3LCN - JenaLib

Molecule 1 - NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN NAB2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET20A
	Expression System Strain	:	BL21(DE3) RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET
	Fragment	:	SEQUENCE DATABASE RESIDUES 1-105
	Gene	:	NAB2, YGL122C
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 2 - MRNA TRANSPORT FACTOR GFD1
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-TEV
	Expression System Strain	:	BL21(DE3) RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PGEX
	Fragment	:	SEQUENCE DATABASE RESIDUES 123-151
	Gene	:	GFD1, YM9920.09, YMR255W
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	GOOD FOR FULL DBP5 ACTIVITY PROTEIN 1

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 2)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:96
 aligned with NAB2_YEAST | P32505 from UniProtKB/Swiss-Prot  Length:525

    Alignment length:96
                                    14        24        34        44        54        64        74        84        94      
           NAB2_YEAST     5 QYTENLKVIVAEKLAGIPNFNEDIKYVAEYIVLLIVNGGTVESVVDELASLFDSVSRDTLANVVQTAFFALEALQQGESAENIVSKIRMMNAQSLG 100
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-100 UniProt: 1-525 [INCOMPLETE]                                               Transcript 1
                 3lcn A   5 QYTENLKVIVAEKLAGIPNFNEDIKYVAEYIVLLIVNGGTVESVVDELASLFDSVSRDTLANVVQTAFFALEALQQGESAENIVSKIRMMNAQSLG 100
                                    14        24        34        44        54        64        74        84        94

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with NAB2_YEAST | P32505 from UniProtKB/Swiss-Prot  Length:525

    Alignment length:97
                                    13        23        33        43        53        63        73        83        93       
           NAB2_YEAST     4 EQYTENLKVIVAEKLAGIPNFNEDIKYVAEYIVLLIVNGGTVESVVDELASLFDSVSRDTLANVVQTAFFALEALQQGESAENIVSKIRMMNAQSLG 100
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Nab2-3lcnB01 B:4-100                                                                              Pfam domains (1)
           Pfam domains (2) Nab2-3lcnB02 B:4-100                                                                              Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:4-100 UniProt: 1-525 [INCOMPLETE]                                                Transcript 1
                 3lcn B   4 EQYTENLKVIVAEKLAGIPNFNEDIKYVAEYIVLLIVNGGTVESVVDELASLFDSVSRDTLANVVQTAFFALEALQQGESAENIVSKIRMMNAQSLG 100
                                    13        23        33        43        53        63        73        83        93

Chain C from PDB  Type:PROTEIN  Length:25
 aligned with GFD1_YEAST | Q04839 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:25
                                   135       145     
           GFD1_YEAST   126 TASKMKLLKKKIEEQREILQKTHHK 150
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 3lcn C 126 TASKMKLLKKKIEEQREILQKTHHK 150
                                   135       145

Chain D from PDB  Type:PROTEIN  Length:22
 aligned with GFD1_YEAST | Q04839 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:22
                                   138       148  
           GFD1_YEAST   129 KMKLLKKKIEEQREILQKTHHK 150
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 3lcn D 129 KMKLLKKKIEEQREILQKTHHK 150
                                   138       148

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (24, 27)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NAB2_YEAST | P32505)

molecular function
	GO:0008097	5S rRNA binding	Interacting selectively and non-covalently with 5S ribosomal RNA, the smallest RNA constituent of a ribosome.
	GO:0008312	7S RNA binding	Interacting selectively and non-covalently with 7S RNA, the RNA component of the signal recognition particle (SRP).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008143	poly(A) binding	Interacting selectively and non-covalently with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0033204	ribonuclease P RNA binding	Interacting selectively and non-covalently with the RNA subunit of ribonuclease P.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0006378	mRNA polyadenylation	The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
	GO:1900364	negative regulation of mRNA polyadenylation	Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation.
	GO:1900152	negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	Any process that stops, prevents or reduces the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.
	GO:0016973	poly(A)+ mRNA export from nucleus	The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
	GO:0045945	positive regulation of transcription from RNA polymerase III promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase III promoter.
	GO:0043488	regulation of mRNA stability	Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain C,D (GFD1_YEAST | Q04839)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys D:129 - Met D:130	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3lcn
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GFD1_YEAST \| Q04839
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	NAB2_YEAST \| P32505
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description

Compounds