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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REACTIVE LOOP CLEAVED CORTICOSTEROID BINDING GLOBULIN COMPLEXED WITH CORTISOL
 
Authors :  A. Zhou, Z. Wei, R. J. Read
Date :  13 Oct 07  (Deposition) - 13 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycoprotein, Lipid-Binding, Steroid-Binding, Disease Mutation, Corticosteroid Binding Globulin, Transport Protein, Cbg, Serpin, Cleaved, Secreted, Cortisol, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Zhou, Z. Wei, P. L. Stanley, R. J. Read, P. E. Stein, R. W. Carrell
The S-To-R Transition Of Corticosteroid-Binding Globulin And The Mechanism Of Hormone Release.
J. Mol. Biol. V. 380 244 2008
PubMed-ID: 18513745  |  Reference-DOI: 10.1016/J.JMB.2008.05.012

(-) Compounds

Molecule 1 - CORTICOSTEROID-BINDING GLOBULIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI,
    Expression System PlasmidPSUMO3-CBG
    Expression System StrainBL21(DE3)
    Expression System VectorPSUMO3
    FragmentRESIDUES 33-405
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCOMPLEXED WITH CORTISOL
    SynonymCBG, TRANSCORTIN, SERPIN A6, HUMAN CORTICOSTEROID-BINDING GLOBULIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1HCY2Ligand/Ion(11ALPHA,14BETA)-11,17,21-TRIHYDROXYPREGN-4-ENE-3,20-DIONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HCY1Ligand/Ion(11ALPHA,14BETA)-11,17,21-TRIHYDROXYPREGN-4-ENE-3,20-DIONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HCY1Ligand/Ion(11ALPHA,14BETA)-11,17,21-TRIHYDROXYPREGN-4-ENE-3,20-DIONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:19 , GLN A:232 , ILE A:263 , ASN A:264 , SER A:267 , HIS A:368 , TRP A:371 , HOH A:2109BINDING SITE FOR RESIDUE HCY A1384
2AC2SOFTWARESER B:19 , GLN B:232 , ARG B:260 , ASN B:264 , SER B:267 , HIS B:368 , TRP B:371BINDING SITE FOR RESIDUE HCY B1384

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VDY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VDY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_007111L115HCBG_HUMANDisease (CBG deficiency)113418909A/BL93H
2UniProtVAR_024350S246ACBG_HUMANPolymorphism2228541A/BS224A
3UniProtVAR_016223D389NCBG_HUMANDisease (CBG deficiency)28929488A/BD367N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_007111L115HCBG_HUMANDisease (CBG deficiency)113418909AL93H
2UniProtVAR_024350S246ACBG_HUMANPolymorphism2228541AS224A
3UniProtVAR_016223D389NCBG_HUMANDisease (CBG deficiency)28929488AD367N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_007111L115HCBG_HUMANDisease (CBG deficiency)113418909BL93H
2UniProtVAR_024350S246ACBG_HUMANPolymorphism2228541BS224A
3UniProtVAR_016223D389NCBG_HUMANDisease (CBG deficiency)28929488BD367N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.CBG_HUMAN377-387
 
  2A:355-365
B:355-365
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.CBG_HUMAN377-387
 
  1A:355-365
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.CBG_HUMAN377-387
 
  1-
B:355-365

(-) Exons   (0, 0)

(no "Exon" information available for 2VDY)

(-) 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:361
 aligned with CBG_HUMAN | P08185 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:368
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397        
            CBG_HUMAN    38 GLASANVDFAFSLYKHLVALSPKKNIFISPVSISMALAMLSLGTCGHTRAQLLQGLGFNLTERSETEIHQGFQHLHQLFAKSDTSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQGKIVDLFSGLDSPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTISYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLYIPKVTISGVYDLGDVLEEMGIADLFTNQANFSRITQDAQLKSSKVVHKAVLQLNEEGVDTAGSTGVTLNLTSKPIILRFNQPFIIMIFDHFTWSSLFLARVMNPV 405
               SCOP domains d2vdya_ A: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2vdyA01 A:16-184,A:280-333 Antithrombin, subunit I, domain 2                                                                                                             2vdyA02 A:185-279,A:339-382 Alpha-1-antitrypsin, domain 1                                      2vdyA01 A:16-184,A:280-333                            -----2vdyA02 A:1 85-279,A:339-382                - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhh..hhhhhhhhhhhh....---.hhhhhhhhhhhhhhh.ee....eeeeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh........---.....eeeeeeeeeeee.....hhhhheeeeee.....eeeeeeeeeeeeeeeee.....eeeeeee....eeeeeeee...hhhhhhh..hhhhhhhhhhhheeeeeeeeee..eeeeeeehhhhhhhh..hhhhh.............eeeeeeeeeeeeee...eeeeeeeeeeeeee.-..eeee....eeeeeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------------------------------------N---------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vdy A  16 GLASANVDFAFSLYKHLVALSPKKNIFISPVSISMALAMLSLGTCGHTRAQLLQGLGFNL---SETEIHQGFQHLHQLFAKSDTSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQGKIVDLF---DSPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTISYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLYIPKVTISGVYDLGDVLEEMGIADLFTTQANFSRITQDAQLKSSKVVHKAVLQLNEEGTEAAGAMFLEAIPR-KPIILRFNQPFIIMIFDHFTWSSLFLARVMNPV 383
                                    25        35        45        55        65        75   |    85        95       105       115       125       135       145       155        |-  |    175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345   | | 355       365       375        
                                                                                      75  79                                                                                  164 168                                                                                                                                                                                  349 |                                
                                                                                                                                                                                                                                                                                                                                                                         351                                

Chain B from PDB  Type:PROTEIN  Length:361
 aligned with CBG_HUMAN | P08185 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:368
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397        
            CBG_HUMAN    38 GLASANVDFAFSLYKHLVALSPKKNIFISPVSISMALAMLSLGTCGHTRAQLLQGLGFNLTERSETEIHQGFQHLHQLFAKSDTSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQGKIVDLFSGLDSPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTISYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLYIPKVTISGVYDLGDVLEEMGIADLFTNQANFSRITQDAQLKSSKVVHKAVLQLNEEGVDTAGSTGVTLNLTSKPIILRFNQPFIIMIFDHFTWSSLFLARVMNPV 405
               SCOP domains d2vdyb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2vdyB01 B:16-184,B:280-333 Antithrombin, subunit I, domain 2                                                                                                             2vdyB02 B:185-279,B:339-382 Alpha-1-antitrypsin, domain 1                                      2vdyB01 B:16-184,B:280-333                            -----2vdyB02 B:1 85-279,B:339-382                - CATH domains
           Pfam domains (1) ---Serpin-2vdyB01 B:19-382                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (1)
           Pfam domains (2) ---Serpin-2vdyB02 B:19-382                                                                                                                                                                                                                                                                                                                                                     - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh....---hhhhhhhhhhhhhhhh.ee...eeeeeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh.........---....eeeeeeeeeeee.....hhhhheeeeee.....eeeeeeeeeeeeeeeee.....eeeeeee....eeeeeeee...hhhhhhh..hhhhhhhhhhhheeeeeeeeee..eeeeeeehhhhhhhh..hhhhh.............eeeeeeeeeeeeee...eeeeeeeeeeeeee.-..eeee....eeeeeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------------------------------------------------------------------N---------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vdy B  16 GLASANVDFAFSLYKHLVALSPKKNIFISPVSISMALAMLSLGTCGHTRAQLLQGLGFNL---SETEIHQGFQHLHQLFAKSDTSLEMTMGNALFLDGSLELLESFSADIKHYYESEVLAMNFQDWATASRQINSYVKNKTQGKIVDLFS---SPAILVLVNYIFFKGTWTQPFDLASTREENFYVDETTVVKVPMMLQSSTISYLHDSELPCQLVQMNYVGNGTVFFILPDKGKMNTVIAALSRDTINRWSAGLTSSQVDLYIPKVTISGVYDLGDVLEEMGIADLFTTQANFSRITQDAQLKSSKVVHKAVLQLNEEGTEAAGAMFLEAIPR-KPIILRFNQPFIIMIFDHFTWSSLFLARVMNPV 383
                                    25        35        45        55        65        75   |    85        95       105       115       125       135       145       155       165   |   175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345   | | 355       365       375        
                                                                                      75  79                                                                                   165 169                                                                                                                                                                                 349 |                                
                                                                                                                                                                                                                                                                                                                                                                         351                                

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CBG_HUMAN | P08185)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
    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.
biological process
    GO:0008211    glucocorticoid metabolic process    The chemical reactions and pathways involving glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBG_HUMAN | P081852vdx 4bb2 4c41 4c49

(-) Related Entries Specified in the PDB File

2vdx CRYSTAL STRUCTURE OF THE REACTIVE LOOP CLEAVED CORTICOSTEROID BINDING GLOBULIN