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(-) Description

Title :  HUMAN RPRD1B CID IN COMPLEX WITH A RPB1-CTD DERIVED SER2 PHOSPHORYLATED PEPTIDE
 
Authors :  Z. Ni, C. Xu, W. Tempel, M. El Bakkouri, P. Loppnau, C. Bountra, C. H. Arr A. M. Edwards, J. Min, J. F. Greenblatt, Structural Genomics Consor (Sgc)
Date :  29 Apr 14  (Deposition) - 18 Jun 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Ni, C. Xu, X. Guo, G. O. Hunter, O. V. Kuznetsova, W. Tempel, E. Marcon G. Zhong, H. Guo, W. H. Kuo, J. Li, P. Young, J. B. Olsen, C. Wan, P. Loppnau, M. El Bakkouri, G. A. Senisterra, H. He, H. Huang, S. S. Sidhu, A. Emili, S. Murphy, A. L. Mosley, C. H. Arrowsmith, J. Min, J. F. Greenblatt
Rprd1A And Rprd1B Are Human Rna Polymerase Ii C-Terminal Domain Scaffolds For Ser5 Dephosphorylation.
Nat. Struct. Mol. Biol. V. 21 686 2014
PubMed-ID: 24997600  |  Reference-DOI: 10.1038/NSMB.2853

(-) Compounds

Molecule 1 - REGULATION OF NUCLEAR PRE-MRNA DOMAIN-CONTAINING PROTEIN 1B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15-MHL
    Expression System Strain: BL21-V2R-PRARE2
    Expression System Taxid: 562
    Gene: RPRD1B, C20ORF77, CREPT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL CYCLE-RELATED AND EXPRESSION-ELEVATED PROTEIN IN TUMOR
 
Molecule 2 - RPB1-CTD
    Chains: C, D
    Engineered: YES
    Other Details: SYNTHETIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  B D
Biological Unit 2 (1x): A C 
Biological Unit 3 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1NH22Mod. Amino AcidAMINO GROUP
2SEP2Mod. Amino AcidPHOSPHOSERINE
3SO43Ligand/IonSULFATE ION
4UNX19Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
2SEP1Mod. Amino AcidPHOSPHOSERINE
3SO41Ligand/IonSULFATE ION
4UNX9Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (4, 14)
No.NameCountTypeFull Name
1NH21Mod. Amino AcidAMINO GROUP
2SEP1Mod. Amino AcidPHOSPHOSERINE
3SO42Ligand/IonSULFATE ION
4UNX10Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 3 (4, 26)
No.NameCountTypeFull Name
1NH22Mod. Amino AcidAMINO GROUP
2SEP2Mod. Amino AcidPHOSPHOSERINE
3SO43Ligand/IonSULFATE ION
4UNX19Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:19 , HIS A:21 , SER A:22 , HOH A:306 , HOH A:312 , HOH A:322 , HOH A:334 , SER C:1628 , HOH C:1803BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWARESER A:3 , PHE A:4 , HIS A:33 , LYS A:35 , HIS A:36 , HOH A:301 , HOH A:309BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWARESER B:19 , HIS B:21 , SER B:22 , HOH B:303 , HOH B:304 , HOH B:311 , HOH B:326 , SER D:1628 , TYR D:1629 , HOH D:1808BINDING SITE FOR RESIDUE SO4 B 201

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:100 -B:100

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Q94)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q94)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q94)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q94)

(-) 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:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                4q94 A    2 SSFSESALEKKLSELSNSQHSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSME  130
                                    11        21        31        41        51        61        71        81        91       101       111       121         


Chain B from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                  
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                4q94 B    2 SSFSESALEKKLSELSNSQHSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSME  130
                                    11        21        31        41        51        61        71        81        91       101       111       121         


Chain C from PDB  Type:PROTEIN  Length:13
                                              
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                4q94 C 1619 SPSYsPTSPSYSx 1631
                                | 1628  |
                             1623-SEP   |
                                     1631-NH2


Chain D from PDB  Type:PROTEIN  Length:13
                                              
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                4q94 D 1619 SPSYsPTSPSYSx 1631
                                | 1628  |
                                |       |
                             1623-SEP   |
                                     1631-NH2
   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 4Q94)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q94)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q94)

(-) Gene Ontology  (14, 14)

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  RPR1B_HUMAN | Q9NQG5
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 Related Entries

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

UniProtKB/Swiss-Prot
        RPR1B_HUMAN | Q9NQG5: 4fla 4fu3 4hfg 4nad 4q96

(-) Related Entries Specified in the PDB File

4q96