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(-) Description

Title :  HUMAN NUCLEAR RECEPTOR LIVER RECEPTOR HOMOLOGUE-1, LRH-1, BOUND TO AN E. COLI PHOSPHOLIPID AND A FRAGMENT OF TIF-2
 
Authors :  E. A. Ortlund, P. M. Musille
Date :  16 May 14  (Deposition) - 16 Dec 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Nuclear Receptor, Phospholipid, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. M. Musille, B. R. Kossmann, J. A. Kohn, I. Ivanov, E. A. Ortlund
Unexpected Allosteric Network Contributes To Lrh-1 Co-Regulator Selectivity.
J. Biol. Chem. V. 291 1411 2016
PubMed-ID: 26553876  |  Reference-DOI: 10.1074/JBC.M115.662874

(-) Compounds

Molecule 1 - NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 2
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 301-541
    Gene: NR5A2, B1F, CPF, FTF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 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 COACTIVATOR 2
    Chains: B, D, F, H
    Engineered: YES
    Fragment: UNP RESIDUES 740-753
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NCOA-2,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75,BHLHE75, TRANSCRIPTIONAL INTERMEDIARY FACTOR 2,HTIF2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1CPS12Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2EPH4Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CPS3Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2EPH1Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CPS2Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2EPH1Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1CPS5Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2EPH1Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1CPS2Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2EPH1Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:341 , PHE A:342 , MET A:345 , LEU A:386 , HIS A:390 , ILE A:415 , ILE A:416 , GLN A:419 , ALA A:420 , GLY A:421 , LEU A:424 , LEU A:427 , MET A:428 , ALA A:431 , ALA A:513 , TYR A:516 , LYS A:520 , HOH A:714binding site for residue EPH A 601
02AC2SOFTWAREMET A:323 , LEU A:326 , GLN A:330 , THR A:341 , LEU A:344 , LEU A:405 , THR A:407 , GLN A:409 , HOH A:734 , HOH A:757binding site for residue CPS A 602
03AC3SOFTWARETYR A:518 , LEU A:536 , LEU G:482binding site for residue CPS A 603
04AC4SOFTWAREGLU A:515 , TYR A:519 , HIS E:336 , GLU G:471 , GLN G:474 , GLU G:475 , ASN G:478binding site for residue CPS A 604
05AC5SOFTWARETHR C:341 , PHE C:342 , MET C:345 , LEU C:386 , HIS C:390 , ILE C:416 , GLN C:419 , ALA C:420 , GLY C:421 , LEU C:424 , LEU C:427 , MET C:428 , ILE C:509 , TYR C:516 , LYS C:520 , HOH C:711binding site for residue EPH C 601
06AC6SOFTWAREMET C:323 , LEU C:326 , GLN C:330 , THR C:341 , LEU C:344 , THR C:407 , GLN C:409 , HOH C:706 , HOH C:708 , HOH C:741binding site for residue CPS C 602
07AC7SOFTWARELEU C:482binding site for residue CPS C 603
08AC8SOFTWARETHR E:341 , PHE E:342 , MET E:345 , LEU E:386 , ILE E:387 , HIS E:390 , ILE E:415 , ILE E:416 , GLN E:419 , GLY E:421 , LEU E:424 , MET E:428 , ALA E:513 , GLU E:514 , TYR E:516 , LYS E:520binding site for residue EPH E 601
09AC9SOFTWAREGLU E:475 , ASN E:478 , LEU E:482 , CPS E:604 , HIS G:336binding site for residue CPS E 602
10AD1SOFTWAREGLU A:471 , GLU A:475 , ASN A:478 , THR E:423 , GLU E:515 , TYR E:519 , CPS E:606 , HOH E:723 , HOH E:736binding site for residue CPS E 603
11AD2SOFTWARELEU E:482 , CPS E:602binding site for residue CPS E 604
12AD3SOFTWAREMET E:323 , LEU E:326 , GLN E:330 , LEU E:344 , THR E:407 , GLN E:409 , HOH E:712 , HOH E:733binding site for residue CPS E 605
13AD4SOFTWARETYR E:518 , LEU E:536 , CPS E:603 , HOH E:771binding site for residue CPS E 606
14AD5SOFTWARETHR G:341 , PHE G:342 , MET G:345 , LEU G:386 , ILE G:387 , HIS G:390 , ILE G:415 , ILE G:416 , GLN G:419 , GLY G:421 , LEU G:424 , MET G:428 , TYR G:516 , LYS G:520 , HOH G:703binding site for residue EPH G 601
15AD6SOFTWARETHR G:423 , GLU G:515 , TYR G:519 , HOH G:727binding site for residue CPS G 602
16AD7SOFTWAREMET G:323 , LEU G:326 , GLN G:330 , LEU G:344 , LEU G:405 , THR G:407 , GLN G:409 , HOH G:708binding site for residue CPS G 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PLE)

(-) 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 ....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ple A 298 AASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHA 538
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537 


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4ple B 742 NALLRYLLD 750


Chain C from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ple C 299 ASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHA 538
                                   308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458   ||  469       479       489       499       509       519       529         
                                                                                                                                                                                             462|                                                                          
                                                                                                                                                                                              464                                                                          


Chain D from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4ple D 742 NALLRYLLDK 751
                                   751


Chain E from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ple E 297 AAASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLH 537
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536 


Chain F 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
                 4ple F 742 NALLRYLLDK 751
                                   751


Chain G from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ple G 298 AASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHA 538
                                   307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537 


Chain H 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
                 4ple H 742 NALLRYLLDK 751
                                   751
   Legend:   → Mismatch (orange background)
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  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 4PLE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (84, 94)

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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
        NCOA2_HUMAN | Q15596: 1gwq 1gwr 1m2z 1mv9 1mvc 1mzn 1p93 1t63 1t65 1uhl 1yok 1zdt 1zdu 1zky 2ao6 2b1v 2b1z 2b23 2fai 2g44 2g5o 2ldc 2p15 2p1t 2p1u 2p1v 2q7j 2q7l 2yjd 2zxz 2zy0 3a9e 3cld 3dzu 3dzy 3e00 3e7c 3e94 3erd 3fug 3gn8 3k22 3k23 3kwy 3kyt 3l0e 3l0j 3l0l 3o1d 3o1e 3oap 3ozj 3pcu 3plz 3q95 3q97 3r5m 3up0 3up3 4csj 4dos 4e2j 4fhh 4fhi 4ia1 4ia2 4ia3 4ia7 4iqr 4iu7 4iui 4iv2 4iv4 4ivw 4ivy 4iw6 4iw8 4iwc 4iwf 4k4j 4k6i 4m8e 4m8h 4nie 4nqa 4oc7 4p6w 4p6x 4pld 4poh 4poj 4pp3 4pp5 4pp6 4ppp 4pps 4pxm 4q0a 4qe6 4qe8 4rfw 4rmc 4rmd 4rme 4ruo 4udc 4udd 4wg0 4zn7 4zn9 4znh 4zns 4znt 4znu 4znv 4znw 4zo1 4zsh 5aph 5apj 5di7 5did 5die 5dig 5dk9 5dkb 5dke 5dkg 5dks 5dl4 5dlr 5dmc 5dmf 5dp0 5drj 5drm 5dtv 5du5 5due 5dug 5duh 5dvs 5dvv 5dwe 5dwg 5dwi 5dwj 5dx3 5dxb 5dxe 5dxg 5dxk 5dxm 5dxp 5dxq 5dxr 5dy8 5dyb 5dyd 5dz0 5dz1 5dz3 5dzh 5dzi 5e0w 5e0x 5e14 5e15 5e19 5e1c 5ec9 5egv 5ehj 5ei1 5eit 5g3j 5g42 5g43 5g44 5g45 5g46 5g5w 5h1e 5hyr 5i4v 5iaw 5ick 5kcc 5kcd 5kce 5kcf 5kct 5kcu 5kcw 5kd9 5kr9 5kra 5krc 5krf 5krh 5kri 5krj 5krk 5krl 5krm 5kro 5l11 5lga 5syz 5tld 5tlf 5tlg 5tll 5tlm 5tlo 5tlp 5tlt 5tlu 5tlv 5tlx 5tly 5tm1 5tm2 5tm3 5tm4 5tm5 5tm6 5tm7 5tm8 5tm9 5tml 5tmm 5tmo 5tmq 5tmr 5tms 5tmt 5tmu 5tmv 5tmw 5tmz 5tn1 5tn3 5tn4 5tn5 5tn6 5tn7 5tn8 5u2d
        NR5A2_HUMAN | O00482: 1yok 1yuc 1zdu 2a66 3plz 3tx7 4dor 4dos 4is8 4oni 4pld 4rwv 5l0m 5l11 5syz 5unj

(-) Related Entries Specified in the PDB File

4pld