Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  INTEGRATION HOST FACTOR/DNA COMPLEX
 
Authors :  P. A. Rice, S. -W. Yang, K. Mizuuchi, H. A. Nash
Date :  21 Aug 96  (Deposition) - 12 Feb 97  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Complex (Transcription Regulation-Dna), Transcription Factor, Beta Ribbon Motif, Dna Bending Protein, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Rice, S. Yang, K. Mizuuchi, H. A. Nash
Crystal Structure Of An Ihf-Dna Complex: A Protein-Induced Dna U-Turn.
Cell(Cambridge, Mass. ) V. 87 1295 1996
PubMed-ID: 8980235  |  Reference-DOI: 10.1016/S0092-8674(00)81824-3

(-) Compounds

Molecule 1 - DNA (35-MER)
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*GP*GP*CP*CP*AP*AP*AP*AP*AP*AP*GP*CP*AP*TP*T)- 3')
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*C P*AP*CP*C)-3')
    Chains: E
    Engineered: YES
    Synonym: IHF ALPHA CHAIN
    Synthetic: YES
 
Molecule 4 - PROTEIN (INTEGRATION HOST FACTOR (ALPHA) (IHF))
    Chains: A
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: IHF BETA CHAIN
 
Molecule 5 - PROTEIN (INTEGRATION HOST FACTOR (BETA) (IHF))
    Chains: B
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric/Biological Unit (1, 15)
No.NameCountTypeFull Name
1CD15Ligand/IonCADMIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU B:73 , HOH C:424 , DG E:30 , HOH E:425 , HOH E:662BINDING SITE FOR RESIDUE CD E 301
02AC2SOFTWARESER B:52 , HIS B:54 , HIS B:79 , HOH B:564 , HOH B:565BINDING SITE FOR RESIDUE CD B 302
03AC3SOFTWAREDG C:-49 , HOH C:710BINDING SITE FOR RESIDUE CD C 303
04AC4SOFTWARETHR B:60 , DT D:28 , HOH D:641 , HOH D:642BINDING SITE FOR RESIDUE CD D 304
05AC5SOFTWAREDG D:15 , HOH D:521 , HOH D:522BINDING SITE FOR RESIDUE CD D 305
06AC6SOFTWAREDG C:-18 , HOH C:519 , HOH C:525BINDING SITE FOR RESIDUE CD C 306
07AC7SOFTWAREGLU A:10 , ASP A:14BINDING SITE FOR RESIDUE CD A 307
08AC8SOFTWAREGLU A:25 , GLN B:14 , HIS B:16 , HOH B:533BINDING SITE FOR RESIDUE CD B 308
09AC9SOFTWAREDA D:24 , HOH D:450 , HOH D:456 , HOH D:457BINDING SITE FOR RESIDUE CD D 309
10BC1SOFTWAREGLU A:7 , GLU B:41BINDING SITE FOR RESIDUE CD B 310
11BC2SOFTWAREALA A:2 , GLU A:7 , HOH A:555 , GLU B:41BINDING SITE FOR RESIDUE CD A 311
12BC3SOFTWAREARG A:21 , ASP A:22BINDING SITE FOR RESIDUE CD A 312
13BC4SOFTWAREDA C:-41BINDING SITE FOR RESIDUE CD C 313
14BC5SOFTWAREDG C:-36 , HOH C:573 , HOH C:574BINDING SITE FOR RESIDUE CD C 314
15BC6SOFTWAREDG C:-18 , HOH C:520BINDING SITE FOR RESIDUE CD C 315

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IHF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IHF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IHF)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_LIKEPS00045 Bacterial histone-like DNA-binding proteins signature.IHFB_ECOLI47-66  1B:47-66
IHFA_ECOLI48-67  1A:48-67

(-) Exons   (0, 0)

(no "Exon" information available for 1IHF)

(-) 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:96
 aligned with IHFA_ECOLI | P0A6X7 from UniProtKB/Swiss-Prot  Length:99

    Alignment length:96
                                    11        21        31        41        51        61        71        81        91      
           IHFA_ECOLI     2 ALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPK  97
               SCOP domains d1ihfa_ A: Integration host factor alpha subunit (IHFA)                                          SCOP domains
               CATH domains 1ihfA00 A:2-97 HU Protein, subunit A                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....eee...eeeeeeee..eeee......eeee..eeeeeeee.hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ----------------------------------------------HISTONE_LIKE        ------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1ihf A   2 ALTKAEMSEYLFDKLGLSKRDAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEDIPITARRVVTFRPGQKLKSRVENASPK  97
                                    11        21        31        41        51        61        71        81        91      


Chain B from PDB  Type:PROTEIN  Length:94
 aligned with IHFB_ECOLI | P0A6Y1 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:94
                                    10        20        30        40        50        60        70        80        90    
           IHFB_ECOLI     1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG  94
               SCOP domains d1ihfb_ B: Integration host factor beta subunit (IHFB)                                         SCOP domains
               CATH domains 1ihfB00 B:1-94 HU Protein, subunit A                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....eee...eeeeeeee..eeee......eeee..eeeeeeee.hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------HISTONE_LIKE        ---------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 1ihf B   1 MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYG  94
                                    10        20        30        40        50        60        70        80        90    


Chain C from PDB  Type:DNA  Length:35
                                                                   
                 1ihf C -50 CGGTGCAACAAATTGATAAGCAATGCTTTTTTGGC -16
                                   -41       -31       -21     


Chain D from PDB  Type:DNA  Length:15
                                               
                 1ihf D  15 GGCCAAAAAAGCATT  29
                                    24     


Chain E from PDB  Type:DNA  Length:20
                                                    
                 1ihf E  30 GCTTATCAATTTGTTGCACC  49
                                    39        49
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IHF)

(-) Gene Ontology  (12, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IHFA_ECOLI | P0A6X7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain B   (IHFB_ECOLI | P0A6Y1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ihf)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ihf
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  IHFA_ECOLI | P0A6X7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  IHFB_ECOLI | P0A6Y1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  IHFA_ECOLI | P0A6X7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  IHFB_ECOLI | P0A6Y1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IHFA_ECOLI | P0A6X7: 1ouz 1owf 1owg 2ht0 2iie 2iif 5j0n
        IHFB_ECOLI | P0A6Y1: 1ouz 1owf 1owg 2ht0 2iie 2iif 5j0n

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1IHF)