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(-) Description

Title :  STRUCTURE OF HUMAN ORPHAN RECEPTOR LRH1 BOUND TO TWO BACTERIAL PHOSPHOLIPIDS
 
Authors :  M. A. Gorman, M. W. Parker, S. Kusumo
Date :  28 Jan 14  (Deposition) - 11 Feb 15  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Alpha Helical Sandwich Fold, Nuclear Receptor, Co-Factor Binding, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Gorman, M. W. Parker, S. Kusumo
Human Nuclear Receptor Lrh1 Bound To Phosopholipids And Shp Peptide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 (DE3) STAR ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 291-541
    Gene: NR5A2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ORPHAN NUCLEAR RECEPTOR NR5A2, ALPHA-1-FETOPROTEIN TRANSCRIPTION FACTOR, B1-BINDING FACTOR, HB1F, CYP7A PROMOTER-BINDING FACTOR, HEPATOCYTIC TRANSCRIPTION FACTOR, LIVER RECEPTOR HOMOLOG 1, LRH-1
 
Molecule 2 - NUCLEAR RECEPTOR SUBFAMILY 0 GROUP B MEMBER 2
    Chains: C, D
    Engineered: YES
    Fragment: NR BOX1, UNP RESIDUES 12-30
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    Synonym: NUCLEAR RECEPTOR NR0B2, ORPHAN NUCLEAR RECEPTOR SHP, SMALL HETERODIMER PARTNER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1EPH1Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2GOL3Ligand/IonGLYCEROL
3P6L1Ligand/Ion(2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL(8E)-OCTADEC-8-ENOATE
4PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EPH1Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2GOL3Ligand/IonGLYCEROL
3P6L-1Ligand/Ion(2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL(8E)-OCTADEC-8-ENOATE
4PG4-1Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1EPH-1Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2GOL-1Ligand/IonGLYCEROL
3P6L1Ligand/Ion(2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL(8E)-OCTADEC-8-ENOATE
4PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:342 , MET A:345 , HIS A:390 , ILE A:416 , ALA A:420 , GLY A:421 , LEU A:424 , MET A:428 , ALA A:431 , TYR A:516 , LYS A:520 , HOH A:714BINDING SITE FOR RESIDUE EPH A 601
2AC2SOFTWAREGLN A:409BINDING SITE FOR RESIDUE GOL A 602
3AC3SOFTWARELEU A:454 , SER A:458 , ASP A:460 , LEU A:503 , ARG A:507 , HOH A:702 , HOH A:705 , HOH A:718 , HOH A:867BINDING SITE FOR RESIDUE GOL A 603
4AC4SOFTWAREGLN A:351 , GLU A:358 , HOH A:857BINDING SITE FOR RESIDUE GOL A 604
5AC5SOFTWAREPHE B:342 , MET B:345 , SER B:383 , ILE B:387 , HIS B:390 , ILE B:416 , GLN B:419 , ALA B:420 , GLY B:421 , LEU B:424 , LEU B:427 , MET B:428 , ALA B:513 , TYR B:516 , LEU B:517 , LYS B:520 , HOH B:718 , HOH B:835BINDING SITE FOR RESIDUE P6L B 601
6AC6SOFTWARELEU B:326 , GLN B:419 , HOH B:828BINDING SITE FOR RESIDUE PG4 B 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ONI)

(-) 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 A from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oni A 299 ASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAK 539
                                   308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538 


Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oni B 300 SIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAKRA 541
                                   309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539  


Chain C from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 4oni C  13 GAASRPAILYALLSSS  28
                                    22      


Chain D from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4oni D  18 PAILYALLSS  27
                                    27
   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  (0, 0)

(no "SCOP Domain" information available for 4ONI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (60, 70)

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  4oni
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  NR5A2_HUMAN | O00482
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 Related Entries

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

UniProtKB/Swiss-Prot
        NR0B2_HUMAN | Q15466: 1yuc 2q3y 2z4j 4dor
        NR5A2_HUMAN | O00482: 1yok 1yuc 1zdu 2a66 3plz 3tx7 4dor 4dos 4is8 4pld 4ple 4rwv 5l0m 5l11 5syz 5unj

(-) Related Entries Specified in the PDB File

1yok 1yuc