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(-) Description

Title :  STRUCTURAL BASIS OF ESTROGEN RECEPTOR ALPHA METHYLATION MEDIATED BY HISTONE METHYLTRANSFERASE SMYD2
 
Authors :  Y. Jiang, L. Trescott, J. Holcomb, J. Brunzelle, N. Sirinupong, X. Shi,
Date :  20 Dec 13  (Deposition) - 26 Mar 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.82
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Histone Methyltransferase, Smyd2, Estrogen Receptor Er Alpha, Methylation, Estrogen Signaling, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Jiang, L. Trescott, J. Holcomb, X. Zhang, J. Brunzelle, N. Sirinupong, X. Shi, Z. Yang
Structural Insights Into Estrogen Receptor Alpha Methylatio By Histone Methyltransferase Smyd2, A Cellular Event Implicated In Estrogen Signaling Regulation.
J. Mol. Biol. V. 426 3413 2014
PubMed-ID: 24594358  |  Reference-DOI: 10.1016/J.JMB.2014.02.019

(-) Compounds

Molecule 1 - N-LYSINE METHYLTRANSFERASE SMYD2
    Chains: A
    EC Number: 2.1.1.-, 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KMT3C, SMYD2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HSKM-B, HISTONE METHYLTRANSFERASE SMYD2, LYSINE N- METHYLTRANSFERASE 3C, SET AND MYND DOMAIN-CONTAINING PROTEIN 2
 
Molecule 2 - ESTROGEN RECEPTOR
    Chains: B
    Engineered: YES
    Fragment: UNP RESIDUES 261-271
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synonym: ER, ER-ALPHA, ESTRADIOL RECEPTOR, NUCLEAR RECEPTOR SUBFAMILY 3 GROUP A MEMBER 1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1NI2Ligand/IonNICKEL (II) ION
2PE81Ligand/Ion3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4ZN3Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:52 , CYS A:55 , CYS A:74 , CYS A:78BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWARECYS A:65 , CYS A:68 , HIS A:86 , CYS A:90BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWARECYS A:209 , CYS A:262 , CYS A:264 , CYS A:267BINDING SITE FOR RESIDUE ZN A 503
4AC4SOFTWAREGLY A:16 , LYS A:17 , ARG A:19 , HIS A:137 , ASN A:182 , ALA A:203 , ASN A:206 , HIS A:207 , TYR A:240 , TYR A:258 , PHE A:260 , HOH A:615BINDING SITE FOR RESIDUE SAH A 504
5AC5SOFTWAREGLU A:190 , LYS A:309 , TYR A:344 , GLY A:348 , LEU A:351 , TRP A:356 , LYS A:387 , HOH A:661 , ARG B:269BINDING SITE FOR RESIDUE PE8 A 505
6AC6SOFTWARECYS A:13BINDING SITE FOR RESIDUE NI A 506
7AC7SOFTWARECYS A:210 , HOH A:665BINDING SITE FOR RESIDUE NI A 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O6F)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:284 -Pro A:285

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O6F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O6F)

(-) Exons   (0, 0)

(no "Exon" information available for 4O6F)

(-) 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:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.....eeeee........eeeeee..eeee.hhhh..............ee.......ee.hhhhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhh...hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhheeee.....eeeeeehhhhhh.ee.....eeeeee..eeeeee..........ee.......hhhhhhhhhhhhhh....hhhhhhh.hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o6f A   3 AEGLGGLERFCSPGKGRGLRALQPFQVGDLLFSCPAYAYVLTVNERGNHCEYCFTRKEGLSKCGRCKQAFYCNVECQKEDWPMHKLECSPMVVFGENWNPSETVRLTARILAKQKIHPERTPSEKLLAVKEFESHLDKLDNEKKDLIQSDIAALHHFYSKHLEFPDNDSLVVLFAQVNCNGFTIEDEELSHLGSAIFPDVALMNHSCCPNVIVTYKGTLAEVRAVQEIKPGEEVFTSYIDLLYPTEDRNDRLRDSYFFTCECQECTTKDKDKAKVEIRKLSDPPKAEAIRDMVRYARNVIEEFRRAKHYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALQYGQKIIKPYSKHYPLYSLNVASMWLKLGRLYMGLEHKAAGEKALKKAIAIMEVAHGKDHPYISEIKQEIES 432
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432


Chain B from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4o6f B 262 GRMLKHKRQR 271
                                   271
   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 4O6F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O6F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O6F)

(-) Gene Ontology  (116, 124)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:284 - Pro A:285   [ RasMol ]  
 

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  SMYD2_HUMAN | Q9NRG4
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 Related Entries

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

UniProtKB/Swiss-Prot
        ESR1_HUMAN | P03372: 1a52 1akf 1ere 1err 1g50 1gwq 1gwr 1hcp 1hcq 1l2i 1pcg 1qkt 1qku 1r5k 1sj0 1uom 1x7e 1x7r 1xp1 1xp6 1xp9 1xpc 1xqc 1yim 1yin 1zky 2ayr 2b1v 2b1z 2b23 2bj4 2fai 2g44 2g5o 2i0j 2iog 2iok 2jf9 2jfa 2llo 2llq 2ocf 2ouz 2p15 2pog 2q6j 2q70 2qa6 2qa8 2qab 2qe4 2qgt 2qgw 2qh6 2qr9 2qse 2qxm 2qxs 2qzo 2r6w 2r6y 2yat 2yja 3cbm 3cbo 3cbp 3dt3 3erd 3ert 3hlv 3hm1 3l03 3os8 3os9 3osa 3q95 3q97 3uu7 3uua 3uuc 3uud 4aa6 4dma 4iu7 4iui 4iv2 4iv4 4ivw 4ivy 4iw6 4iw8 4iwc 4iwf 4jc3 4jdd 4mg5 4mg6 4mg7 4mg8 4mg9 4mga 4mgb 4mgc 4mgd 4pp6 4ppp 4pps 4pxm 4q13 4q50 4tuz 4tv1 4xi3 4zn7 4zn9 4znh 4zns 4znt 4znu 4znv 4znw 5aau 5aav 5acc 5ak2 5di7 5did 5die 5dig 5dk9 5dkb 5dke 5dkg 5dks 5dl4 5dlr 5dmc 5dmf 5dp0 5drj 5drm 5dtv 5du5 5due 5dug 5duh 5dvs 5dvv 5dwe 5dwg 5dwi 5dwj 5dx3 5dxb 5dxe 5dxg 5dxk 5dxm 5dxp 5dxq 5dxr 5dy8 5dyb 5dyd 5dz0 5dz1 5dz3 5dzh 5dzi 5e0w 5e0x 5e14 5e15 5e19 5e1c 5egv 5ehj 5ei1 5eit 5fqp 5fqr 5fqs 5fqt 5fqv 5hyr 5jmm 5kcc 5kcd 5kce 5kcf 5kct 5kcu 5kcw 5kd9 5kr9 5kra 5krc 5krf 5krh 5kri 5krj 5krk 5krl 5krm 5kro 5n10 5t0x 5t92 5t97 5tld 5tlf 5tlg 5tll 5tlm 5tlo 5tlp 5tlt 5tlu 5tlv 5tlx 5tly 5tm1 5tm2 5tm3 5tm4 5tm5 5tm6 5tm7 5tm8 5tm9 5tml 5tmm 5tmo 5tmq 5tmr 5tms 5tmt 5tmu 5tmv 5tmw 5tmz 5tn1 5tn3 5tn4 5tn5 5tn6 5tn7 5tn8 5tn9 5tnb 5u2b 5u2d
        SMYD2_HUMAN | Q9NRG4: 3rib 3s7b 3s7d 3s7f 3s7j 3tg4 3tg5 4wuy 4ynd 5arf 5arg 5kjk 5kjl 5kjm 5kjn

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4O6F)