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(-) Description

Title :  STRUCTURE OF LSD1:COREST IN COMPLEX WITH SSRNA
 
Authors :  Z. Luka, L. V. Loukachevitch, W. J. Martin, C. Wagner, N. J. Reiter
Date :  16 Dec 14  (Deposition) - 27 Apr 16  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,D
Biol. Unit 1:  A,B,D  (4x)
Keywords :  Lsd1, Lysine Specific Demethylase, Demethylase, Demethylation, Rna, Corest, Rest Co-Repressor 1, Amine Oxidase, Coiled-Coil, Swirm, Chromatin Remodelling Enzyme, Epigenetics, Histone Modifying Enzyme, Non-Coding Rna, Ncrna, Kdm1A, Oxidoreductase-Transcription-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hirschi, W. J. Martin, Z. Luka, L. V. Loukachevitch, N. J. Reiter
G-Quadruplex Rna Binding And Recognition By The Lysine-Specific Histone Demethylase-1 Enzyme.
Rna V. 22 1250 2016
PubMed-ID: 27277658  |  Reference-DOI: 10.1261/RNA.057265.116

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A
    Chains: A
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P1
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 171-836
    Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: RECOMBINANT PLASMID (RESIDUES 171-852)
    Synonym: BRAF35-HDAC COMPLEX PROTEIN BHC110,FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2
 
Molecule 2 - REST COREPRESSOR 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 308-440
    Gene: RCOR1, KIAA0071, RCOR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: AMINO ACIDS RESIDUES 286-482, GIFT FROM DR. PHILLIP COLE.
    Synonym: PROTEIN COREST
 
Molecule 3 - RNA (5'-R(*UP*UP*AP*GP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABD
Biological Unit 1 (4x): ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL1Ligand/IonGLYCEROL
3SO45Ligand/IonSULFATE ION
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL4Ligand/IonGLYCEROL
3SO420Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:285 , GLY A:287 , VAL A:288 , SER A:289 , GLU A:308 , ALA A:309 , ARG A:310 , GLY A:314 , GLY A:315 , ARG A:316 , VAL A:317 , LEU A:329 , GLY A:330 , ALA A:331 , MET A:332 , VAL A:333 , THR A:588 , VAL A:590 , THR A:624 , LEU A:625 , PRO A:626 , VAL A:637 , TRP A:751 , TRP A:756 , SER A:760 , TYR A:761 , GLY A:800 , GLU A:801 , THR A:810 , VAL A:811 , ALA A:814 , HOH A:1003 , HOH A:1004 , HOH A:1011 , HOH A:1015binding site for residue FAD A 901
2AC2SOFTWARETRP A:751 , ASP A:754 , SO4 A:903binding site for residue SO4 A 902
3AC3SOFTWAREARG A:310 , ARG A:312 , SO4 A:902binding site for residue SO4 A 903
4AC4SOFTWARELYS A:374 , SER A:522 , ARG A:524binding site for residue SO4 A 904
5AC5SOFTWARESER A:687 , GLU A:690 , LEU B:389binding site for residue SO4 A 905
6AC6SOFTWARETHR A:189 , SER A:190binding site for residue SO4 A 906
7AC7SOFTWAREGLY A:409 , GLU A:413 , ARG A:526 , PHE A:533 , ARG A:688binding site for residue GOL A 907

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:240 -Pro A:241
2Pro A:470 -Pro A:471
3Gln A:633 -Pro A:634
4Val A:640 -Pro A:641

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XBF)

(-) 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:666
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhhhh....................eeeee..hhhhhhhhhhhhhh..eeeee...........eeee..eeee....ee.....hhhhhhhhhh...eee...............hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh............hhhhh.......eee....hhhhhhhhh...ee..eeeeeeeee..eeeeeeee..eeeeeeeeee.eeee..hhhhhhh.....eee...hhhhhhhhhhhee...eeeeee...........eee.............eee......eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee.............ee......hhhhhhhhh.................eee.hhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xbf A 171 PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTL 836
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830      


Chain B from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh............hhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xbf B 308 RKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE 440
                                   317       327       337       347       357       367       377       387       397       407       417       427       437   


Chain D from PDB  Type:DNA/RNA  Length:5
                                     
                 4xbf D   1 UUAGG   5
   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 4XBF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (71, 85)

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 Related Entries

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

UniProtKB/Swiss-Prot
        KDM1A_HUMAN | O60341: 2com 2dw4 2ejr 2h94 2hko 2iw5 2l3d 2uxn 2uxx 2v1d 2x0l 2xaf 2xag 2xah 2xaj 2xaq 2xas 2y48 2z3y 2z5u 3abt 3abu 3zms 3zmt 3zmu 3zmv 3zmz 3zn0 3zn1 4bay 4czz 4kum 4uv8 4uv9 4uva 4uvb 4uvc 4uxn 5afw 5h6q 5h6r 5it3 5l3b 5l3c 5l3d 5l3e 5l3f 5l3g 5lbq 5lgn 5lgt 5lgu 5lhg 5lhh 5lhi 5x60
        RCOR1_HUMAN | Q9UKL0: 2iw5 2uxn 2uxx 2v1d 2x0l 2xaf 2xag 2xah 2xaj 2xaq 2xas 2y48 3zms 3zmt 3zmu 3zmv 3zmz 3zn0 3zn1 4bay 4kum 4uv8 4uv9 4uva 4uvb 4uvc 4uxn 5h6q 5h6r 5l3b 5l3c 5l3d 5l3e 5l3f 5l3g 5lbq 5lgn 5lgt 5lgu 5lhg 5lhh 5lhi 5x60

(-) Related Entries Specified in the PDB File

4kum