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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SPINDLIN1 IN COMPLEX WITH A HISTONE H3K4(ME3) PEPTIDE
 
Authors :  N. Yang, W. Wang, Y. Wang, M. Wang, Q. Zhao, Z. Rao, B. Zhu, R. M. Xu
Date :  20 Sep 12  (Deposition) - 03 Oct 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tudor Domain, H3K4Me3 Binding, Methylation, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Yang, W. Wang, Y. Wang, M. Wang, Q. Zhao, Z. Rao, B. Zhu, R. M. Xu
Distinct Mode Of Methylated Lysine-4 Of Histone H3 Recognition By Tandem Tudor-Like Domains Of Spindlin1.
Proc. Natl. Acad. Sci. Usa V. 109 17954 2012
PubMed-ID: 23077255  |  Reference-DOI: 10.1073/PNAS.1208517109

(-) Compounds

Molecule 1 - SPINDLIN-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 27-262
    Gene: SPIN1, OCR, SPIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: OVARIAN CANCER-RELATED PROTEIN
 
Molecule 2 - HISTONE H3
    Chains: B
    Engineered: YES
    Fragment: H3K4(ME3) PEPTIDE (UNP RESIDUES 2-9)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
4SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:68 , VAL A:69 , SER A:121 , MET A:162 , ASN A:163 , THR A:164 , TRP A:165 , GLN A:180BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWARESER A:109 , ALA A:110 , HOH A:486BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREASP A:183 , ASP A:184 , GLU A:187 , HOH A:481 , ARG B:2BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWARETRP A:62 , GLU A:64 , TRP A:72 , LYS A:73 , TYR A:91 , LEU A:100 , PHE A:251 , HOH A:436 , HOH A:464 , HOH A:492 , ARG B:8BINDING SITE FOR RESIDUE NHE A 304
5AC5SOFTWAREGLN A:59 , THR B:6 , ALA B:7 , ARG B:8 , HOH B:211BINDING SITE FOR RESIDUE SO4 B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H75)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H75)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H75)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H75)

(-) Exons   (0, 0)

(no "Exon" information available for 4H75)

(-) 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:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeee.....eeeeeeeeeee.......eeeee......eee.......eeeeee...........hhhhhhhhh..eeeeeee.....eeeeeeeeeee.......eeeee..eeeeeeehhhhhhhh..eee........eeeeee...eeeeeeeeee......eeeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h75 A  45 PVSQPRRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLV 259
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194|      220       230       240       250         
                                                                                                                                                                               194|                                                
                                                                                                                                                                                211                                                


Chain B from PDB  Type:PROTEIN  Length:8
                                        
               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
                 4h75 B   1 ARTkQTAR   8
                               |    
                               4-M3L
   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 4H75)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H75)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H75)

(-) Gene Ontology  (16, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  SPIN1_HUMAN | Q9Y657
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q5TEC6_HUMAN | Q5TEC6: 2cnx 2co0 2v83 2v85 2v88 2v89 2vnf 2x0l
        SPIN1_HUMAN | Q9Y657: 2ns2 4mzf 4mzg 4mzh 5jsg 5jsj

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4H75)