2ram
From Proteopedia
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|PDB= 2ram |SIZE=350|CAPTION= <scene name='initialview01'>2ram</scene>, resolution 2.40Å | |PDB= 2ram |SIZE=350|CAPTION= <scene name='initialview01'>2ram</scene>, resolution 2.40Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=DTV:(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL'>DTV</scene> | + | |LIGAND= <scene name='pdbligand=5IU:5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=DTV:(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL'>DTV</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ram FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ram OCA], [http://www.ebi.ac.uk/pdbsum/2ram PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ram RCSB]</span> | ||
}} | }} | ||
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[[Category: Ghosh, G.]] | [[Category: Ghosh, G.]] | ||
[[Category: Ghosh, S.]] | [[Category: Ghosh, S.]] | ||
| - | [[Category: DTV]] | ||
[[Category: activator nuclear protein]] | [[Category: activator nuclear protein]] | ||
[[Category: complex (transcription factor/dna)]] | [[Category: complex (transcription factor/dna)]] | ||
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[[Category: transcription regulation]] | [[Category: transcription regulation]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:58:19 2008'' |
Revision as of 01:58, 31 March 2008
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| , resolution 2.40Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER
Overview
The crystal structure of the NF-kappa B p65 (RelA) homodimer in complex with a DNA target has been determined to 2.4 A resolution. The two p65 subunits are not symmetrically disposed on the DNA target. The homodimer should optimally bind to a pseudo-palindromic nine base pair target with each subunit recognizing a 5'GGAA-3' half site separated by a central A-T base pair. However, one of the subunits (subunit B) encounters a half site of 5'-GAAA-3'. The single base-pair change from G-C to A-T results in highly unfavorable interactions between this half site and the base contacting protein residues in subunit B, which leads to an 18 degrees rotation of the N-terminal terminal domain from its normal conformation. Remarkably, subunit B retains all the interactions with the sugar phosphate backbone of the DNA target. This mode of interaction allows the NF-kappa B p65 homodimer to recognize DNA targets containing only one cognate half site. Differences in the sequence of the other half site provide variations in conformation and affinity of the complex.
About this Structure
2RAM is a Single protein structure of sequence from Mus musculus. Full crystallographic information is available from OCA.
Reference
A novel DNA recognition mode by the NF-kappa B p65 homodimer., Chen YQ, Ghosh S, Ghosh G, Nat Struct Biol. 1998 Jan;5(1):67-73. PMID:9437432
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