3D8C - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   FACTOR INHIBITING HIF-1 ALPHA D201G MUTANT IN COMPLEX WITH ZN(II), ALPHA-KETOGLUTARATE AND HIF-1 ALPHA 19MER

Authors :   M. A. Mcdonough, R. Chowdhury, C. J. Schofield

Date :   23 May 08 (Deposition) - 12 Aug 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Fih, Hif, Dsbh, Oxygenase, Transcription, Hypoxia, Inhibitor 2- Oxoglutarate, Asparaginyl Hydroxylase, Transcription Regulator, Oxidoreductase, Dioxygenase, Iron, Metal-Binding, Nucleus, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. S. Hewitson, S. L. Holmes, D. Ehrismann, A. P. Hardy, R. Chowdhury, C. J. Schofield, M. A. Mcdonough
Evidence That Two Enzyme-Derived Histidine Ligands Are Sufficient For Iron Binding And Catalysis By Factor Inhibiting Hif (Fih).
J. Biol. Chem. V. 283 25971 2008
PubMed-ID: 18611856 | Reference-DOI: 10.1074/JBC.M804999200
(for further references see the PDB file header)

Molecule 1 - HYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR
	Chains	:	A
	EC Number	:	1.14.11.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HIF1AN, FIH1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HYPOXIA-INDUCIBLE FACTOR ASPARAGINE HYDROXYLASE, FACTOR INHIBITING HIF-1, FIH-1

Molecule 2 - HYPOXIA-INDUCIBLE FACTOR 1 ALPHA
	Chains	:	B
	Engineered	:	YES
	Fragment	:	CTAD
	Other Details	:	SYNTHETIC PEPTIDE FRAGMENT OF HIF-1 ALPHA
	Synonym	:	HIF-1 ALPHA, HIF1 ALPHA, ARNT- INTERACTING PROTEIN, MEMBER OF PAS PROTEIN 1, MOP1
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	AKG	1	Ligand/Ion	2-OXOGLUTARIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION
4	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	AKG	2	Ligand/Ion	2-OXOGLUTARIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	4	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	AKG	1	Ligand/Ion	2-OXOGLUTARIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:199 , HIS A:279 , HOH A:1001	BINDING SITE FOR RESIDUE ZN A 350
2	AC2	SOFTWARE	ARG A:138 , GLY A:140 , GLU A:141 , GLU A:142 , HOH A:1139	BINDING SITE FOR RESIDUE SO4 A 501
3	AC3	SOFTWARE	ARG A:143 , GLU A:192 , GLY A:193 , LEU A:285 , ASN A:286	BINDING SITE FOR RESIDUE SO4 A 502
4	AC4	SOFTWARE	TYR A:145 , THR A:196 , HIS A:199 , ASN A:205 , PHE A:207 , LYS A:214 , HIS A:279 , ILE A:281 , ASN A:294 , TRP A:296	BINDING SITE FOR RESIDUE AKG A 1351
5	AC5	SOFTWARE	LYS A:99 , TYR A:230 , SER A:240 , GLN A:241 , ASP A:243 , HOH A:1078	BINDING SITE FOR RESIDUE GOL A 2000

(no "SS Bond" information available for 3D8C)

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)

Biological Unit 2 (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)

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

Biological Unit 2 (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

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:9-59	51
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

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	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:341
 aligned with HIF1N_HUMAN | Q9NWT6 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:341
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348 
          HIF1N_HUMAN     9 VASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN 349
               SCOP domains d3d8ca_ A: Hypoxia-inducible factor HIF ihhibitor (FIH1)                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3d8cA02 A:306-349 Clavaminate synthase-like  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhh......eee..ee...hhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh....eeeeee........hhhhh.........eeeeeehhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhh.hhhhhhhhhhhh....eee.eeeee....eeeee...eeeeeeeee..eeeeeehhhhhhhhh.......................hhhhhhh.eeeeee....eeee....eeeeee......eeeeeeeee............hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.... 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:9-59 UniProt: 1-59 [INCOMPLETE]  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)
                 3d8c A   9 VASGSGEPREEAGALGPAWDESQLRSYSFPTRPIPRLSQSDPRAEELIENEEPVVLTDTNLVYPALKWDLEYLQENIGNGDFSVYSASTHKFLYYDEKKMANFQNFKPRSNREEMKFHEFVEKLQDIQQRGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYGEQQNFFAQIKGYKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMYWWHHIESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGPLLNTMIKGRYN 349
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348

Chain B from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 3d8c B 794 QLTSYDCEVNAPI 806
                                   803

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Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

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)

d3d8ca_

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)

3d8cA02

A:306-349

(no "Pfam Domain" information available for 3D8C)

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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1h2k
1h2l
1h2m
1h2n
1yci
2ilm	FACTOR INHIBITING HIF-1 ALPHA D201A MUTANT IN COMPLEX WITH 2 FE(II), ALPHA-KETOGLUTARATE AND HIF-1 ALPHA 35MER

Description

Compounds

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Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (8, 8)

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SCOP Domains (1, 1)

CATH Domains (1, 1)

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Gene Ontology (32, 32)

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