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(-) Description

Title :  THE CRYSTAL STRUCTURE OF MLL1 (N3861I/Q3867L) IN COMPLEX WITH RBBP5 AND ASH2L
 
Authors :  Y. Li, M. Lei, Y. Chen
Date :  06 Dec 15  (Deposition) - 24 Feb 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,J
Keywords :  Histone Methyltransferase, Histone Methylation, Set Domain, Protein Complex, Protein Binding-Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Li, J. Han, Y. Zhang, F. Cao, Z. Liu, S. Li, J. Wu, C. Hu, Y. Wang, J. Shuai, J. Chen, L. Cao, D. Li, P. Shi, C. Tian, J. Zhang, Y. Dou, G. Li, Y. Chen, M. Lei
Structural Basis For Activity Regulation Of Mll Family Methyltransferases.
Nature V. 530 447 2016
PubMed-ID: 26886794  |  Reference-DOI: 10.1038/NATURE16952

(-) Compounds

Molecule 1 - RETINOBLASTOMA-BINDING PROTEIN 5
    Chains: J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B-SUMO
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 330-356
    Gene: RBBP5, RBQ3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RBBP-5,RETINOBLASTOMA-BINDING PROTEIN RBQ-3
 
Molecule 2 - SET1/ASH2 HISTONE METHYLTRANSFERASE COMPLEX SUBUNIT ASH2
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B-SUMO
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 380-496, 539-598
    Gene: ASH2L, ASH2L1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ASH2-LIKE PROTEIN
 
Molecule 3 - HISTONE-LYSINE N-METHYLTRANSFERASE 2A
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B-SUMO
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 3813-3969
    Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LYSINE N-METHYLTRANSFERASE 2A,ALL-1,CXXC-TYPE ZINC FINGER PROTEIN 7,MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA,MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA PROTEIN 1,TRITHORAX-LIKE PROTEIN,ZINC FINGER PROTEIN HRX

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:3838 , HIS A:3839 , GLY A:3840 , ARG A:3841 , ARG A:3903 , PHE A:3904 , ASN A:3906 , HIS A:3907 , TYR A:3944 , PRO A:3956 , CYS A:3957 , ASN A:3958 , LEU A:3968 , HOH A:4108 , HOH A:4156binding site for residue SAH A 4001
2AC2SOFTWARECYS A:3909 , CYS A:3957 , CYS A:3959 , CYS A:3964binding site for residue ZN A 4002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F6L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly B:485 -Pro B:486

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F6L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F6L)

(-) Exons   (0, 0)

(no "Exon" information available for 5F6L)

(-) 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:153
                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhheeeee.....eeeee........eeee...eeee..hhhhhhhhhhhh.....eee....eeee...eehhhhhhee.....eeeeeeee..eeeeeeee..........ee........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5f6l A 3814 LPMPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGIVIRSILTDKREKYYDSKGIGCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDKLPCNCGAKKCRKFLN 3969
                                  3823      3833      3843      3853      3863      3873      3883      3893      3903      3913      3923      3933      3943      3956      3966   
                                                                                                                                                                 3950|               
                                                                                                                                                                  3954               


Chain B from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....ee.....eee.....eeeee......eeeeeeeeeee.....eeeeeee...............eeeee.....eee..eee..........eeeeeeee.....eeeeee..eeeeeeee.......eeeeeee...eeeee..............ee.hhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5f6l B  285 SRVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEGSSEIIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTVSINFGPCFKYPPKDLTYRPMSDMG  504
                                   294       304       314       324       334       344       354       364       374       384       394     ||446       456       466       476       486       496        
                                                                                                                                             400|                                                             
                                                                                                                                              443                                                             


Chain J from PDB  Type:PROTEIN  Length:19
                                                    
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .ee....ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                5f6l J  336 FKELDENVEYEERESEFDI  354
                                   345
   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 5F6L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F6L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F6L)

(-) Gene Ontology  (72, 103)

Asymmetric/Biological Unit(hide GO term definitions)

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  ASH2L_HUMAN | Q9UBL3
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  KMT2A_HUMAN | Q03164
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  RBBP5_HUMAN | Q15291
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 Related Entries

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

UniProtKB/Swiss-Prot
        ASH2L_HUMAN | Q9UBL3: 3rsn 3s32 3toj 4riq 4x8n 4x8p 5f6k
        KMT2A_HUMAN | Q03164: 2agh 2j2s 2jyi 2kkf 2ku7 2kyu 2lxs 2lxt 2msr 2mtn 2w5y 2w5z 3eg6 3emh 3lqh 3lqi 3lqj 3p4f 3u85 3u88 4esg 4gq6 4nw3 5f5e
        RBBP5_HUMAN | Q15291: 3p4f 4x8n 4x8p 5f6k

(-) Related Entries Specified in the PDB File

5f59
5f5e THE SAME MLL1 PROTEIN IN APO FORM
5f6k