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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH 5ALPHA-ANDROSTANE-3BETA,17ALPHA-DIOL
 
Authors :  I. Grishkovskaya, G. V. Avvakumov, G. L. Hammond, M. G. Catalano, Y. A. Muller
Date :  17 Apr 02  (Deposition) - 23 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Shbg, 17A-Dha, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Grishkovskaya, G. V. Avvakumov, G. L. Hammond, M. G. Catalano, Y. A. Muller
Steroid Ligands Bind Human Sex Hormone-Binding Globulin In Specific Orientations And Produce Distinct Changes In Protein Conformation
J. Biol. Chem. V. 277 32086 2002
PubMed-ID: 12065592  |  Reference-DOI: 10.1074/JBC.M203999200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SEX HORMONE-BINDING GLOBULIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LG-LIKE 1 DOMAIN, RESIDUES 30-218
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SHBG, SEX STEROID-BINDING PROTEIN, SBP, TESTIS- SPECIFIC ANDROGEN-BINDING PROTEIN, ABP

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1AON1Ligand/Ion5-ALPHA-ANDROSTANE-3-BETA,17-ALPHA-DIOL
2CA1Ligand/IonCALCIUM ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1AON2Ligand/Ion5-ALPHA-ANDROSTANE-3-BETA,17-ALPHA-DIOL
2CA-1Ligand/IonCALCIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:50 , GLU A:52 , ALA A:160 , HOH A:506 , HOH A:511 , HOH A:524BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREASP A:65 , HIS A:83 , HIS A:136 , HOH A:537BINDING SITE FOR RESIDUE ZN A 501
3AC3SOFTWARETHR A:40 , SER A:41 , SER A:42 , ASP A:65 , TRP A:66 , PHE A:67 , VAL A:105 , MET A:107 , HOH A:549BINDING SITE FOR RESIDUE AON A 301

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:164 -A:188

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LHN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016182P185LSHBG_HUMANPolymorphism6258AP156L
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016182P185LSHBG_HUMANPolymorphism6258AP156L
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.SHBG_HUMAN45-217  1A:16-188
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LAM_G_DOMAINPS50025 Laminin G domain profile.SHBG_HUMAN45-217  2A:16-188

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003804502bENSE00001943779chr17:7533468-7533601134SHBG_HUMAN1-37370--
1.3ENST000003804503ENSE00001650558chr17:7533734-753382592SHBG_HUMAN38-68311A:13-3927
1.4ENST000003804504ENSE00000887379chr17:7533998-7534187190SHBG_HUMAN68-131641A:39-10264
1.5ENST000003804505ENSE00000887381chr17:7534518-7534679162SHBG_HUMAN132-185541A:103-156 (gaps)54
1.6ENST000003804506ENSE00000887383chr17:7534907-7535066160SHBG_HUMAN186-239541A:157-18933
1.7ENST000003804507ENSE00000887385chr17:7535197-7535333137SHBG_HUMAN239-284460--
1.8ENST000003804508ENSE00000887386chr17:7536070-7536277208SHBG_HUMAN285-354700--
1.9bENST000003804509bENSE00001828732chr17:7536522-7536701180SHBG_HUMAN354-402490--

(-) 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:176
 aligned with SHBG_HUMAN | P04278 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:177
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
           SHBG_HUMAN    42 PPAVHLSNGPGQEPIAVMTFDLTKITKTSSSFEVRTWDPEGVIFYGDTNPKDDWFMLGLRDGRPEIQLHNHWAQLTVGAGPRLDDGRWHQVEVKMEGDSVLLEVDGEEVLRLRQVSGPLTSKRHPIMRIALGGLLFPASNLRLPLVPALDGCLRRDSWLDKQAEISASAPTSLRSCD 218
               SCOP domains d1lhna_ A: Sex hormone-binding globulin                                                                                                                                           SCOP domains
               CATH domains 1lhnA00 A:13-189  [code=2.60.120.200, no name defined]                                                                                                                            CATH domains
               Pfam domains ---------------------------------Laminin_G_1-1lhnA01 A:46-176                                                                                                       ------------- Pfam domains
         Sec.struct. author ..eee..........eeeeee.hhh....eeeeeee....eeeeeeeee...eeeeeeee..eeeeeee....eeeee..........eeeeeeee..eeeeee..eeeeee..........-..eeeeee.....hhhhh.........eeeeeeee.hhh.eeeee......... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------L--------------------------------- SAPs(SNPs)
                    PROSITE ---LAM_G_DOMAIN  PDB: A:16-188 UniProt: 45-217                                                                                                                                  - PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:13-39     ---------------------------------------------------------------Exon 1.5  PDB: A:103-156 (gaps) UniProt: 132-185      Exon 1.6  PDB: A:157-189          Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.4  PDB: A:39-102 UniProt: 68-131                         --------------------------------------------------------------------------------------- Transcript 1 (2)
                 1lhn A  13 PPAVHLSNGPGQEPIAVMTFDLTKITKTSSSFEVRTWDPEGVIFYGDTNPKDDWFMLGLRDGRPEIQLHNHWAQLTVGAGPRLDDGRWHQVEVKMEGDSVLLEVDGEEVLRLRQVSGPLTSK-HPIMRIALGGLLFPASNLRLPLVPALDGCLRRDSWLDKQAEISASAPTSLRSCD 189
                                    22        32        42        52        62        72        82        92       102       112       122       132 | |   142       152       162       172       182       
                                                                                                                                                   134 |                                                     
                                                                                                                                                     136
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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  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (SHBG_HUMAN | P04278)
molecular function
    GO:0005497    androgen binding    Interacting selectively and non-covalently with any androgen, male sex hormones.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0005496    steroid binding    Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1lhn
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  SHBG_HUMAN | P04278
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 Related Entries

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

UniProtKB/Swiss-Prot
        SHBG_HUMAN | P04278: 1d2s 1f5f 1kdk 1kdm 1lho 1lhu 1lhv 1lhw

(-) Related Entries Specified in the PDB File

1d2s CRYSTAL STRUCTURE OF THE N-TERMINAL LAMININ G-LIKE DOMAINOF SHBG IN COMPLEX WITH DIHYDROTESTOSTERONE
1f5f CRYSTAL STRUCTURE OF THE N-TERMINAL G-DOMAIN OF SHBG IN COMPLEX WITH ZINC
1kdk THE STRUCTURE OF THE N-TERMINAL LG DOMAIN OF SHBG IN CRYSTALS SOAKED WITH EDTA
1kdm THE CRYSTAL STRUCTURE OF THE HUMAN SEX HORMONE-BINDING GLOBULIN (TETRAGONAL CRYSTAL FORM)
1lho CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH 5ALPHA-ANDROSTANE-3BETA,17BETA-DIOL
1lhu CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH ESTRADIOL
1lhv CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH NORGESTREL
1lhw CRYSTAL STRUCTURE OF THE N-TERMINAL LG-DOMAIN OF SHBG IN COMPLEX WITH 2-METHOXYESTRADIOL