2KW3 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   HETEROTRIMERIC INTERACTION BETWEEN RFX5 AND RFXAP

Authors :   K. M. Laird, L. L. Briggs, J. M. Boss, M. F. Summers, C. W. Garvie

Date :   30 Mar 10 (Deposition) - 25 Aug 10 (Release) - 25 Aug 10 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C  (20x)
NMR Structure *: A,B,C  (1x)

Keywords :   Mhcii, Rfx5, Rfxap, Enhanceosome, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. M. Laird, L. L. Briggs, J. M. Boss, M. F. Summers, C. W. Garvie
Solution Structure Of The Heterotrimeric Complex Between Rfx5 And Rfxap Reveals Molecular Details Associated With Mhcii Gene Expression
To Be Published
PubMed: search

Molecule 1 - DNA-BINDING PROTEIN RFX5
	Chains	:	A, B
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 24-90
	Gene	:	RFX5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	REGULATORY FACTOR X 5

Molecule 2 - REGULATORY FACTOR X-ASSOCIATED PROTEIN
	Chains	:	C
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 214-271
	Gene	:	RFXAP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RFX-ASSOCIATED PROTEIN, RFX DNA-BINDING COMPLEX 36 KDA SUBUNIT

		1	2	3
NMR Structure (20x)	:	A	B	C
NMR Structure * (1x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2KW3)

(no "Site" information available for 2KW3)

(no "SS Bond" information available for 2KW3)

(no "Cis Peptide Bond" information available for 2KW3)

(no "SAP(SNP)/Variant" information available for 2KW3)

(no "PROSITE Motif" information available for 2KW3)

(no "Exon" information available for 2KW3)

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:68
 aligned with RFX5_HUMAN | P48382 from UniProtKB/Swiss-Prot  Length:616

    Alignment length:71
                                    29        39        49        59        69        79        89 
           RFX5_HUMAN    20 GGAEAGEPTTLLQRLRGTISKAVQNKVEGILQDVQKFSDNDKLYLYLQLPSGPTTGDKSSEPSTLSNEEYM  90
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------RFX_DN Pfam domains
         Sec.struct. author .---.....hhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.....hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 2kw3 A  23 G---AGEPTTLLQRLRGTISKAVQNKVEGILQDVQKFSDNDKLYLYLQLPSGPTTGDKSSEPSTLSNEEYM  90
                            |   |   29        39        49        59        69        79        89 
                            |  24                                                                  
                           23

Chain B from PDB  Type:PROTEIN  Length:68
 aligned with RFX5_HUMAN | P48382 from UniProtKB/Swiss-Prot  Length:616

    Alignment length:71
                                    29        39        49        59        69        79        89 
           RFX5_HUMAN    20 GGAEAGEPTTLLQRLRGTISKAVQNKVEGILQDVQKFSDNDKLYLYLQLPSGPTTGDKSSEPSTLSNEEYM  90
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---.....hhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 2kw3 B  23 G---AGEPTTLLQRLRGTISKAVQNKVEGILQDVQKFSDNDKLYLYLQLPSGPTTGDKSSEPSTLSNEEYM  90
                            |   |   29        39        49        59        69        79        89 
                           23  24

Chain C from PDB  Type:PROTEIN  Length:62
 aligned with RFXAP_HUMAN | O00287 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:78
                                   204       214       224       234       244       254       264        
          RFXAP_HUMAN   195 GNVKLEESADNILSIVKQRTGSFGDRPARPTLLEQVLNQKRLSLLRSPEVVQFLQKQQQLLNQQVLEQRQQQFPGTSM 272
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .----------------.............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 2kw3 C 211 G----------------HGTGSFGDRPARPTLLEQVLNQKRLSLLRSPEVVQFLQKQQQLLNQQVLEQRQQQFPGTSM 272
                            |        -       214       224       234       244       254       264        
                          211              212

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 '\|'

(no "SCOP Domain" information available for 2KW3)

(no "CATH Domain" information available for 2KW3)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: RFX_DNA_binding (1)

Homo sapiens (Human) (1)

RFX_DNA_binding-2kw3A01

A:85-90

NMR Structure(hide GO term definitions)

Chain A,B (RFX5_HUMAN | P48382)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA 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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates 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: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.

Chain C (RFXAP_HUMAN | O00287)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:1903506	regulation of nucleic acid-templated transcription	Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
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.

NMR Structure
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	2kw3
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	RFX5_HUMAN \| P48382
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	RFXAP_HUMAN \| O00287
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	RFX5_HUMAN \| P48382	:	3v30

(no "Related Entries Specified in the PDB File" available for 2KW3)

Description

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Ligands, Modified Residues, Ions (0, 0)

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