3D9J - JenaLib

Title :   SNAPSHOTS OF THE RNA PROCESSING FACTOR SCAF8 BOUND TO DIFFERENT PHOSPHORYLATED FORMS OF THE CARBOXY-TERMINAL DOMAIN OF RNA-POLYMERASE II

Authors :   R. Becker, B. Loll, A. Meinhart

Date :   27 May 08 (Deposition) - 10 Jun 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Scaf8, Rna Polymerase Ii Ctd Interacting Domain, Arm Repeats, Phospho-Ctd, Phosphoprotein, Rna-Binding, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Becker, B. Loll, A. Meinhart
Snapshots Of The Rna Processing Factor Scaf8 Bound To Different Phosphorylated Forms Of The Carboxyl-Terminal Domain Of Rna Polymerase Ii.
J. Biol. Chem. V. 283 22659 2008
PubMed-ID: 18550522 | Reference-DOI: 10.1074/JBC.M803540200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 26)

Sites (26, 26)

Asymmetric Unit (26, 26)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:48 , PHE A:88 , ILE A:92 , THR A:95	BINDING SITE FOR RESIDUE NH4 A 301
02	AC2	SOFTWARE	PRO A:56 , GLU A:57 , LYS A:59 , ASP A:106	BINDING SITE FOR RESIDUE NH4 A 302
03	AC3	SOFTWARE	PHE A:77 , LYS A:81 , ASP A:133	BINDING SITE FOR RESIDUE NH4 A 303
04	AC4	SOFTWARE	ILE A:37 , SER A:73 , PHE A:77 , ASP A:82	BINDING SITE FOR RESIDUE NH4 A 304
05	AC5	SOFTWARE	ASP A:67 , ARG A:71 , LEU A:116 , TRP A:117	BINDING SITE FOR RESIDUE NH4 A 305
06	AC6	SOFTWARE	TYR A:12 , PHE A:50 , LYS A:53 , CYS A:54	BINDING SITE FOR RESIDUE NH4 A 306
07	AC7	SOFTWARE	ILE B:37 , SER B:73 , ASP B:82	BINDING SITE FOR RESIDUE NH4 B 307
08	AC8	SOFTWARE	ILE B:21 , SER B:22	BINDING SITE FOR RESIDUE NH4 B 308
09	AC9	SOFTWARE	LYS B:38 , PHE B:39 , TYR B:40 , LYS B:41	BINDING SITE FOR RESIDUE NH4 B 309
10	BC1	SOFTWARE	ILE B:37 , PHE B:77 , LYS B:81	BINDING SITE FOR RESIDUE NH4 B 310
11	BC2	SOFTWARE	TYR B:40 , PRO B:86	BINDING SITE FOR RESIDUE NH4 B 311
12	BC3	SOFTWARE	PRO B:20 , ILE B:21 , PRO B:61 , TYR B:64	BINDING SITE FOR RESIDUE NH4 B 312
13	BC4	SOFTWARE	LYS A:35 , ASN A:91 , SER A:94	BINDING SITE FOR RESIDUE SO4 A 2000
14	BC5	SOFTWARE	TYR A:40 , ARG A:87 , ASN A:90	BINDING SITE FOR RESIDUE SO4 A 2001
15	BC6	SOFTWARE	LYS A:41 , ARG A:87	BINDING SITE FOR RESIDUE SO4 A 2002
16	BC7	SOFTWARE	ARG A:71 , LEU A:116 , ASN A:120 , ALA B:136 , HIS B:140	BINDING SITE FOR RESIDUE SO4 A 2003
17	BC8	SOFTWARE	PRO A:20 , TYR A:64 , LYS A:109	BINDING SITE FOR RESIDUE SO4 A 2004
18	BC9	SOFTWARE	GLU A:10 , TYR A:17 , LYS A:25 , GLN A:28 , TYR B:12 , LYS B:49	BINDING SITE FOR RESIDUE SO4 A 2005
19	CC1	SOFTWARE	TYR B:40 , ARG B:87 , ASN B:90	BINDING SITE FOR RESIDUE SO4 B 2006
20	CC2	SOFTWARE	LYS B:41 , ARG B:87	BINDING SITE FOR RESIDUE SO4 B 2007
21	CC3	SOFTWARE	LYS B:35 , ASN B:91 , SER B:94	BINDING SITE FOR RESIDUE SO4 B 2008
22	CC4	SOFTWARE	PRO B:103 , GLY B:104	BINDING SITE FOR RESIDUE SO4 B 2009
23	CC5	SOFTWARE	GLN A:72 , HIS A:75 , GLN A:97 , ARG A:101	BINDING SITE FOR RESIDUE GOL A 1000
24	CC6	SOFTWARE	LYS A:31 , ARG A:101	BINDING SITE FOR RESIDUE GOL A 1001
25	CC7	SOFTWARE	TYR A:17 , ASN B:8 , TYR B:12 , SER B:46 , LYS B:49 , PHE B:50	BINDING SITE FOR RESIDUE GOL B 1002
26	CC8	SOFTWARE	LYS A:35 , ALA A:36 , ILE A:37 , LYS A:38 , SER A:89 , ASN A:90 , ILE A:127	BINDING SITE FOR RESIDUE GOL A 1003

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (5, 10)

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:137
 aligned with SCAF8_HUMAN | Q9UPN6 from UniProtKB/Swiss-Prot  Length:1271

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
          SCAF8_HUMAN     2 EAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAGI 138
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1aExon 1.3  PDB: A:11-38      Exon 1.4       Exon 1.5  PDB: A:54-107 UniProt: 54-107               Exon 1.6c  PDB: A:108-138       Transcript 1
                 3d9j A   2 EAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAAL 138
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain B from PDB  Type:PROTEIN  Length:140
 aligned with SCAF8_HUMAN | Q9UPN6 from UniProtKB/Swiss-Prot  Length:1271

    Alignment length:140
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
          SCAF8_HUMAN     2 EAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAGIPPP 141
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1aExon 1.3  PDB: B:11-38      Exon 1.4       Exon 1.5  PDB: B:54-107 UniProt: 54-107               Exon 1.6c  PDB: B:108-141          Transcript 1
                 3d9j B   2 EAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAALEHH 141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141

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 (0, 0)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SCAF8_HUMAN | Q9UPN6)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0043175	RNA polymerase core enzyme binding	Interacting selectively and non-covalently with an RNA polymerase core enzyme, containing a specific subunit composition defined as the core enzyme.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
cellular component
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.
	GO:0005681	spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NH4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]
		CC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Pro A:19 - Pro A:20	[ RasMol ]
		Pro B:19 - Pro B:20	[ RasMol ]

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

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3d9j
		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
	SCAF8_HUMAN \| Q9UPN6
		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

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

6404	BACKBONE ASSIGNMENT OF PCF11 CTD BINDING DOMAIN
1sz9	THE RNA POLYMERASE II CTD IN MRNA PROCESSING: BETA-TURN RECOGNITION AND BETA-SPIRAL
1sza	THE RNA POLYMERASE II CTD IN MRNA PROCESSING: BETA-TURN RECOGNITION AND BETA-SPIRAL
2bf0	CRYSTAL STRUCTURE OF THE RPR OF PCF11
3clj	STRUCTURE OF THE RNA POLYMERASE II CTD-INTERACTING DOMAIN OF NRD1
3d9i	SNAPSHOTS OF THE RNA PROCESSING FACTOR SCAF8 BOUND TO DIFFERENT PHOSPHORYLATED FORMS OF THE CARBOXY-TERMINAL DOMAIN OF RNA-POLYMERASE II
3d9k	SNAPSHOTS OF THE RNA PROCESSING FACTOR SCAF8 BOUND TO DIFFERENT PHOSPHORYLATED FORMS OF THE CARBOXY-TERMINAL DOMAIN OF RNA-POLYMERASE II (CTD PHOSPHORYLATED AT SER2 AND SER5)
3d9l	SNAPSHOTS OF THE RNA PROCESSING FACTOR SCAF8 BOUND TO DIFFERENT PHOSPHORYLATED FORMS OF THE CARBOXY-TERMINAL DOMAIN OF RNA-POLYMERASE II (CTD PHOSPHORYLATED AT SER2)
3d9m	SNAPSHOTS OF THE RNA PROCESSING FACTOR SCAF8 BOUND TO DIFFERENT PHOSPHORYLATED FORMS OF THE CARBOXY-TERMINAL DOMAIN OF RNA-POLYMERASE II (CTD PHOSPHORYLATED AT SER5)
3d9n	SNAPSHOTS OF THE RNA PROCESSING FACTOR SCAF8 BOUND TO DIFFERENT PHOSPHORYLATED FORMS OF THE CARBOXY-TERMINAL DOMAIN OF RNA-POLYMERASE II (CTD PHOSPHORYLATED AT SER2 AND SER7)
3d9o	SNAPSHOTS OF THE RNA PROCESSING FACTOR SCAF8 BOUND TO DIFFERENT PHOSPHORYLATED FORMS OF THE CARBOXY-TERMINAL DOMAIN OF RNA-POLYMERASE II (CTD UNPHOSPHORYLATED)
3d9p	SNAPSHOTS OF THE RNA PROCESSING FACTOR SCAF8 BOUND TO DIFFERENT PHOSPHORYLATED FORMS OF THE CARBOXY-TERMINAL DOMAIN OF RNA-POLYMERASE II (CTD PHOSPHORYLATED AT SER2 AND SER5)

Description