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(-) Description

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 :  1.91
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

Molecule 1 - RNA-BINDING PROTEIN 16
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)-RIL
    Expression System Vector Type: PLASMID
    Fragment: CTD INTERACTING DOMAIN OF SCAF8, UNP RESIDUES 1-136
    Gene: RBM16, KIAA1116
    Mutation: YES
    Organism Common: MAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RNA-BINDING MOTIF PROTEIN 16

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric Unit (3, 21)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NH46Ligand/IonAMMONIUM ION
3SO411Ligand/IonSULFATE ION
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NH42Ligand/IonAMMONIUM ION
3SO46Ligand/IonSULFATE ION
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NH44Ligand/IonAMMONIUM ION
3SO45Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:35 , ASN A:91 , SER A:94BINDING SITE FOR RESIDUE SO4 A 146
02AC2SOFTWARETYR A:40 , LYS A:41 , ARG A:87 , ASN A:90BINDING SITE FOR RESIDUE SO4 A 147
03AC3SOFTWARELYS A:41 , ARG A:87BINDING SITE FOR RESIDUE SO4 A 148
04AC4SOFTWAREARG A:71 , LEU A:116 , ASN A:120 , ALA B:136 , HIS B:140BINDING SITE FOR RESIDUE SO4 A 149
05AC5SOFTWAREPRO A:20 , TYR A:64 , LYS A:109BINDING SITE FOR RESIDUE SO4 A 150
06AC6SOFTWAREGLU A:10 , LYS A:25 , TYR B:12BINDING SITE FOR RESIDUE SO4 A 151
07AC7SOFTWARETYR B:40 , ARG B:87 , ASN B:90BINDING SITE FOR RESIDUE SO4 B 146
08AC8SOFTWAREGLU B:2 , LYS B:41 , ARG B:87BINDING SITE FOR RESIDUE SO4 B 147
09AC9SOFTWARELYS B:35 , ASN B:91 , SER B:94BINDING SITE FOR RESIDUE SO4 B 148
10BC1SOFTWAREPRO B:103 , GLY B:104BINDING SITE FOR RESIDUE SO4 B 149
11BC2SOFTWARELYS B:124 , SER B:125BINDING SITE FOR RESIDUE SO4 B 150
12BC3SOFTWAREPHE A:77 , LYS A:81 , ASP A:133BINDING SITE FOR RESIDUE NH4 A 303
13BC4SOFTWAREILE A:37 , SER A:73 , PHE A:77 , ASP A:82BINDING SITE FOR RESIDUE NH4 A 304
14BC5SOFTWAREILE B:37 , SER B:73 , PHE B:77 , ASP B:82BINDING SITE FOR RESIDUE NH4 B 307
15BC6SOFTWARELYS B:38 , PHE B:39 , TYR B:40 , LYS B:41BINDING SITE FOR RESIDUE NH4 B 309
16BC7SOFTWARETYR B:40BINDING SITE FOR RESIDUE NH4 B 311
17BC8SOFTWAREPRO B:20 , ILE B:21 , PRO B:61 , TYR B:64BINDING SITE FOR RESIDUE NH4 B 312
18BC9SOFTWAREGLN A:72 , HIS A:75 , GLN A:97 , ARG A:101BINDING SITE FOR RESIDUE GOL A 1000
19CC1SOFTWAREASN B:8 , LEU B:11 , SER B:46 , LYS B:49 , PHE B:50BINDING SITE FOR RESIDUE GOL B 1001
20CC2SOFTWARELYS A:35 , ALA A:36 , ILE A:37 , LYS A:38 , SER A:89 , ASN A:90 , ILE A:127BINDING SITE FOR RESIDUE GOL A 1002
21CC3SOFTWARESER A:13 , ASP A:16 , LYS A:25 , ASN B:8BINDING SITE FOR RESIDUE GOL A 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D9I)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:19 -Pro A:20
2Pro B:19 -Pro B:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D9I)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CIDPS51391 CID domain profile.SCAF8_HUMAN1-139  1B:1-136
Biological Unit 1 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CIDPS51391 CID domain profile.SCAF8_HUMAN1-139  0-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CIDPS51391 CID domain profile.SCAF8_HUMAN1-139  1B:1-136

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003671781aENSE00001428900chr6:155054459-155055064606SCAF8_HUMAN1-10102A:2-10
B:1-10		9
10
1.3ENST000003671783ENSE00002165709chr6:155095123-15509520684SCAF8_HUMAN11-38282A:11-38
B:11-38		28
28
1.4ENST000003671784ENSE00002190306chr6:155099135-15509917945SCAF8_HUMAN39-53152A:39-53
B:39-53		15
15
1.5ENST000003671785ENSE00002183742chr6:155108995-155109156162SCAF8_HUMAN54-107542A:54-107
B:54-107		54
54
1.6cENST000003671786cENSE00001237781chr6:155113957-155114110154SCAF8_HUMAN108-159522A:108-139
B:108-140		32
33
1.7ENST000003671787ENSE00000813828chr6:155116143-155116273131SCAF8_HUMAN159-202440--
1.8ENST000003671788ENSE00001237766chr6:155123105-155123281177SCAF8_HUMAN203-261590--
1.9ENST000003671789ENSE00000813830chr6:155124678-15512475780SCAF8_HUMAN262-288270--
1.10ENST0000036717810ENSE00000813831chr6:155126503-155126620118SCAF8_HUMAN288-327400--
1.11ENST0000036717811ENSE00001237750chr6:155129204-155129335132SCAF8_HUMAN328-371440--
1.12ENST0000036717812ENSE00000813833chr6:155129820-155129932113SCAF8_HUMAN372-409380--
1.13ENST0000036717813ENSE00001237733chr6:155131149-155131342194SCAF8_HUMAN409-474660--
1.14ENST0000036717814ENSE00001375840chr6:155136850-155136950101SCAF8_HUMAN474-507340--
1.15ENST0000036717815ENSE00001190014chr6:155139613-155139726114SCAF8_HUMAN508-545380--
1.16ENST0000036717816ENSE00001237706chr6:155141311-155141467157SCAF8_HUMAN546-598530--
1.17bENST0000036717817bENSE00001237697chr6:155143410-155143543134SCAF8_HUMAN598-642450--
1.18ENST0000036717818ENSE00000813840chr6:155145368-155145512145SCAF8_HUMAN643-691490--
1.20ENST0000036717820ENSE00001237676chr6:155148306-15514837469SCAF8_HUMAN691-714240--
1.21ENST0000036717821ENSE00000813842chr6:155152056-155152274219SCAF8_HUMAN714-787740--
1.22bENST0000036717822bENSE00001812832chr6:155153073-1551551922120SCAF8_HUMAN787-12714850--

(-) 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:138
 aligned with SCAF8_HUMAN | Q9UPN6 from UniProtKB/Swiss-Prot  Length:1271

    Alignment length:138
                                    11        21        31        41        51        61        71        81        91       101       111       121       131        
          SCAF8_HUMAN     2 EAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAGIP 139
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE CID  PDB: - UniProt: 1-139                                                                                                                 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:108-139        Transcript 1
                 3d9i A   2 EAVKTFNSELYSLMDMKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAALE 139
                                    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
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
          SCAF8_HUMAN     1 MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAGIPP 140
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CID  PDB: B:1-136 UniProt: 1-139                                                                                                           - PROSITE
               Transcript 1 Exon 1.1a Exon 1.3  PDB: B:11-38      Exon 1.4       Exon 1.5  PDB: B:54-107 UniProt: 54-107               Exon 1.6c  PDB: B:108-140         Transcript 1
                 3d9i B   1 MEAVKTFNSELYSLMDMKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMAAALEH 140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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)

(no "SCOP Domain" information available for 3D9I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D9I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D9I)

(-) 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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        SCAF8_HUMAN | Q9UPN6: 2diw 3d9j 3d9k 3d9l 3d9m 3d9n 3d9o 3d9p

(-) Related Entries Specified in the PDB File

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3d9j 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)