1IZ3 - JenaLib

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Title :   DIMERIC STRUCTURE OF FIH (FACTOR INHIBITING HIF)

Authors :   C. Lee, S. -J. Kim, D. -G. Jeong, S. M. Lee, S. -E. Ryu

Date :   19 Sep 02 (Deposition) - 10 Jun 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Double Beta-Sheet Helix, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Lee, S. J. Kim, D. G. Jeong, S. M. Lee, S. E. Ryu
Structure Of Human Fih-1 Reveals A Unique Active Site Pocke And Interaction Sites For Hif-1 And Von Hippel-Lindau.
J. Biol. Chem. V. 278 7558 2003
PubMed-ID: 12482756 | Reference-DOI: 10.1074/JBC.M210385200

Molecule 1 - FIH
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	FACTOR INHIBITING HIF1

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:107 , ARG A:238 , ARG A:320 , LYS A:324	BINDING SITE FOR RESIDUE SO4 A 501

(no "SS Bond" information available for 1IZ3)

Asymmetric Unit

No.	Residues
1	Tyr A:308	-	Pro A:309

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051028	P	41	A	HIF1N_HUMAN	Polymorphism	2295778	A	P	41	A

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

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051028	P	41	A	HIF1N_HUMAN	Polymorphism	2295778	A	P	41	A

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	HIF1N_HUMAN	142-312	1	A:142-312

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JMJC	PS51184	JmjC domain profile.	HIF1N_HUMAN	142-312	2	A:142-312

Asymmetric Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000299163	2b	ENSE00001695622	chr10:102295616-102295892	277	HIF1N_HUMAN	1-59	59	1	A:12-59	48
1.3b	ENST00000299163	3b	ENSE00001100126	chr10:102296168-102296418	251	HIF1N_HUMAN	60-143	84	1	A:60-143	84
1.4b	ENST00000299163	4b	ENSE00001100124	chr10:102300391-102300539	149	HIF1N_HUMAN	143-193	51	1	A:143-193	51
1.5a	ENST00000299163	5a	ENSE00001100127	chr10:102304708-102304853	146	HIF1N_HUMAN	193-241	49	1	A:193-241	49
1.6b	ENST00000299163	6b	ENSE00001100128	chr10:102305700-102305806	107	HIF1N_HUMAN	242-277	36	1	A:242-277	36
1.7	ENST00000299163	7	ENSE00001100132	chr10:102306275-102306338	64	HIF1N_HUMAN	277-298	22	1	A:277-298	22
1.8b	ENST00000299163	8b	ENSE00001100130	chr10:102306897-102307007	111	HIF1N_HUMAN	299-335	37	1	A:299-335	37
1.9b	ENST00000299163	9b	ENSE00001212367	chr10:102307850-102309763	1914	HIF1N_HUMAN	336-349	14	1	A:336-349	14

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
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Chain A from PDB  Type:PROTEIN  Length:338
 aligned with HIF1N_HUMAN | Q9NWT6 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:338
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341        
          HIF1N_HUMAN    12 GSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN 349
               SCOP domains d1iz3a_ A: Hypoxia-inducible factor HIF ihhibitor (FIH1)                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1iz3A02 A:306-349 Clavaminate synthase-like  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhh......eee..ee...hhhhhhhhhh....ee.....hhhhhhhhhhhhhhhh...eeeeeee........hhhhhhhhh......eeeeeehhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee....eeeeee...eeeeeeee..eeeeeehhhhhhhhh.......................hhhhhhh.eeeeee....eeee....eeeeee......eeeeeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------JMJC  PDB: A:142-312 UniProt: 142-312                                                                                                                                      ------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:12-59 UniProt: 1-59           Exon 1.3b  PDB: A:60-143 UniProt: 60-143                                            -------------------------------------------------Exon 1.5a  PDB: A:193-241 UniProt: 193-241       Exon 1.6b  PDB: A:242-277           ---------------------Exon 1.8b  PDB: A:299-335            Exon 1.9b      Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------Exon 1.4b  PDB: A:143-193 UniProt: 143-193         -----------------------------------------------------------------------------------Exon 1.7              --------------------------------------------------- Transcript 1 (2)
                 1iz3 A  12 GSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKmANFQNFKPRSNREEmKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGGKIVmDFLGFNWNWINKQQGKRGWGQLTSNLLLIGmEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPmYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAImRNIEKmLGEALGNPQEVGPLLNTmIKGRYN 349
                                    21        31        41        51        61        71        81        91       101      |111       121 |     131       141       151       161       171       181       191       201       211       221       231       241       251       261       271   |   281       291       301       311       321   |   331       341 |      
                                                                                                                          108-MSE        123-MSE                              160-MSE                        191-MSE                                                                             275-MSE                                     319-MSE |               343-MSE  
                                                                                                                                                                                                                                                                                                                                                   325-MSE

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Double-stranded beta-helix (580)

Superfamily: Clavaminate synthase-like (197)

Family: Hypoxia-inducible factor HIF ihhibitor (FIH1) (26)

Protein domain: Hypoxia-inducible factor HIF ihhibitor (FIH1) (26)

Human (Homo sapiens) [TaxId: 9606] (26)

d1iz3a_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: Clavaminate synthase-like (17)

Human (Homo sapiens) (17)

1iz3A02

A:306-349

(no "Pfam Domain" information available for 1IZ3)

Asymmetric Unit(hide GO term definitions)

Chain A (HIF1N_HUMAN | Q9NWT6)

molecular function
	GO:0051059	NF-kappaB binding	Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.
	GO:0005112	Notch binding	Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor.
	GO:0071532	ankyrin repeat binding	Interacting selectively and non-covalently with an ankyrin repeat of a protein. Ankyrin repeats are tandemly repeated modules of about 33 amino acids; each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90-degree angle, and repeats stack to form an L-shaped structure.
	GO:0031406	carboxylic acid binding	Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0048037	cofactor binding	Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016706	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors	Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
	GO:0019826	oxygen sensor activity	Interacting selectively and non-covalently with and responding, e.g. by conformational change, to changes in the cellular level of oxygen (O2).
	GO:0036140	peptidyl-asparagine 3-dioxygenase activity	Catalysis of the reaction: peptidyl L-asparagine + 2-oxoglutarate + O2 = peptidyl 3-hydroxy-L-asparagine + succinate + CO2.
	GO:0036139	peptidyl-histidine dioxygenase activity	Catalysis of the reaction: peptidyl L-histidine + 2-oxoglutarate + O2 = peptidyl hydroxy-L-histidine + succinate + CO2.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0045746	negative regulation of Notch signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of the Notch signaling pathway.
	GO:0061428	negative regulation of transcription from RNA polymerase II promoter in response to hypoxia	Any process that decreases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0042265	peptidyl-asparagine hydroxylation	The hydroxylation of peptidyl-asparagine to form peptidyl-hydroxyasparagine.
	GO:0042264	peptidyl-aspartic acid hydroxylation	The hydroxylation of peptidyl-aspartic acid to form peptidyl-hydroxyaspartic acid.
	GO:0036138	peptidyl-histidine hydroxylation	The hydroxylation of peptidyl-histidine to form peptidyl-hydroxyhistidine.
	GO:0045663	positive regulation of myoblast differentiation	Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
	GO:2001214	positive regulation of vasculogenesis	Any process that activates or increases the frequency, rate or extent of vasculogenesis.
	GO:0061418	regulation of transcription from RNA polymerase II promoter in response to hypoxia	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

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	1iz3
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Description

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Ligands, Modified Residues, Ions (2, 9)

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SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (8, 8)

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