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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN JMJD2D/KDM4D IN COMPLEX WITH AN H3K9ME3 PEPTIDE AND 2-OXOGLUTARATE
 
Authors :  S. Krishnan, R. C. Trievel
Date :  22 Oct 12  (Deposition) - 21 Nov 12  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,F,G
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,G  (1x)
Keywords :  Jumonji C Demethylase, Jmjd2/Kdm4 Family, Beta Barrel Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Krishnan, R. C. Trievel
Structural And Functional Analysis Of Jmjd2D Reveals Molecular Basis For Site-Specific Demethylation Among Jmjd2 Demethylases.
Structure V. 21 98 2013
PubMed-ID: 23219879  |  Reference-DOI: 10.1016/J.STR.2012.10.018

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4D
    Chains: A, B
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHT4
    Expression System Strain: BL21(ROSETTA 2)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 12-341
    Gene: JHDM3D, JMJD2D, KDM4D
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, JUMONJI DOMAIN-CONTAINING PROTEIN 2D
 
Molecule 2 - HISTONE H3 PEPTIDE
    Chains: F, G
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABFG
Biological Unit 1 (1x): A F 
Biological Unit 2 (1x):  B G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 31)

Asymmetric Unit (7, 31)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
3NI2Ligand/IonNICKEL (II) ION
4NO312Ligand/IonNITRATE ION
5PDO5Ligand/Ion1,3-PROPANDIOL
6SCN6Ligand/IonTHIOCYANATE ION
7ZN2Ligand/IonZINC ION
Biological Unit 1 (5, 17)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3NI-1Ligand/IonNICKEL (II) ION
4NO38Ligand/IonNITRATE ION
5PDO4Ligand/Ion1,3-PROPANDIOL
6SCN3Ligand/IonTHIOCYANATE ION
7ZN-1Ligand/IonZINC ION
Biological Unit 2 (5, 10)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
3NI-1Ligand/IonNICKEL (II) ION
4NO34Ligand/IonNITRATE ION
5PDO1Ligand/Ion1,3-PROPANDIOL
6SCN3Ligand/IonTHIOCYANATE ION
7ZN-1Ligand/IonZINC ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:136 , PHE A:189 , HIS A:192 , GLU A:194 , SER A:200 , ASN A:202 , LYS A:210 , TRP A:212 , HIS A:280 , NI A:402 , PDO A:415 , HOH A:507 , M3L F:9 , HOH F:101BINDING SITE FOR RESIDUE AKG A 401
02AC2SOFTWAREHIS A:192 , GLU A:194 , HIS A:280 , AKG A:401 , HOH A:507BINDING SITE FOR RESIDUE NI A 402
03AC3SOFTWARECYS A:238 , HIS A:244 , CYS A:310 , CYS A:312BINDING SITE FOR RESIDUE ZN A 403
04AC4SOFTWARELYS A:150 , GLN A:151 , SCN A:406BINDING SITE FOR RESIDUE SCN A 404
05AC5SOFTWAREGLU A:27BINDING SITE FOR RESIDUE SCN A 405
06AC6SOFTWARELYS A:58 , THR A:149 , SCN A:404BINDING SITE FOR RESIDUE SCN A 406
07AC7SOFTWAREGLU A:224 , ALA A:240 , PHE A:241 , LEU A:242 , HOH A:664 , HOH A:683BINDING SITE FOR RESIDUE NO3 A 407
08AC8SOFTWARELYS A:305 , ARG A:332 , LEU A:335 , TRP A:336 , HOH A:549 , ASP B:302 , MET B:306BINDING SITE FOR RESIDUE NO3 A 408
09AC9SOFTWARELYS A:305 , MET A:321 , TRP A:336 , GLN A:340 , HOH A:630 , HOH A:652BINDING SITE FOR RESIDUE NO3 A 409
10BC1SOFTWAREASP A:302 , MET A:306 , HOH A:602 , HOH A:697 , LYS B:305 , ARG B:332 , LEU B:335 , TRP B:336BINDING SITE FOR RESIDUE NO3 A 410
11BC2SOFTWAREGLU A:314 , ALA A:315 , ARG A:316 , VAL A:317 , ALA F:7 , ARG F:8BINDING SITE FOR RESIDUE NO3 A 411
12BC3SOFTWAREPRO A:113 , LYS A:124 , ASN A:128 , TRP A:185 , LYS A:186 , HOH A:510BINDING SITE FOR RESIDUE NO3 A 412
13BC4SOFTWAREHOH A:720BINDING SITE FOR RESIDUE NO3 A 413
14BC5SOFTWARESER A:67 , VAL A:98 , GLY A:99 , ARG A:102BINDING SITE FOR RESIDUE NO3 A 414
15BC6SOFTWAREPHE A:189 , ALA A:190 , HIS A:192 , LYS A:245 , AKG A:401 , HOH A:507 , HOH A:537 , SER F:10 , THR F:11 , HOH F:101BINDING SITE FOR RESIDUE PDO A 415
16BC7SOFTWARETHR A:87 , TYR A:89 , PHE A:231 , PRO A:232 , HOH A:536 , HOH A:561BINDING SITE FOR RESIDUE PDO A 416
17BC8SOFTWAREGLY A:142 , SER A:143BINDING SITE FOR RESIDUE PDO A 417
18BC9SOFTWAREMET A:19 , ILE A:20 , ILE B:20 , PHE B:21 , HIS B:22 , TYR B:34 , HOH B:570BINDING SITE FOR RESIDUE PDO A 418
19CC1SOFTWARETYR B:136 , PHE B:189 , HIS B:192 , GLU B:194 , SER B:200 , ASN B:202 , LYS B:210 , TRP B:212 , HIS B:280 , ALA B:292 , NI B:402 , HOH B:508 , HOH B:524 , M3L G:9BINDING SITE FOR RESIDUE AKG B 401
20CC2SOFTWAREHIS B:192 , GLU B:194 , HIS B:280 , AKG B:401 , HOH B:508BINDING SITE FOR RESIDUE NI B 402
21CC3SOFTWARECYS B:238 , HIS B:244 , CYS B:310 , CYS B:312BINDING SITE FOR RESIDUE ZN B 403
22CC4SOFTWAREARG B:60 , ASN B:65BINDING SITE FOR RESIDUE SCN B 404
23CC5SOFTWARELYS B:58 , THR B:149 , HOH B:655BINDING SITE FOR RESIDUE SCN B 405
24CC6SOFTWAREGLU A:68 , LYS B:124 , ASN B:128 , HOH B:576BINDING SITE FOR RESIDUE SCN B 406
25CC7SOFTWAREGLU B:224 , ALA B:240 , PHE B:241 , LEU B:242BINDING SITE FOR RESIDUE NO3 B 407
26CC8SOFTWAREPRO A:217 , GLU A:218 , TYR A:277 , TYR A:303 , HOH A:625 , ASP B:334 , LEU B:335 , ARG B:338BINDING SITE FOR RESIDUE NO3 B 408
27CC9SOFTWAREASP A:334 , LEU A:335 , ARG A:338 , PRO B:217 , GLU B:218 , TYR B:277 , TYR B:303 , HOH B:594BINDING SITE FOR RESIDUE NO3 B 409
28DC1SOFTWARELYS B:124 , ASN B:128 , TRP B:185 , LYS B:186 , HOH B:521 , HOH B:584BINDING SITE FOR RESIDUE NO3 B 410
29DC2SOFTWAREILE B:140 , SER B:143BINDING SITE FOR RESIDUE PDO B 411

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HON)

(-) 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:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee...hhhhhhhhhhhhhhhhhhhhhh.eeee..................ee...eeeeeeee..eeeeeeee...eehhhhhhhhh..........hhhhhhhhhhhh......eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhh........hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee.hhhhhhhhhhh.............hhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hon A  12 QNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQD 341
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341


Chain B from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee...hhhhhhhhhhhhhhhhhhhhhh.eeee.............hhhh.ee...eeeeeeee..eeeeeeee...eehhhhhhhhhh.........hhhhhhhhhhhh......eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhh.hhhhhh.hhhhhh.eeehhhhhhhh....eeeee....eeee....eeeeee...eeeeeeee.hhhhhhhhhhh.............hhhhhhhhh..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hon B  12 QNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQD 341
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341


Chain F 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
                 4hon F   6 TARkSTGGKA  15
                               |    15
                               9-M3L  


Chain G from PDB  Type:PROTEIN  Length:7
                                       
               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
                 4hon G   7 ARkSTGG  13
                              |    
                              9-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 4HON)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (44, 46)

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  4hon
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  H31_HUMAN | P68431
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  KDM4D_HUMAN | Q6B0I6
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  1.14.11.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        H31_HUMAN | P68431: 1cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
        KDM4D_HUMAN | Q6B0I6: 3dxt 3dxu 4d6q 4d6r 4d6s 4hoo 5f5a 5f5c 5fp4 5fp7 5fp8 5fp9 5fpa 5fpb 5ph0 5ph1 5ph2 5ph3 5ph4 5ph5 5ph6 5ph7 5ph8 5ph9 5pha 5phb 5phc 5phd 5phe 5phf 5phg 5phh 5phi 5phj 5phk 5phl 5phm 5phn 5pho 5php 5phq 5phr 5phs 5pht 5phu 5phv 5phw 5phx 5phy 5phz 5pi0 5pi1 5pi2 5pi3 5pi4 5pi5 5pi6 5pi7 5pi8 5pi9 5pia 5pib 5pic 5pid 5pie 5pif 5pig 5pih 5pii 5pij 5pik 5pil 5pim 5pin 5pio 5pip 5piq 5pir 5pis 5pit 5piu 5piv 5piw 5pix 5piy 5piz 5pj0 5pj1 5pj2 5pj3 5pj4 5pj5 5pj6 5pj7 5pj8 5pj9 5pja 5pjb 5pjc 5pjd 5pje 5pjf 5pjg 5pjh 5pji 5pjj 5pjk 5pjl 5pjm 5pjn 5pjo 5pjp 5pjq 5pjr 5pjs 5pjt 5pju 5pjv 5pjw 5pjx 5pjy 5pjz 5pk0 5pk1 5pk2 5pk3 5pk4 5pk5 5pk6 5pk7 5pk8 5pk9 5pka 5pkb 5pkc 5pkd 5pke 5pkf 5pkg 5pkh 5pki 5pkj 5pkk 5pkl 5pkm 5pkn 5pko 5pkp 5pkq 5pkr 5pks 5pkt 5pku 5pkv 5pkw 5pkx 5pky 5pkz 5pl0 5pl1 5pl2 5pl3 5pl4 5pl5 5pl6 5pl7 5pl8 5pl9 5pla 5plb 5plc 5pld 5ple 5plf 5plg 5plh 5pli 5plj 5plk 5pll 5plm 5pln 5plo 5plp 5plq 5plr 5pls 5plt 5plu 5plv 5plw 5plx 5ply 5plz 5pm0 5pm1 5pm2 5pm3 5pm4 5pm5 5pm6 5pm7 5pm8 5pm9 5pma 5pmb 5pmc 5pmd 5pme 5pmf 5pmg 5pmh 5pmi 5pmj 5pmk 5pml 5pmm 5pmn 5pmo 5pmp 5pmq 5pmr 5pms 5pmt 5pmu 5pmv 5pmw 5pmx 5pmy 5pmz 5pn0 5pn1 5pn2 5pn3 5pn4 5pn5 5pn6 5pn7 5pn8 5pn9 5pna 5pnb 5pnc 5pnd 5pne 5pnf 5png 5pnh 5pni 5pnj 5pnk 5pnl 5pnm 5pnn 5pno 5pnp 5pnq 5pnr 5pns 5pnu 5pnv 5pnw

(-) Related Entries Specified in the PDB File

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