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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIGH AFFINITY HETERODIMER OF HIF2 ALPHA AND ARNT C-TERMINAL PAS DOMAINS IN COMPLEX WITH A BENZOXADIAZOLE ANTAGONIST
 
Authors :  T. H. Scheuermann, J. Key, U. K. Tambar, R. K. Bruick, K. H. Gardner
Date :  07 Aug 12  (Deposition) - 27 Feb 13  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pas Fold, Protein : Protein Interactions, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. H. Scheuermann, Q. Li, H. W. Ma, J. Key, L. Zhang, R. Chen, J. A. Garcia J. Naidoo, J. Longgood, D. E. Frantz, U. K. Tambar, K. H. Gardner, R. K. Bruick
Allosteric Inhibition Of Hypoxia Inducible Factor-2 With Small Molecules.
Nat. Chem. Biol. V. 9 271 2013
PubMed-ID: 23434853  |  Reference-DOI: 10.1038/NCHEMBIO.1185

(-) Compounds

Molecule 1 - ENDOTHELIAL PAS DOMAIN-CONTAINING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS-GB1-PARALLEL
    Expression System Strain: BL21(DE3)CODONPLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL PAS DOMAIN, UNP RESIDUES 239-350
    Gene: BHLHE73, EPAS1, HIF2A, MOP2, PASD2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EPAS-1, BASIC-HELIX-LOOP-HELIX-PAS PROTEIN MOP2, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 73, BHLHE73, HIF-1-ALPHA-LIKE FACTOR, HLF, HYPOXIA-INDUCIBLE FACTOR 2-ALPHA, HIF-2-ALPHA, HIF2-ALPHA, MEMBER OF PAS PROTEIN 2, PAS DOMAIN-CONTAINING PROTEIN 2
 
Molecule 2 - ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS-GB1-PARALLEL
    Expression System Strain: BL21(DE3)CODONPLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL PAS DOMAIN, UNP RESIDUES 356-470
    Gene: ARNT, BHLHE2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ARNT PROTEIN, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 2, BHLHE2, DIOXIN RECEPTOR, NUCLEAR TRANSLOCATOR, HYPOXIA-INDUCIBLE FACTOR 1-BETA, HIF-1-BETA, HIF1-BETA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
10X31Ligand/IonN-(3-CHLORO-5-FLUOROPHENYL)-4-NITRO-2,1,3-BENZOXADIAZOL-5-AMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:244 , SER A:246 , HIS A:248 , MET A:252 , ALA A:277 , TYR A:281 , MET A:289 , SER A:292 , HIS A:293 , LEU A:296 , SER A:304 , TYR A:307 , ILE A:337 , CYS A:339 , ASN A:341BINDING SITE FOR RESIDUE 0X3 A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GHI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GHI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GHI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GHI)

(-) Exons   (0, 0)

(no "Exon" information available for 4GHI)

(-) Sequences/Alignments

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:107
                                                                                                                                           
               SCOP domains d4ghia_ A: automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeee.....eeee.hhhhhhhh.hhhhhh..hhhhh....hhhhhhhhhhhhhhhheee...eeee.....eeeeeeeeeee...eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4ghi A   0 FKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYPQCIMCVNYVLSEIE 348
                              ||   245       255       265       275       285       295       305       315       325 ||    341       
                              2|                                                                                     327|              
                             239                                                                                      334              


Chain B from PDB  Type:PROTEIN  Length:110
                                                                                                                                              
               SCOP domains d4ghib_ B: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....eeee..hhhhhhh.hhhhhh..hhhhhh...hhhhhhhhhhhhh......eeeeeeee.....eeeeeeeeeee.........eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 4ghi B 358 CQPTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNS 467
                                   367       377       387       397       407       417       427       437       447       457       467
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GHI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GHI)

(-) Gene Ontology  (60, 79)

Asymmetric/Biological Unit(hide GO term definitions)

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  ARNT_HUMAN | P27540
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  EPAS1_HUMAN | Q99814
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ARNT_HUMAN | P27540: 1d7g 1x0o 2a24 2arn 2b02 2hv1 2k7s 3f1n 3f1o 3f1p 3h7w 3h82 4eq1 4gs9 4h6j 4lpz 4pky 4xt2 5nj8 5tbm 5ufp 5v0l
        EPAS1_HUMAN | Q99814: 1p97 2a24 3f1n 3f1o 3f1p 3h7w 3h82 4gs9 4pky 4xt2 5kiz 5tbm 5ufp

(-) Related Entries Specified in the PDB File

2hv1 NMR-GUIDED MODEL OF THE HETERODIMER OF WILDTYPE HIF2ALPHA PAS-B AND ARNT PAS-B DOMAINS
3f1n CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF AN ARTIFICIAL HIF2 LIGAND IN COMPLEX WITH AN ENGINEERED HIGH AFFINITY HIF2ALPHA PAS-B : ARNT PAS-B PROTEIN HETERODIMER
3f1o CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF AN ARTIFICIAL HIF2 LIGAND IN COMPLEX WITH AN ENGINEERED HIGH AFFINITY HIF2ALPHA PAS-B : ARNT PAS-B PROTEIN HETERODIMER
3f1p CRYSTAL STRUCTURE OF AN ENGINEERED HIGH AFFINITY HIF2ALPHA : PAS-B ARNT PAS-B PROTEIN HETERODIMER
3h7w CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF AN ARTIFICIAL HIF2 LIGAND IN COMPLEX WITH AN ENGINEERED HIGH AFFINITY HIF2ALPHA PAS-B : ARNT PAS-B PROTEIN HETERODIMER
3h82 CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF AN ARTIFICIAL HIF2 LIGAND IN COMPLEX WITH AN ENGINEERED HIGH AFFINITY HIF2ALPHA PAS-B : ARNT PAS-B PROTEIN HETERODIMER