-specific chromatin binding
D	1990904	cellular_component	ribonucleoprotein complex
F	0003676	molecular_function	nucleic acid binding
F	0003723	molecular_function	RNA binding
F	0003729	molecular_function	mRNA binding
F	0003730	molecular_function	mRNA 3'-UTR binding
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0005840	cellular_component	ribosome
F	0006397	biological_process	mRNA processing
F	0006417	biological_process	regulation of translation
F	0006446	biological_process	regulation of translational initiation
F	0008143	molecular_function	poly(A) binding
F	0008266	molecular_function	poly(U) RNA binding
F	0008428	molecular_function	ribonuclease inhibitor activity
F	0010494	cellular_component	cytoplasmic stress granule
F	0031124	biological_process	mRNA 3'-end processing
F	0043232	cellular_component	intracellular non-membrane-bounded organelle
F	0051028	biological_process	mRNA transport
F	0060211	biological_process	regulation of nuclear-transcribed mRNA poly(A) tail shortening
F	0140693	molecular_function	molecular condensate scaffold activity
F	1990841	molecular_function	promoter-specific chromatin binding
F	1990904	cellular_component	ribonucleoprotein complex
H	0003676	molecular_function	nucleic acid binding
H	0003723	molecular_function	RNA binding
H	0003729	molecular_function	mRNA binding
H	0003730	molecular_function	mRNA 3'-UTR binding
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0005840	cellular_component	ribosome
H	0006397	biological_process	mRNA processing
H	0006417	biological_process	regulation of translation
H	0006446	biological_process	regulation of translational initiation
H	0008143	molecular_function	poly(A) binding
H	0008266	molecular_function	poly(U) RNA binding
H	0008428	molecular_function	ribonuclease inhibitor activity
H	0010494	cellular_component	cytoplasmic stress granule
H	0031124	biological_process	mRNA 3'-end processing
H	0043232	cellular_component	intracellular non-membrane-bounded organelle
H	0051028	biological_process	mRNA transport
H	0060211	biological_process	regulation of nuclear-transcribed mRNA poly(A) tail shortening
H	0140693	molecular_function	molecular condensate scaffold activity
H	1990841	molecular_function	promoter-specific chromatin binding
H	1990904	cellular_component	ribonucleoprotein complex
N	0000289	biological_process	nuclear-transcribed mRNA poly(A) tail shortening
N	0003723	molecular_function	RNA binding
N	0004672	molecular_function	protein kinase activity
N	0005524	molecular_function	ATP binding
N	0006397	biological_process	mRNA processing
N	0006468	biological_process	protein phosphorylation
N	0031251	cellular_component	PAN complex
O	0000288	biological_process	nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
O	0000289	biological_process	nuclear-transcribed mRNA poly(A) tail shortening
O	0000932	cellular_component	P-body
O	0003723	molecular_function	RNA binding
O	0004672	molecular_function	protein kinase activity
O	0005515	molecular_function	protein binding
O	0005524	molecular_function	ATP binding
O	0005737	cellular_component	cytoplasm
O	0006281	biological_process	DNA repair
O	0006301	biological_process	postreplication repair
O	0006397	biological_process	mRNA processing
O	0006468	biological_process	protein phosphorylation
O	0008143	molecular_function	poly(A) binding
O	0008270	molecular_function	zinc ion binding
O	0031251	cellular_component	PAN complex
O	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue MG E 101

Chain	Residue
A	HIS1015
A	LEU1047
E	A65
E	A66
E	MG102

site_id	AC2
Number of Residues	5
Details	binding site for residue MG E 102

Chain	Residue
E	MG101
A	HIS1015
A	LEU1047
A	SER1048
E	A65

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	29
Details	ZN_FING: C3H1-type => ECO:0000255\|HAMAP-Rule:MF_03181

Chain	Residue	Details
O	TRP8-ASN37
N	ASP376
N	ARG430
A	CYS716

site_id	SWS_FT_FI2
Number of Residues	3
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_03181

Chain	Residue	Details
O	LYS325
O	ASP376
O	ARG430

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:18407956

Chain	Residue	Details
O	THR57
F	SER249
H	SER249

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18407956

Chain	Residue	Details
O	SER252
D	SER405
F	SER332
F	SER405
H	SER332
H	SER405

site_id	SWS_FT_FI5
Number of Residues	9
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744\|PubMed:22106047

Chain	Residue	Details
D	LYS7
D	LYS337
F	LYS7
F	LYS337
H	LYS7
H	LYS337

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)