1IC8 | PD0208 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   HEPATOCYTE NUCLEAR FACTOR 1A BOUND TO DNA : MODY3 GENE PRODUCT

Authors :   Y-. I. Chi, J. D. Frantz, B-. C. Oh, L. Hansen, S. Dhe-Paganon, S. E. Shoel

Date :   30 Mar 01 (Deposition) - 27 Nov 02 (Release) - 01 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B,E,F

Keywords :   Transcription Regulation; Dna-Binding; Pou Domain; Diabetes; Disease Mutation; Mody3, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y-. I. Chi, J. D. Frantz, B-. C. Oh, L. Hansen, S. Dhe-Paganon, S. E. Shoelson
Diabetes Mutations Delineate An Atypical Pou Domains In Hnf1-Alpha
Mol. Cell V. 10 1129 2002
PubMed-ID: 12453420 | Reference-DOI: 10.1016/S1097-2765(02)00704-9

*Molecule 1 - 5'-D(CPTPTPGPGPTPTPAPAPTPAPAPTPTPCPAPCPCP APGPA)-3'**
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'-D(TPCPTPGPGPTPGPAPAPTPTPAPTPTPAPAPCPCP APAPG)-3'**
	Chains	:	F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - HEPATOCYTE NUCLEAR FACTOR 1-ALPHA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1IC8)

(no "Site" information available for 1IC8)

(no "SS Bond" information available for 1IC8)

(no "Cis Peptide Bond" information available for 1IC8)

Asymmetric/Biological Unit (37, 74)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_010540	A	98	V	HNF1A_HUMAN	Polymorphism	1800574	A/B	A	98	V
02	UniProt	VAR_010541	L	107	R	HNF1A_HUMAN	Disease (MODY3)	---	A/B	L	107	R
03	UniProt	VAR_010542	K	117	E	HNF1A_HUMAN	Disease (MODY3)	---	A/B	K	117	E
04	UniProt	VAR_003756	Y	122	C	HNF1A_HUMAN	Disease (MODY3)	---	A/B	Y	122	C
05	UniProt	VAR_033088	N	127	Y	HNF1A_HUMAN	Unclassified	---	A/B	N	127	Y
06	UniProt	VAR_010543	I	128	N	HNF1A_HUMAN	Disease (MODY3)	---	A/B	I	128	N
07	UniProt	VAR_010544	P	129	T	HNF1A_HUMAN	Disease (MODY3)	---	A/B	P	129	T
08	UniProt	VAR_010545	R	131	Q	HNF1A_HUMAN	Disease (MODY3)	---	A/B	R	131	Q
09	UniProt	VAR_010546	R	131	W	HNF1A_HUMAN	Disease (MODY3)	---	A/B	R	131	W
10	UniProt	VAR_010547	V	133	M	HNF1A_HUMAN	Disease (MODY3)	---	A/B	V	133	M
11	UniProt	VAR_003757	S	142	F	HNF1A_HUMAN	Disease (MODY3)	---	A/B	S	142	F
12	UniProt	VAR_010548	H	143	Y	HNF1A_HUMAN	Disease (MODY3)	---	A/B	H	143	Y
13	UniProt	VAR_010549	K	158	N	HNF1A_HUMAN	Disease (MODY3)	---	A/B	K	158	N
14	UniProt	VAR_003758	R	159	Q	HNF1A_HUMAN	Disease (MODY3)	---	A/B	R	159	Q
15	UniProt	VAR_010550	R	159	W	HNF1A_HUMAN	Disease (MODY3)	---	A/B	R	159	W
16	UniProt	VAR_010551	A	161	T	HNF1A_HUMAN	Disease (MODY3)	---	A/B	A	161	T
17	UniProt	VAR_033089	W	165	C	HNF1A_HUMAN	Unclassified	---	A/B	W	165	C
18	UniProt	VAR_010554	R	203	C	HNF1A_HUMAN	Disease (MODY3)	---	A/B	R	203	C
19	UniProt	VAR_012484	R	203	H	HNF1A_HUMAN	Disease (MODY3)	---	A/B	R	203	H
20	UniProt	VAR_010555	K	205	Q	HNF1A_HUMAN	Disease (MODY3)	---	A/B	K	205	Q
21	UniProt	VAR_033090	W	206	C	HNF1A_HUMAN	Unclassified	---	A/B	W	206	C
22	UniProt	VAR_033091	W	206	L	HNF1A_HUMAN	Unclassified	---	A/B	W	206	L
23	UniProt	VAR_010556	R	229	Q	HNF1A_HUMAN	Disease (MODY3)	---	A/B	R	229	Q
24	UniProt	VAR_033092	N	237	S	HNF1A_HUMAN	Unclassified	---	A/B	N	237	S
25	UniProt	VAR_010557	C	241	G	HNF1A_HUMAN	Disease (MODY3)	---	A/B	C	241	G
26	UniProt	VAR_033093	R	244	G	HNF1A_HUMAN	Unclassified	---	A/B	R	244	G
27	UniProt	VAR_033094	Q	250	P	HNF1A_HUMAN	Unclassified	---	A/B	Q	250	P
28	UniProt	VAR_010558	L	254	M	HNF1A_HUMAN	Unclassified	---	A/B	L	254	M
29	UniProt	VAR_010559	V	259	D	HNF1A_HUMAN	Disease (MODY3)	---	A/B	V	259	D
30	UniProt	VAR_010560	T	260	M	HNF1A_HUMAN	Disease (MODY3)	---	A/B	T	260	M
31	UniProt	VAR_010561	R	263	C	HNF1A_HUMAN	Disease (MODY3)	---	A/B	R	263	C
32	UniProt	VAR_033095	F	268	C	HNF1A_HUMAN	Unclassified	---	A/B	F	268	C
33	UniProt	VAR_010562	R	271	W	HNF1A_HUMAN	Disease (MODY3)	---	A/B	R	271	W
34	UniProt	VAR_010563	R	272	C	HNF1A_HUMAN	Unclassified	---	A/B	R	272	C
35	UniProt	VAR_003759	R	272	H	HNF1A_HUMAN	Disease (MODY3)	---	A/B	R	272	H
36	UniProt	VAR_033096	K	273	E	HNF1A_HUMAN	Unclassified	---	A/B	K	273	E
37	CancerSNP	VAR_HNF1A_HUMAN_CCDS9209_1_01 *	K	273	E	HNF1A_HUMAN	Disease (Breast cancer)	---	A/B	K	273	E
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HOMEOBOX_2	PS50071	'Homeobox' domain profile.	HNF1A_HUMAN	197-278	2	A:201-276 B:201-278
2	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	HNF1A_HUMAN	253-276	2	A:253-276 B:253-276

Asymmetric/Biological Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000257555	1a	ENSE00001893688	chr12:121416346-121416897	552	HNF1A_HUMAN	1-109	109	2	A:87-109 B:85-109	23 25
1.2	ENST00000257555	2	ENSE00000756493	chr12:121426636-121426835	200	HNF1A_HUMAN	109-176	68	2	A:109-176 B:109-176	68 68
1.3	ENST00000257555	3	ENSE00000756490	chr12:121431323-121431509	187	HNF1A_HUMAN	176-238	63	2	A:176-238 (gaps) B:176-238 (gaps)	63 63
1.4	ENST00000257555	4	ENSE00000564735	chr12:121431967-121432208	242	HNF1A_HUMAN	238-319	82	2	A:238-276 B:238-278	39 41
1.5	ENST00000257555	5	ENSE00000756487	chr12:121434065-121434216	152	HNF1A_HUMAN	319-369	51	0	-	-
1.6a	ENST00000257555	6a	ENSE00000940088	chr12:121434344-121434545	202	HNF1A_HUMAN	370-437	68	0	-	-
1.6e	ENST00000257555	6e	ENSE00000756464	chr12:121435277-121435468	192	HNF1A_HUMAN	437-501	65	0	-	-
1.7	ENST00000257555	7	ENSE00000756456	chr12:121437071-121437192	122	HNF1A_HUMAN	501-541	41	0	-	-
1.8	ENST00000257555	8	ENSE00000756450	chr12:121437286-121437430	145	HNF1A_HUMAN	542-590	49	0	-	-
1.9a	ENST00000257555	9a	ENSE00000835338	chr12:121438868-121440899	2032	HNF1A_HUMAN	590-631	42	0	-	-

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:170
 aligned with HNF1A_HUMAN | P20823 from UniProtKB/Swiss-Prot  Length:631

    Alignment length:190
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276
          HNF1A_HUMAN    87 KELENLSPEEAAHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA 276
               SCOP domains d1ic8a2 A:87-180 Hepatocyte nuclear factor 1a (LFB1/HNF1)                                     --------------------d1ic8a1 A:201-276 Hepatocyte nuclear factor 1a (LFB1/HNF1)                   SCOP domains
               CATH domains 1ic8A01 A:87-180 lambda repressor-like DNA-binding domains                                    ----------------------1ic8A02 A:203-276 Homeodomain-like                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhh...........--------------------......hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.........hhhhh.hhhhhhhhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) -----------V--------R---------E----C----YNT-Q-M--------FY--------------NQ-T---C-------------------------------------C-QC----------------------Q-------S---G--G-----P---M----DM--C----C--WCE--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------W---------------------------W-------------------------------------------H--L-----------------------------------------------------------------HE--- SAPs(SNPs) (2)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------HOMEOBOX_2  PDB: A:201-276 UniProt: 197-278                                      PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------HOMEOBOX_1               PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:87-10------------------------------------------------------------------Exon 1.3  PDB: A:176-238 (gaps) UniProt: 176-238               -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.2  PDB: A:109-176 UniProt: 109-176                           -------------------------------------------------------------Exon 1.4  PDB: A:238-276 [INCOMPLETE]   Transcript 1 (2)
                 1ic8 A  87 KELENLSPEEAAHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAALYTWYVRKQREVAQQFTHA--------------------RNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA 276
                                    96       106       116       126       136       146       156       166       176   |     -         -    |  206       216       226       236       246       256       266       276
                                                                                                                       180                  201

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with HNF1A_HUMAN | P20823 from UniProtKB/Swiss-Prot  Length:631

    Alignment length:194
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274    
          HNF1A_HUMAN    85 ILKELENLSPEEAAHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR 278
               SCOP domains d1ic8b2 B:85-179 Hepatocyte nuclear factor 1a (LFB1/HNF1)                                      ---------------------d1ic8b1 B:201-278 Hepatocyte nuclear factor 1a (LFB1/HNF1)                     SCOP domains
               CATH domains --1ic8B01 B:87-201 lambda repressor-like DNA-binding domains                                                         -1ic8B02 B:203-276 Homeodomain-like                                        -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhh.........---------------------......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.........hhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) -------------V--------R---------E----C----YNT-Q-M--------FY--------------NQ-T---C-------------------------------------C-QC----------------------Q-------S---G--G-----P---M----DM--C----C--WCE----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------W---------------------------W-------------------------------------------H--L-----------------------------------------------------------------HE----- SAPs(SNPs) (2)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------HOMEOBOX_2  PDB: B:201-278 UniProt: 197-278                                        PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------HOMEOBOX_1              -- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: B:85-109 ------------------------------------------------------------------Exon 1.3  PDB: B:176-238 (gaps) UniProt: 176-238               ---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.2  PDB: B:109-176 UniProt: 109-176                           -------------------------------------------------------------Exon 1.4  PDB: B:238-278 UniProt: 238-319 Transcript 1 (2)
                 1ic8 B  85 ILKELENLSPEEAAHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAALYTWYVRKQREVAQQFTH---------------------RNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFR 278
                                    94       104       114       124       134       144       154       164       174    |    -         -      |204       214       224       234       244       254       264       274    
                                                                                                                        179                   201

Chain E from PDB  Type:DNA  Length:21
                                                     
                 1ic8 E 301 CTTGGTTAATAATTCACCAGA 321
                                   310       320

Chain F from PDB  Type:DNA  Length:21
                                                     
                 1ic8 F 401 TCTGGTGAATTATTAACCAAG 421
                                   410       420

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: 434 Repressor (Amino-terminal Domain) (116)

Homologous Superfamily: lambda repressor-like DNA-binding domains (100)

[unclassified] (45)

1a	1ic8A01	A:87-180
1b	1ic8B01	B:87-201

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: Homeodomain-like (288)

[unclassified] (65)

2a	1ic8A02	A:203-276
2b	1ic8B02	B:203-276

(no "Pfam Domain" information available for 1IC8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HNF1A_HUMAN | P20823)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific 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 (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
	GO:0042593	glucose homeostasis	Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
	GO:0046323	glucose import	The directed movement of the hexose monosaccharide glucose into a cell or organelle.
	GO:0030073	insulin secretion	The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0060261	positive regulation of transcription initiation from RNA polymerase II promoter	Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
	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:0035565	regulation of pronephros size	Any process that modulates the size of a pronephric kidney.
	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:0035623	renal glucose absorption	A renal system process in which glucose is taken up from the collecting ducts and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	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: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.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Asymmetric/Biological Unit
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(no "Sites" information available for 1ic8)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ic8)

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	1ic8
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	HNF1A_HUMAN \| P20823
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	HNF1A_HUMAN \| P20823	:	2gyp

1au7	PIT-1 DIMER BOUND TO DNA
1lfb	HNF1A HOMEODOMAIN
1oct	OCT-1 MONOMER BOUND TO DNA
2lfb	HNF1A HOEMODOMAIN NMR STRUCTURES

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (37, 74)

PROSITE Motifs (2, 4)

Exons (4, 8)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (23, 23)

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