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(-) Description

Title :  MULTI-DOMAIN ORGANIZATION OF THE HNF4ALPHA NUCLEAR RECEPTOR COMPLEX ON DNA
 
Authors :  V. Chandra, P. Huang, Y. Kim, F. Rastinejad
Date :  13 Jan 13  (Deposition) - 20 Mar 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,I,J  (1x)
Biol. Unit 2:  E,F,G,H,K,L  (1x)
Keywords :  Transcription Factor, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Chandra, P. Huang, N. Potluri, D. Wu, Y. Kim, F. Rastinejad
Multidomain Integration In The Structure Of The Hnf-4 Alpha Nuclear Receptor Complex.
Nature V. 495 394 2013
PubMed-ID: 23485969  |  Reference-DOI: 10.1038/NATURE11966

(-) Compounds

Molecule 1 - HEPATOCYTE NUCLEAR FACTOR 4-ALPHA
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 55-377
    Gene: HNF4A, HNF4, NR2A1, TCF14
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HNF-4-ALPHA, NUCLEAR RECEPTOR SUBFAMILY 2 GROUP A MEMBER 1, TRANSCRIPTION FACTOR 14, TCF-14, TRANSCRIPTION FACTOR HNF-4
 
Molecule 2 - DNA (5'- D(*GP*GP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3')
    Chains: C, G
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*CP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*C)-3')
    Chains: D, H
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - NUCLEAR RECEPTOR COACTIVATOR 2
    Chains: I, J, K, L
    Engineered: YES
    Fragment: LXXLL MOTIF PEPTIDE (UNP RESIDUES 685-697)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NCOA-2, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75, BHLHE75, TRANSCRIPTIONAL INTERMEDIARY FACTOR 2, HTIF2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCD    IJ  
Biological Unit 2 (1x):     EFGH  KL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1MYR4Ligand/IonMYRISTIC ACID
2ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MYR2Ligand/IonMYRISTIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MYR2Ligand/IonMYRISTIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:181 , GLN A:185 , ARG A:226 , LEU A:236 , GLY A:237 , MET A:252 , GLN A:345BINDING SITE FOR RESIDUE MYR A 401
02AC2SOFTWARECYS A:51 , CYS A:54 , CYS A:68 , CYS A:71BINDING SITE FOR RESIDUE ZN A 402
03AC3SOFTWARECYS A:87 , CYS A:93 , CYS A:103 , CYS A:106BINDING SITE FOR RESIDUE ZN A 403
04AC4SOFTWAREVAL B:178 , SER B:181 , GLN B:185 , ARG B:226 , LEU B:236 , GLY B:237 , MET B:252BINDING SITE FOR RESIDUE MYR B 401
05AC5SOFTWARECYS B:51 , CYS B:54 , CYS B:68 , CYS B:71BINDING SITE FOR RESIDUE ZN B 402
06AC6SOFTWARECYS B:87 , CYS B:93 , CYS B:103 , CYS B:106BINDING SITE FOR RESIDUE ZN B 403
07AC7SOFTWAREVAL E:178 , SER E:181 , MET E:182 , GLN E:185 , ARG E:226 , LEU E:236 , GLY E:237 , MET E:252 , SER E:256 , ILE E:259BINDING SITE FOR RESIDUE MYR E 401
08AC8SOFTWARECYS E:51 , CYS E:54 , CYS E:68 , CYS E:71BINDING SITE FOR RESIDUE ZN E 402
09AC9SOFTWARECYS E:87 , CYS E:93 , CYS E:103 , CYS E:106BINDING SITE FOR RESIDUE ZN E 403
10BC1SOFTWARESER F:181 , GLN F:185 , ALA F:223 , ARG F:226 , MET F:252 , VAL F:255 , SER F:256 , ILE F:259 , ILE F:346BINDING SITE FOR RESIDUE MYR F 401
11BC2SOFTWARECYS F:51 , CYS F:54 , CYS F:68 , CYS F:71BINDING SITE FOR RESIDUE ZN F 402
12BC3SOFTWARECYS F:87 , CYS F:93 , CYS F:103 , CYS F:106BINDING SITE FOR RESIDUE ZN F 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IQR)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee..ee.hhhhhhhhhhhhhhh....................hhhhhhhhhhhh............hhhhhhhhhh...........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....eee.....eee.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4iqr A   49 ALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNEINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGG  368
                                    58        68        78        88        98       108       118     ||146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366  
                                                                                                     124|                                                                                                                                                                                                                                 
                                                                                                      143                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..eeehhhhhhhhhhhhhh..............hhhhh..hhhhhhhhhhh...............................hhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eee..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4iqr B   49 ALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERDRISTRRSSYEDSSLPSINALLQAEVLSDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGG  368
                                    58        68        78        88        98       108       118       128       138       148    || 170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360        
                                                                                                                                  153|                                                                                                                                                                                                          
                                                                                                                                   166                                                                                                                                                                                                          


Chain C from PDB  Type:DNA  Length:20
                                                     
                4iqr C 3001 GGAACTAGGTCAAAGGTCAG 3020
                                  3010      3020


Chain D from PDB  Type:DNA  Length:20
                                                     
                4iqr D 4000 CCTGACCTTTGACCTAGTTC 4019
                                  4009      4019


Chain E from PDB  Type:PROTEIN  Length:303
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee..ee.hhhhhhhhhhhhhhh....................hhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eee.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4iqr E   49 ALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNPSINALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGG  368
                                    58        68        78        88        98       108       118    || 145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365   
                                                                                                    123|                                                                                                                                                                                                                                   
                                                                                                     141                                                                                                                                                                                                                                   


Chain F from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee..ee.hhhhhhhhhhhhhh.....................hhhhhhhhhhhhh.hhhhh....................hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....eee..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4iqr F   49 ALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERDRISTRRSSYEDSSLPSINALLQAEVLSRSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGG  368
                                    58        68        78        88        98       108       118       128       138       148     ||164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364    
                                                                                                                                   154|                                                                                                                                                                                                               
                                                                                                                                    161                                                                                                                                                                                                               


Chain G from PDB  Type:DNA  Length:20
                                                     
                4iqr G 3001 GGAACTAGGTCAAAGGTCAG 3020
                                  3010      3020


Chain H from PDB  Type:DNA  Length:20
                                                     
                4iqr H 4000 CCTGACCTTTGACCTAGTTC 4019
                                  4009      4019


Chain I from PDB  Type:PROTEIN  Length:8
                                         
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                4iqr I  688 KILHRLLQ  695


Chain J from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                4iqr J  687 HKILHRLLQD  696
                                   696


Chain K from PDB  Type:PROTEIN  Length:8
                                         
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                4iqr K  688 KILHRLLQ  695


Chain L from PDB  Type:PROTEIN  Length:8
                                         
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                4iqr L  688 KILHRLLQ  695
   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 4IQR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (109, 119)

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  4iqr
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 Related Entries

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

UniProtKB/Swiss-Prot
        HNF4A_HUMAN | P41235: 1pzl 3cbb 3fs1 4b7w
        NCOA2_HUMAN | Q15596: 1gwq 1gwr 1m2z 1mv9 1mvc 1mzn 1p93 1t63 1t65 1uhl 1yok 1zdt 1zdu 1zky 2ao6 2b1v 2b1z 2b23 2fai 2g44 2g5o 2ldc 2p15 2p1t 2p1u 2p1v 2q7j 2q7l 2yjd 2zxz 2zy0 3a9e 3cld 3dzu 3dzy 3e00 3e7c 3e94 3erd 3fug 3gn8 3k22 3k23 3kwy 3kyt 3l0e 3l0j 3l0l 3o1d 3o1e 3oap 3ozj 3pcu 3plz 3q95 3q97 3r5m 3up0 3up3 4csj 4dos 4e2j 4fhh 4fhi 4ia1 4ia2 4ia3 4ia7 4iu7 4iui 4iv2 4iv4 4ivw 4ivy 4iw6 4iw8 4iwc 4iwf 4k4j 4k6i 4m8e 4m8h 4nie 4nqa 4oc7 4p6w 4p6x 4pld 4ple 4poh 4poj 4pp3 4pp5 4pp6 4ppp 4pps 4pxm 4q0a 4qe6 4qe8 4rfw 4rmc 4rmd 4rme 4ruo 4udc 4udd 4wg0 4zn7 4zn9 4znh 4zns 4znt 4znu 4znv 4znw 4zo1 4zsh 5aph 5apj 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 5ec9 5egv 5ehj 5ei1 5eit 5g3j 5g42 5g43 5g44 5g45 5g46 5g5w 5h1e 5hyr 5i4v 5iaw 5ick 5kcc 5kcd 5kce 5kcf 5kct 5kcu 5kcw 5kd9 5kr9 5kra 5krc 5krf 5krh 5kri 5krj 5krk 5krl 5krm 5kro 5l11 5lga 5syz 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 5u2d

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