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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SPINDLIN1 BOUND TO HISTONE H3K4ME3 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 :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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
    Chains: A, C
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H3/M, HISTONE H3/O
    Synthetic: YES
 
Molecule 2 - SPINDLIN-1
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSFDUET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 50-262
    Gene: SPIN1, OCR, SPIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SP1, OVARIAN CANCER-RELATED PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
3MG1Ligand/IonMAGNESIUM ION
4MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3MG-1Ligand/IonMAGNESIUM ION
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3MG-1Ligand/IonMAGNESIUM ION
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5MRD-1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:8 , TRP B:62 , TRP B:72 , TYR B:98 , HOH B:432 , HOH B:434BINDING SITE FOR RESIDUE MRD B 301
2AC2SOFTWAREGLU B:171 , VAL B:242 , VAL B:255 , ASP B:257BINDING SITE FOR RESIDUE MPD B 302
3AC3SOFTWAREHOH B:414 , HOH B:428 , HOH B:431 , HOH D:421 , HOH D:422 , HOH D:428BINDING SITE FOR RESIDUE MG B 303
4AC4SOFTWAREARG B:152 , LYS B:172BINDING SITE FOR RESIDUE CL B 304
5AC5SOFTWARETRP D:62 , TRP D:72 , TYR D:98 , LEU D:100 , PHE D:251BINDING SITE FOR RESIDUE MPD D 301
6AC6SOFTWAREMET D:154 , GLU D:171 , HOH D:502 , HOH D:526BINDING SITE FOR RESIDUE MPD D 302
7AC7SOFTWAREARG B:152 , ARG D:152 , LYS D:172BINDING SITE FOR RESIDUE CL D 303
8AC8SOFTWARETRP D:165BINDING SITE FOR RESIDUE CL D 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MZG)

(-) 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: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
                 4mzg A   1 ARTkQTARK   9
                               |     
                               |     
                               4-M3L 


Chain B from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee.......eeeeeeeeee.......eeeee......eee.......eeeeeeeeee.......hhhhhhhhh..eeeeeee.....eeeeeeeeeee.......eeeee..eeeeeeehhhhhhhh..eee........eeeee.....eeeeeeeee......eeeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mzg B  48 SMRRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLV 259
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       213       223       233       243       253      
                                                                                                                                                                             195|                                               
                                                                                                                                                                              212                                               


Chain C from PDB  Type:PROTEIN  Length:6
                                      
               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
                 4mzg C   1 ARTkQT   6
                               |  
                               4-M3L


Chain D from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee.......eeeeeeeeeee..eeeeeeeee......eee.......eeeeee...........hhhhhhhhh..eeeeeee.....eeeeeeeeeee.......eeeee..eeeeeeehhhhhhhh..eee..........ee....eeeeee......eeeee.......eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mzg D  48 SMRRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDVDSLVGKQVEYRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLV 259
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       211       228       238       248       258 
                                                                                                                                                                             195|       220|                               
                                                                                                                                                                              210        228
   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 4MZG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 29)

Asymmetric Unit(hide GO term definitions)

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  4mzg
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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
        H32_HUMAN | Q71DI3: 2iij 2x4w 2x4x 2x4y 3av1 3db3 3mo8 3qo2 3r93 4mzf 4mzh 4ouc 5b0y 5b0z 5b40 5bo0 5ciu 5vac
        SPIN1_HUMAN | Q9Y657: 2ns2 4h75 4mzf 4mzh 5jsg 5jsj

(-) Related Entries Specified in the PDB File

4mzf 4mzh