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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PHF5A
 
Authors :  J. H. C. Tsai, T. Teng, P. Zhu, P. Fekkes, N. A. Larsen
Date :  10 Aug 16  (Deposition) - 07 Sep 16  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Core Component, Sf3B Complex, Human Spliceosome, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Teng, J. H. Tsai, X. Puyang, M. Seiler, S. Peng, S. Prajapati, D. Aird S. Buonamici, B. Caleb, B. Chan, L. Corson, J. Feala, P. Fekkes, B. Gerard, C. Karr, M. Korpal, X. Liu, J. T Lowe, Y. Mizui, J. Palacino, E. Park, P. G. Smith, V. Subramanian, Z. J. Wu, J. Zou, L. Yu, A. Chicas, M. Warmuth, N. Larsen, P. Zhu
Splicing Modulators Act At The Branch Point Adenosine Binding Pocket Defined By The Phf5A-Sf3B Complex.
Nat Commun V. 8 15522 2017
PubMed-ID: 28541300  |  Reference-DOI: 10.1038/NCOMMS15522

(-) Compounds

Molecule 1 - PHD FINGER-LIKE DOMAIN-CONTAINING PROTEIN 5A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21*
    Expression System Taxid: 562
    Gene: PHF5A
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PHD FINGER-LIKE DOMAIN PROTEIN 5A, SPLICING FACTOR 3B- ASSOCIATED 14 KDA PROTEIN, SF3B14B, P14B, RDS3 HOMOLOG

 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  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:11 , CYS A:46 , CYS A:49 , CYS A:85binding site for residue ZN A 201
02AC2SOFTWARECYS A:30 , CYS A:33 , CYS A:72 , CYS A:75binding site for residue ZN A 202
03AC3SOFTWARECYS A:23 , CYS A:26 , CYS A:58 , CYS A:61binding site for residue ZN A 203
04AC4SOFTWAREGLY A:16 , VAL A:17 , ASP A:47 , HOH A:309binding site for residue EDO A 204
05AC5SOFTWAREPHE A:10 , ARG A:12 , LYS A:80 , ASP A:83 , HOH A:302binding site for residue EDO A 205
06AC6SOFTWARECYS B:11 , CYS B:46 , CYS B:49 , CYS B:85binding site for residue ZN B 201
07AC7SOFTWARECYS B:30 , CYS B:33 , CYS B:72 , CYS B:75binding site for residue ZN B 202
08AC8SOFTWARECYS B:23 , CYS B:26 , CYS B:58 , CYS B:61binding site for residue ZN B 203
09AC9SOFTWAREPHE B:10 , ARG B:12 , LYS B:80 , ASP B:83 , HOH B:301binding site for residue EDO B 204
10AD1SOFTWAREGLY B:16 , VAL B:17 , ASP B:47binding site for residue EDO B 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5SYB)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:3 -His A:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5SYB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5SYB)

(-) Exons   (0, 0)

(no "Exon" information available for 5SYB)

(-) 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:90
                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee.......ee.ee................eeee.eehhhhhh...............ee.eeehhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  5syb A  2 AKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPSTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTIQEKDRDGCPKIVNL 91
                                    11        21        31        41        51        61        71        81        91


Chain B from PDB  Type:PROTEIN  Length:90
                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee.......ee.ee................eeee.ee.....hhhhh...........ee.eeehhhhhhhhhhhh...eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  5syb B  3 KHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPSTLVRICDECNYGSYQGRCVICGGPGVSDAYYCKECTIQEKDRDGCPKIVNLG 92
                                    12        22        32        42        52        62        72        82        92
   Legend:   → Mismatch (orange background)
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  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 5SYB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5SYB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5SYB)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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        PHF5A_HUMAN | Q7RTV0: 5ife

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