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(-) Description

Title :  CRYSTAL STRUCTURE OF HNF-6ALPHA DNA-BINDING DOMAIN IN COMPLEX WITH THE TTR PROMOTER
 
Authors :  D. Iyaguchi, M. Yao, N. Watanabe, J. Nishihira, I. Tanaka
Date :  07 Nov 05  (Deposition) - 05 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Transcription Factor, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Iyaguchi, M. Yao, N. Watanabe, J. Nishihira, I. Tanaka
Dna Recognition Mechanism Of The Onecut Homeodomain Of Transcription Factor Hnf-6
Structure V. 15 75 2007
PubMed-ID: 17223534  |  Reference-DOI: 10.1016/J.STR.2006.11.004

(-) Compounds

Molecule 1 - 5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3'
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3'
    Chains: D, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - HEPATOCYTE NUCLEAR FACTOR 6
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-156
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: HNF-6, ONE CUT DOMAIN FAMILY MEMBER 1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:101 , HOH B:4010 , HOH E:187 , DA E:2010 , DT E:2011 , DT F:2020 , DG F:2021BINDING SITE FOR RESIDUE ACT E 3001
2AC2SOFTWAREPHE A:144 , ASN A:147 , ARG A:151 , DT D:1020 , DG D:1021BINDING SITE FOR RESIDUE ACT D 3002
3AC3SOFTWAREHIS B:113 , PHE B:144 , ASN B:147 , ALA B:148 , ARG B:151 , DT F:2020 , DG F:2021BINDING SITE FOR RESIDUE GOL B 4001
4AC4SOFTWAREPRO A:69 , PHE A:71 , HOH A:173 , ASP B:106 , VAL B:107 , ARG B:110BINDING SITE FOR RESIDUE GOL B 4002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D5V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D5V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D5V)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_2PS50071 'Homeobox' domain profile.HNF6_RAT383-443
 		  2A:100-155
B:100-155
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_2PS50071 'Homeobox' domain profile.HNF6_RAT383-443
 		  1A:100-155
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_2PS50071 'Homeobox' domain profile.HNF6_RAT383-443
 		  1-
B:100-155

(-) Exons   (0, 0)

(no "Exon" information available for 2D5V)

(-) 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:135
 aligned with HNF6_RAT | P70512 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:155
                                   298       308       318       328       338       348       358       368       378       388       398       408       418       428       438     
            HNF6_RAT    289 MEEINTKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQRMSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDK  443
               SCOP domains d2d5va1 A:1-79 automated matches                                               --------------------d2d5va2 A:100-155 automated matches                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--------------------.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------HOMEOBOX_2  PDB: A:100-155 UniProt: 383-443                   PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2d5v A    1 MEEINTKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQRMSALRL--------------------PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDK  155
                                    10        20        30        40        50        60        70        |-         -       100       110       120       130       140       150     
                                                                                                         79                  100                                                       


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with HNF6_RAT | P70512 from UniProtKB/Swiss-Prot  Length:465

    Alignment length:155
                                   298       308       318       328       338       348       358       368       378       388       398       408       418       428       438     
            HNF6_RAT    289 MEEINTKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQRMSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDK  443
               SCOP domains d2d5vb1 B:1-79 automated matches                                               --------------------d2d5vb2 B:100-155 automated matches                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--------------------.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------HOMEOBOX_2  PDB: B:100-155 UniProt: 383-443                   PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2d5v B    1 MEEINTKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQRMSALRL--------------------PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDK  155
                                    10        20        30        40        50        60        70        |-         -       100       110       120       130       140       150     
                                                                                                         79                  100                                                       


Chain C from PDB  Type:DNA  Length:14
                                               
                2d5v C 1001 TCTAAGTCAATAAT 1014
                                  1010    


Chain D from PDB  Type:DNA  Length:13
                                              
                2d5v D 1015 ATTATTGACTTAG 1027
                                  1024   


Chain E from PDB  Type:DNA  Length:14
                                               
                2d5v E 2001 TCTAAGTCAATAAT 2014
                                  2010    


Chain F from PDB  Type:DNA  Length:12
                                             
                2d5v F 2015 ATTATTGACTTA 2026
                                  2024
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D5V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D5V)

(-) Gene Ontology  (11, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HNF6_RAT | P70512)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    GO:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048731    system development    The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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