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Intramural Research > Online Research Resources > Homeodomain Resource

Structures of homeodomain proteins and protein-DNA complexes

The following table contains information on solved three-dimensional structures of both homeodomain proteins and protein-DNA complexes. The homeodomain structures are manually compiled from the NCBI Entrez Structure database. Each entry in the table below was inspected to assure that the solved structure contains the homeodomain region of the protein.

Each entry is cross-linked to the corresponding entries in both PDB and NCBI Entrez. Users can follow the Entrez links to view the Entrez Structure record for an entry of interest. The Entrez Structure records contain links to manuscripts in PubMed that describe how these structures were experimentally determined. Users can follow the PDB links to view still images and download the three-dimensional coordinates of a structure of interest.

PDB Entrez (MMDB) Descriptor Experimental Technique Source Title Publication Year
2H1K 45003 Pdx1 X-RAY DIFFRACTION Mesocricetus auratus Structural basis for induced fit mechanisms in DNA recognition by the pdx1 homeodomain 2007
2P81 46519 Engrailed NMR, 25 STRUCTURES Drosophila melanogaster The helix-turn-helix motif as an ultrafast independently folding domain: The pathway of folding of Engrailed homeodomain. 2007
1ZQ3 37491 Bicoid Homeodomain NMR, 20 STRUCTURES Drosophila melanogaster The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site. 2006
2HI3 43356 homeodomain-only protein HOP NMR, 20 STRUCTURES Mus musculus Analysis of the structure and function of the transcriptional coregulator HOP 2006
2HOS 43361 Engrailed homeodomain X-RAY DIFFRACTION Drosophila melanogaster Structure and properties of a re-engineered homeodomain protein-DNA interface. 2006
2HOT 43362 Engrailed homeodomain X-RAY DIFFRACTION Drosophila melanogaster Structure and properties of a re-engineered homeodomain protein-DNA interface. 2006
1XPX 32857 Prospero X-RAY DIFFRACTION Drosophila melanogaster Structural Basis of Prospero-DNA Interaction: Implications for Transcription Regulationin Developing Cells. 2005
1YZ8 32985 PITX2 NMR, 20 STRUCTURES Homo sapiens Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome. 2005
1ZTR 35559 Engrailed homeodomain L16A mutant NMR, 25 STRUCTURES Drosophila melanogaster Solution structure of a protein denatured state and folding intermediate. 2005
1S7E 30852 HNF-6 NMR, 20 STRUCTURES Mus Musculus Structure of the Hepatocyte Nuclear Factor 6Alpha and its Interaction with DNA. 2004
1WH5 30558 Zf-Hd Homeobox Family Protein NMR, 20 STRUCTURES Arabidopsis thaliana Solution Structure Of Homeobox Domain Of Arabidopsisthaliana Zinc Finger Homeobox Family Protein 2004
1WI3 30585 SATB2 NMR, 20 STRUCTURES Homo sapiens Solution structure of the homeodomain of KIAA1034 protein 2004
1LFU 21702 Pbx NMR Mus Musculus Lock and Key Binding of the Hox Ypwm Peptide to the Pbx Homeodomain 2003
1MH3 20725 Maltose Binding-A1 Homeodomain Protein X-RAY DIFFRACTION Saccharomyces cerevisiae Insights Into Binding Cooperativity of MATa1/MATalpha2 from the Crystal Structure of a MATa1 Homeodomain-Maltose Binding Protein Chimera 2003
1MH4 20726 Maltose Binding-A1 Homeodomain Protein X-RAY DIFFRACTION Saccharomyces cerevisiae Insights Into Binding Cooperativity of MATa1/MATalpha2 from the Crystal Structure of a MATa1 Homeodomain-Maltose Binding Protein Chimera 2003
1P7I 25046 ENGRAILED MUTANT X-RAY DIFFRACTION Drosophila melanogaster Crystal Structures of Engrailed Homeodomain Mutants: Implications for Stability and Dynamics 2003
1P7J 25047 ENGRAILED MUTANT X-RAY DIFFRACTION Drosophila melanogaster Crystal Structures of Engrailed Homeodomain Mutants: Implications for Stability and Dynamics 2003
1PUF 23939 HOXA9 & PBX1 X-RAY DIFFRACTION Mus Musculus Structure of Hoxa9 and Pbx1 Bound to DNA: Hox Hexapeptide and DNA Recognition Anterior to Posterior 2003
1QRY 10619 VND NMR, 20 STRUCTURES Drosophila melanogaster Distortion of the three-dimensional structure of the vnd/NK-2 homeodomain bound to DNA induced by an embryonically lethal A35T point mutation. 2003
1UHS 28757 HOP NMR, 20 STRUCTURES Mus Musculus Solution structure of mouse homeodomain-only protein HOP 2003
1IC8 21086 Hepatocyte Nuclear Factor 1a X-RAY DIFFRACTION Homo sapiens Diabetes Mutations Delineate an Atypical POU Domains in HNF1-Alpha 2002
1K61 21373 MATALPHA2 X-RAY DIFFRACTION SYNTHETIC CONSTRUCT A Hoogsteen base pair embedded in undistorted B-DNA 2002
1KZ0 19081 ANTENNAPEDIA PROTEIN NMR, 26 STRUCTURES Synthetic construct Investigation of Penetratin Peptides. Part 1. The Environment Dependent Conformational Properties of Penetratin and Two of its Derivatives 2002
1KZ2 19082 ANTENNAPEDIA PROTEIN NMR, 39 STRUCTURES Synthetic construct Investigation of Penetratin Peptides. Part 1. The Environment Dependent Conformational Properties of Penetratin and Two of its Derivatives 2002
1KZ5 19083 ANTENNAPEDIA PROTEIN NMR, 16 STRUCTURES Synthetic construct Investigation of Penetratin Peptides. Part 1. The Environment Dependent Conformational Properties of Penetratin and Two of its Derivatives 2002
1LE8 19631 MATING-TYPE PROTEIN X-RAY DIFFRACTION Saccharomyces cerevisiae Structural and Thermodynamic Characterization of the DNA Binding Properties of a Triple Alanine Mutant of MATalpha2 2002
1MIJ 21235 Prospero X-RAY DIFFRACTION Drosophila melanogaster Structure of the DNA Binding Region of Prospero Reveals a Novel Homeo-Prospero Domain 2002
1IG7 16229 HOMEOTIC PROTEIN MSX-1 X-RAY DIFFRACTION Mus Musculus Crystal Structure of the MSX-1 homeodomain/DNA complex 2001
1JGG 17029 EVEN-SKIPPED X-RAY DIFFRACTION Drosophila melanogaster Structure of the Even-Skipped Homeodomain Complexed to AT-Rich DNA: New Perspectives on Homeodomain Specificity 2001
1DU0 13731 ENGRAILED HOMEODOMAIN X-RAY DIFFRACTION Drosophila melanogaster Exploring the Role of Glutamine 50 in the Homeodomain-DNA Interface: Crystal Structure of Engrailed (Gln50-->Ala) Complex at 2.0 A 2000
1DU6 14150 PBX NMR, 30 STRUCTURES Mus Musculus Conformational Changes in the Pbx Homeodomain and C-Terminal Extension Upon Binding DNA and Hox-Derived Ypwm Peptides 2000
1F43 13835 MATING-TYPE PROTEIN NMR, 20 STRUCTURES Saccharomyces cerevisiae Cooperative Ordering in Homeodomain-DNA Recognition: Solution Structure and Dynamics of the MATa1 Homeodomain 2000
1B72 9588 PBX1 X-RAY DIFFRACTION Homo sapiens Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation. 1999
1B8I 13531 ULTRABITHORAX X-RAY DIFFRACTION Drosophila melanogaster Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex. 1999
1BW5 10482 Isl-1 NMR, 50 STRUCTURES Rattus norvegicus The solution structure of the homeodomain of the rat insulin-gene enhancer protein isl-1. Comparison with other homeodomains. 1999
6PAX 11064 Pax-6 X-RAY DIFFRACTION Homo sapiens Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding. 1999
1AKH 7748 MATING-TYPE PROTEIN X-RAY DIFFRACTION Saccharomyces cerevisiae Crystal structure of the MATa1/MATalpha2 homeodomain heterodimer in complex with DNA containing an A-tract. 1998
1NK2 9575 VND NMR, 20 STRUCTURES Drosophila melanogaster Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity. 1998
1NK3 9716 VND NMR Drosophila melanogaster Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity. 1998
3HDD 8560 ENGRAILED HOMEODOMAIN X-RAY DIFFRACTION Drosophila melanogaster Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures. 1998
9ANT 8759 ANTENNAPEDIA PROTEIN X-RAY DIFFRACTION Drosophila melanogaster Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex. 1998
1MNM 7281 MATING-TYPE PROTEIN X-RAY DIFFRACTION Saccharomyces cerevisiae Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. 1997
2HDD 7633 ENGRAILED HOMEODOMAIN X-RAY DIFFRACTION Drosophila melanogaster Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity. 1997
2LFB 5036 LIVER TRANSCRIPTION FACTOR (LFB1) NMR, 20 STRUCTURES Rattus rattus The NMR solution structure of the non-classical homeodomain from the rat liver LFB1/HNF1 transcription factor. 1997
1FTT 3904 THYROID TRANSCRIPTION FACTOR 1 HOMEODOMAIN NMR, 20 STRUCTURES Rattus norvegicus Analysis of the solution structure of the homeodomain of rat thyroid transcription factor 1 by 1H-NMR spectroscopy and restrained molecular mechanics. 1996
1VND 5683 VND NMR, 30 STRUCTURES Drosophila melanogaster The three-dimensional solution structure of the NK-2 homeodomain from Drosophila. 1996
1FJL 4645 PAIRED HOMEODOMAIN X-RAY DIFFRACTION Drosophila melanogaster High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. 1995
1OCP 3722 OCT-3 POU NMR, 20 STRUCTURES Mus musculus Structure of the Oct-3 POU-Homeodomain in Solution, as Determined by Triple Resonance Heteronuclear Multidimensional NMR Spectroscopy 1995
1YRN 3857 MATING-TYPE PROTEIN X-RAY DIFFRACTION Saccharomyces cerevisiae Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA. 1995
1ENH 864 ENGRAILED HOMEODOMAIN X-RAY DIFFRACTION Drosophila melanogaster Structural studies of the engrailed homeodomain. 1994
1FTZ 986 FUSHI TARAZU PROTEIN NMR, 20 STRUCTURES Drosophila melanogaster Nuclear magnetic resonance solution structure of the fushi tarazu homeodomain from Drosophila and comparison with the Antennapedia homeodomain. 1994
1HDP 1139 OCT-2 POU NMR Homo sapiens Solution structure of a POU-specific homeodomain: 3D-NMR studies of human B-cell transcription factor Oct-2. 1994
1POG 3800 OCT-1 POU NMR, 13 STRUCTURES Homo sapiens Solution structure of the Oct-1 POU homeodomain determined by NMR and restrained molecular dynamics. 1994
1SAN 2152 ANTENNAPEDIA PROTEIN NMR, 20 STRUCTURES Drosophila melanogaster The des(1-6)antennapedia homeodomain: comparison of the NMR solution structure and the DNA-binding affinity with the intact Antennapedia homeodomain. 1994
1AHD 208 ANTENNAPEDIA PROTEIN NMR, 16 STRUCTURES Drosophila melanogaster Determination of the nuclear magnetic resonance solution structure of an Antennapedia homeodomain-DNA complex. 1993
1LFB 1523 LIVER TRANSCRIPTION FACTOR (LFB1) X-RAY DIFFRACTION Rattus norvegicus The X-ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1/HNF1 and implications for DNA binding. 1993
1APL 255 MATING-TYPE PROTEIN X-RAY DIFFRACTION Saccharomyces cerevisiae Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. 1991
2HOA 2725 ANTENNAPEDIA PROTEIN NMR, 20 STRUCTURES Drosophila melanogaster Structure determination of the Antp (C39----S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS and GLOMSA. 1991
1HDD 1136 ENGRAILED HOMEODOMAIN X-RAY DIFFRACTION Drosophila melanogaster Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions. 1990
1HOM 1232 ANTENNAPEDIA PROTEIN NMR, 19 STRUCTURES Drosophila melanogaster Determination of the three-dimensional structure of the Antennapedia homeodomain from Drosophila in solution by 1H nuclear magnetic resonance spectroscopy. 1990
1WH7 30560 F22K18.140 NMR, 20 STRUCTURES Arabidopsis thaliana Solution structure of homeobox domain of Arabidopsis thaliana hypothetical protein F22K18.140 To be Published
1X2L 35477 Cux-2 NMR, 20 STRUCTURES Homo sapiens Solution structure of the CUT domain of human homeobox protein Cux-2 (Cut-like 2) To be Published
1X2N 35479 PKNOX1 NMR, 20 STRUCTURES Homo sapiens Solution structure of the homeobox domain of human homeobox protein PKNOX1 To be Published
2CRA 36365 Hox-B13 NMR, 20 STRUCTURES Homo sapiens Solution structure of the homeobox domain of human homeo box B13 To be Published
2CUE 36437 Pax-6 NMR, 20 STRUCTURES Homo sapiens Solution structure of the homeobox domain of the human paired box protein Pax-6 To be Published
2CUF 36438 FLJ21616 NMR, 20 STRUCTURES Homo sapiens Solution structure of the homeobox domain of the human hypothetical protein FLJ21616 To be Published
2DA1 39738 ATBF1 NMR, 20 STRUCTURES Homo sapiens Solution structure of the first homeobox domain of AT-binding transcription factor 1 (ATBF1) To be Published
2DA2 39739 ATBF1 NMR, 20 STRUCTURES Homo sapiens Solution structure of the second homeobox domain of AT-binding transcription factor 1 (ATBF1) To be Published
2DA3 39740 ATBF1 NMR, 20 STRUCTURES Homo sapiens Solution structure of the third homeobox domain of AT-binding transcription factor 1 (ATBF1) To be Published
2DA5 39742 Triple homeobox 1 protein NMR, 20 STRUCTURES Homo sapiens Solution structure of the second homeobox domain of Zinc fingers and homeoboxes protein 3 (Triple homeobox 1 protein) To be Published
2DA6 43218 HNF-1beta NMR, 20 STRUCTURES Homo sapiens Solution structure of the homeobox domain of Hepatocyte nuclear factor 1-beta (HNF-1beta) To be Published
2DA7 43219 Smad interacting protein 1 NMR, 20 STRUCTURES Homo sapiens Solution structure of the homeobox domain of Zinc finger homeobox protein 1b (Smad interacting protein 1) To be Published
2DJN 41990 DLX-5 NMR, 20 STRUCTURES Homo sapiens The solution structure of the homeobox domain of human Homeobox protein DLX-5 To be Published
2DMN 42060 TGIF2LX NMR, 20 STRUCTURES Homo sapiens The solution structure of the homeobox domain of human homeobox protein TGIF2LX To be Published
2DMP 42061 Zinc fingers and homeoboxes protein 2 NMR, 20 STRUCTURES Homo sapiens Solution structure of the third homeobox domain of Zinc fingers and homeoboxes protein 2 To be Published
2DMQ 42062 Lhx9 NMR, 20 STRUCTURES Homo sapiens Solution structure of the homeobox domain of LIM/homeobox protein Lhx9 To be Published
2DMS 42063 OTX2 NMR, 20 STRUCTURES Mus musculus Solution structure of the homeobox domain of Homeobox protein OTX2 To be Published
2DMT 42064 BarH-like 1 NMR, 20 STRUCTURES Homo sapiens Solution structure of the homeobox domain of Homeobox protein BarH-like 1 To be Published
2DMU 42065 goosecoid NMR, 20 STRUCTURES Homo sapiens Solution structure of the homeobox domain of Homeobox protein goosecoid To be Published
2DN0 42071 Zinc fingers and homeoboxes protein 3 NMR, 20 STRUCTURES Homo sapiens Solution structure of the second homeobox domain of human zinc fingers and homeoboxes protein 3 To be Published
2E19 45595 NIL-2-A zinc finger protein, transcription factor 8 NMR, 20 STRUCTURES Homo sapiens Solution structure of the homeobox domain from human NIL-2-A zinc finger protein, transcription factor 8 To be Published
2E1O 42680 Homeobox protein PRH NMR, 20 STRUCTURES Homo sapiens Solution structure of RSGI RUH-028, a homeobox domain from human cDNA To be Published
2ECB 44385 Zinc fingers and homeoboxes protein 1 NMR, 20 STRUCTURES Homo sapiens The solution structure of the third homeobox domain of human Zinc fingers and homeoboxes protein To be Published
2ECC 44386 HOMEZ NMR, 20 STRUCTURES Homo sapiens Solution Structure Of The Homeobox Domain Of Human Homeodomain Leucine Zipper-Encoding Gene To be Published


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