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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SPINDLIN1 BOUND TO HISTONE H3(K4ME3-R8ME2A) PEPTIDE
 
Authors :  X. Su, X. Ding, H. Li
Date :  30 Sep 13  (Deposition) - 26 Mar 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Wnt Signal, Histone H3, Nuclear, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Su, G. Zhu, X. Ding, S. Y. Lee, Y. Dou, B. Zhu, W. Wu, H. Li
Molecular Basis Underlying Histone H3 Lysine-Arginine Methylation Pattern Readout By Spin/Ssty Repeats Of Spindlin1
Genes Dev. V. 28 622 2014
PubMed-ID: 24589551  |  Reference-DOI: 10.1101/GAD.233239.113

(-) Compounds

Molecule 1 - PEPTIDE FROM HISTONE H3.2
    ChainsA
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHISTONE H3/M, HISTONE H3/O
    SyntheticYES
 
Molecule 2 - SPINDLIN-1
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSFDUET
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 50-262
    GeneSPIN1, OCR, SPIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSP1, OVARIAN CANCER-RELATED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2DA21Mod. Amino AcidNG,NG-DIMETHYL-L-ARGININE
3M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:152 , LYS B:172BINDING SITE FOR RESIDUE CL B 301
2AC2SOFTWAREHIS B:234 , GLU B:237 , HOH B:413BINDING SITE FOR RESIDUE CL B 302
3AC3SOFTWAREHOH B:447 , HOH B:463 , HOH B:464BINDING SITE FOR RESIDUE MG B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MZF)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His B:43 -His B:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MZF)

(-) Sequences/Alignments

Asymmetric/Biological 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:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .ee...... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4mzf A   1 ARTkQTArK   9
                               |   | 
                               |   | 
                               4-M3L 
                                   8-DA2

Chain B from PDB  Type:PROTEIN  Length:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee.....eeeeeeee.....eeeeeeeeeee.......eeeee......eee.......eeeeeeeeee.......hhhhhhhhh..eeeeeee.....eeeeeeeeeee.......eeeee..eeeeeeehhhhhhhh..eee......eeeee.....eeeeeeeee......eeeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mzf B  39 GSSHHHHHHGSRRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLV 259
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188    || 216       226       236       246       256   
                                                                                                                                                                                    193|                                               
                                                                                                                                                                                     212                                               

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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 4MZF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    His B:43 - His B:44   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        H32_HUMAN | Q71DI32iij 2x4w 2x4x 2x4y 3av1 3db3 3mo8 3qo2 3r93 4mzg 4mzh 4ouc 5b0y 5b0z 5b40 5bo0 5ciu 5vac
        SPIN1_HUMAN | Q9Y6572ns2 4h75 4mzg 4mzh 5jsg 5jsj

(-) Related Entries Specified in the PDB File

4mzg 4mzh