1DP7 | PD0111 - JenaLib

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Biol. Unit 1 - sites

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Description

Title :   COCRYSTAL STRUCTURE OF RFX-DBD IN COMPLEX WITH ITS COGNATE X-BOX BINDING SITE

Authors :   K. S. Gajiwala, H. Chen, F. Cornille, B. P. Roques, W. Reith, B. Mach, S. K. Burley

Date :   23 Dec 99 (Deposition) - 06 Mar 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : D,P
Biol. Unit 1: D,P  (2x)

Keywords :   Winged Helix, Mhc Class Ii Transcription Factor, Protein- Dna Cocrystal Structure, Novel Mode Of Dna Recognition, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. S. Gajiwala, H. Chen, F. Cornille, B. P. Roques, W. Reith, B. Mach, S. K. Burley
Structure Of The Winged-Helix Protein Hrfx1 Reveals A New Mode Of Dna Binding.
Nature V. 403 916 2000
PubMed-ID: 10706293 | Reference-DOI: 10.1038/35002634
(for further references see the PDB file header)

Compounds

*Molecule 1 - DNA (5'-D(CPGP(BRU)PTPAPCPCPAP(BRU) PGPGPTPAPAPCPG)-3')*
	Chains	:	D
	Engineered	:	YES
	Fragment	:	X-BOX
	Synthetic	:	YES

Molecule 2 - MHC CLASS II TRANSCRIPTION FACTOR HRFX1
	Chains	:	P
	Engineered	:	YES
	Fragment	:	DNA BINDING DOMAIN
	Mutation	:	YES
	Other Details	:	SEQUENCE TAKEN FROM HUMAN MHC CLASS II TRANSCRIPTION FACTOR
	Synonym	:	REGULATORY FACTOR X
	Synthetic	:	YES

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	D	P
Biological Unit 1 (2x)	:	D	P

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 5)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	BRU	2	Mod. Nucleotide	5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	BRU	4	Mod. Nucleotide	5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH D:37 , HOH D:43 , THR P:56 , HOH P:563	BINDING SITE FOR RESIDUE EDO P 501
2	AC2	SOFTWARE	VAL P:2 , SER P:49 , VAL P:50 , HOH P:549	BINDING SITE FOR RESIDUE EDO P 502
3	AC3	SOFTWARE	PRO P:18 , THR P:21 , MET P:52 , GLY P:53 , ARG P:55 , HOH P:523	BINDING SITE FOR RESIDUE PEG P 503

SS Bonds (0, 0)

(no "SS Bond" information available for 1DP7)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1DP7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1DP7)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RFX_DBD	PS51526	RFX-type winged-helix DNA-binding domain profile.	RFX1_HUMAN	438-513	1	P:1-76

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RFX_DBD	PS51526	RFX-type winged-helix DNA-binding domain profile.	RFX1_HUMAN	438-513	2	P:1-76

Exons (3, 3)

Asymmetric Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000254325	1	ENSE00001348294	chr19:14117097-14116915	183	RFX1_HUMAN	-	0	0	-	-
1.2	ENST00000254325	2	ENSE00001055458	chr19:14104707-14104337	371	RFX1_HUMAN	1-107	107	0	-	-
1.3	ENST00000254325	3	ENSE00000902153	chr19:14094407-14094298	110	RFX1_HUMAN	107-143	37	0	-	-
1.4	ENST00000254325	4	ENSE00000902152	chr19:14094082-14093999	84	RFX1_HUMAN	144-171	28	0	-	-
1.5	ENST00000254325	5	ENSE00000902151	chr19:14093040-14092933	108	RFX1_HUMAN	172-207	36	0	-	-
1.6	ENST00000254325	6	ENSE00000902150	chr19:14091501-14091385	117	RFX1_HUMAN	208-246	39	0	-	-
1.7	ENST00000254325	7	ENSE00000902149	chr19:14090354-14090259	96	RFX1_HUMAN	247-278	32	0	-	-
1.8	ENST00000254325	8	ENSE00000902148	chr19:14088898-14088804	95	RFX1_HUMAN	279-310	32	0	-	-
1.9	ENST00000254325	9	ENSE00000902147	chr19:14083939-14083555	385	RFX1_HUMAN	310-438	129	1	P:1-1	1
1.10	ENST00000254325	10	ENSE00000902146	chr19:14080987-14080806	182	RFX1_HUMAN	439-499	61	1	P:2-62	61
1.11	ENST00000254325	11	ENSE00000902145	chr19:14079706-14079587	120	RFX1_HUMAN	499-539	41	1	P:62-76	15
1.12	ENST00000254325	12	ENSE00000902144	chr19:14079492-14079377	116	RFX1_HUMAN	539-578	40	0	-	-
1.13	ENST00000254325	13	ENSE00000902143	chr19:14077563-14077445	119	RFX1_HUMAN	578-617	40	0	-	-
1.14	ENST00000254325	14	ENSE00000902142	chr19:14077342-14077233	110	RFX1_HUMAN	618-654	37	0	-	-
1.15	ENST00000254325	15	ENSE00000902141	chr19:14076589-14076438	152	RFX1_HUMAN	654-705	52	0	-	-
1.16	ENST00000254325	16	ENSE00000902140	chr19:14076358-14076261	98	RFX1_HUMAN	705-737	33	0	-	-
1.17	ENST00000254325	17	ENSE00000902139	chr19:14074819-14074670	150	RFX1_HUMAN	738-787	50	0	-	-
1.18	ENST00000254325	18	ENSE00000902138	chr19:14074558-14074350	209	RFX1_HUMAN	788-857	70	0	-	-
1.19	ENST00000254325	19	ENSE00001794399	chr19:14074087-14073934	154	RFX1_HUMAN	857-908	52	0	-	-
1.20	ENST00000254325	20	ENSE00000902136	chr19:14073851-14073806	46	RFX1_HUMAN	909-924	16	0	-	-
1.21	ENST00000254325	21	ENSE00001385967	chr19:14073676-14072353	1324	RFX1_HUMAN	924-979	56	0	-	-

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 D from PDB  Type:DNA  Length:16
                                                
                 1dp7 D   1 CGuTACCAuGGTAACG  16
                              |     10      
                              3-BRU 9-BRU

Chain P from PDB  Type:PROTEIN  Length:76
 aligned with RFX1_HUMAN | P22670 from UniProtKB/Swiss-Prot  Length:979

    Alignment length:76
                                   447       457       467       477       487       497       507      
           RFX1_HUMAN   438 TVQWLLDNYETAEGVSLPRSTLYCHYLLHCQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA 513
               SCOP domains d1dp7p_ P: Class II MHC transcription factor RFX1                            SCOP domains
               CATH domains 1dp7P00 P:1-76 'winged helix' repressor DNA binding domain                   CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhheeeeeeeeeehhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...eeeee......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RFX_DBD  PDB: P:1-76 UniProt: 438-513                                        PROSITE
           Transcript 1 (1) 1Exon 1.10  PDB: P:2-62 UniProt: 439-499                      -------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.11       Transcript 1 (2)
                 1dp7 P   1 TVQWLLDNYETAEGVSLPRSTLYNHYLLHSQEQKLEPVNAASFGKLIRSVFMGLRTRRLGTRGNSKYHYYGLRIKA  76
                                    10        20        30        40        50        60        70

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 (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: P4 origin-binding domain-like (2)

Protein domain: Class II MHC transcription factor RFX1 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d1dp7p_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

[unclassified] (77)

1dp7P00

P:1-76

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 1DP7)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain P (RFX1_HUMAN | P22670)

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: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.
biological process
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	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:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (3, 3)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File