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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT ALPHA 1-MACROGLOBULIN RECEPTOR BINDING DOMAIN
 
Authors :  T. Xiao, D. L. Decamp, S. R. Sprang
Date :  28 Jan 00  (Deposition) - 01 Dec 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Beta Sandwich, Pseudo-Symmetric Dimer, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Xiao, D. L. Decamp, S. R. Spran
Structure Of A Rat Alpha 1-Macroglobulin Receptor-Binding Domain Dimer.
Protein Sci. V. 9 1889 2000
PubMed-ID: 11106161
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA 1-MACROGLOBULIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Taxid: 562
    Fragment: RECEPTOR BINDING DOMAIN
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Tissue: PLASMA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1EDY)

(-) Sites  (0, 0)

(no "Site" information available for 1EDY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EDY)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EDY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EDY)

(-) Exons   (6, 11)

Asymmetric Unit (6, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000094671ENSRNOE00000061288chr4:165551145-165551009137A1M_RAT1-29290--
1.2ENSRNOT000000094672ENSRNOE00000061503chr4:165549994-165549811184A1M_RAT29-90620--
1.3ENSRNOT000000094673ENSRNOE00000061664chr4:165548811-165548658154A1M_RAT91-142520--
1.4ENSRNOT000000094674ENSRNOE00000376989chr4:165548470-16554841853A1M_RAT142-159180--
1.5ENSRNOT000000094675ENSRNOE00000376985chr4:165547431-16554741121A1M_RAT160-16670--
1.6ENSRNOT000000094676ENSRNOE00000061988chr4:165546883-165546715169A1M_RAT167-223570--
1.7ENSRNOT000000094677ENSRNOE00000062151chr4:165545886-16554580285A1M_RAT223-251290--
1.8ENSRNOT000000094678ENSRNOE00000062308chr4:165542552-165542429124A1M_RAT251-292420--
1.9ENSRNOT000000094679ENSRNOE00000062465chr4:165539632-165539518115A1M_RAT293-331390--
1.10ENSRNOT0000000946710ENSRNOE00000062620chr4:165538978-165538869110A1M_RAT331-367370--
1.11ENSRNOT0000000946711ENSRNOE00000062790chr4:165536648-165536487162A1M_RAT368-421540--
1.12ENSRNOT0000000946712ENSRNOE00000062948chr4:165535737-165535510228A1M_RAT422-497760--
1.13ENSRNOT0000000946713ENSRNOE00000063097chr4:165534524-16553446164A1M_RAT498-519220--
1.14ENSRNOT0000000946714ENSRNOE00000063254chr4:165527893-165527751143A1M_RAT519-566480--
1.15ENSRNOT0000000946715ENSRNOE00000063406chr4:165525360-165525211150A1M_RAT567-616500--
1.16ENSRNOT0000000946716ENSRNOE00000063572chr4:165523870-165523706165A1M_RAT617-671550--
1.17ENSRNOT0000000946717ENSRNOE00000063747chr4:165521191-16552109894A1M_RAT672-703320--
1.18ENSRNOT0000000946718ENSRNOE00000063897chr4:165519302-165519128175A1M_RAT703-761590--
1.19ENSRNOT0000000946719ENSRNOE00000064021chr4:165518734-165518506229A1M_RAT761-837770--
1.20ENSRNOT0000000946720ENSRNOE00000064193chr4:165517914-165517788127A1M_RAT838-880430--
1.21ENSRNOT0000000946721ENSRNOE00000064356chr4:165517405-165517284122A1M_RAT880-920410--
1.22ENSRNOT0000000946722ENSRNOE00000064527chr4:165517079-16551702852A1M_RAT921-938180--
1.23ENSRNOT0000000946723ENSRNOE00000064695chr4:165513810-16551372784A1M_RAT938-966290--
1.24ENSRNOT0000000946724ENSRNOE00000064862chr4:165513268-165513092177A1M_RAT966-1025600--
1.25ENSRNOT0000000946725ENSRNOE00000065032chr4:165512822-16551273291A1M_RAT1025-1055310--
1.26ENSRNOT0000000946726ENSRNOE00000350117chr4:165512261-165512105157A1M_RAT1055-1107530--
1.27ENSRNOT0000000946727ENSRNOE00000344825chr4:165511699-16551162575A1M_RAT1108-1132250--
1.28ENSRNOT0000000946728ENSRNOE00000065559chr4:165511349-165511172178A1M_RAT1133-1192600--
1.29ENSRNOT0000000946729ENSRNOE00000065720chr4:165510481-165510231251A1M_RAT1192-1275840--
1.30ENSRNOT0000000946730ENSRNOE00000065855chr4:165509498-165509280219A1M_RAT1276-1348730--
1.31ENSRNOT0000000946731ENSRNOE00000066003chr4:165509107-165508977131A1M_RAT1349-1392442A:3-33
B:3-33		31
31
1.32ENSRNOT0000000946732ENSRNOE00000066146chr4:165508590-16550850091A1M_RAT1392-1422312A:33-63
B:33-63		31
31
1.33ENSRNOT0000000946733ENSRNOE00000066311chr4:165507986-16550791869A1M_RAT1423-1445232A:64-86
B:64-86		23
23
1.34ENSRNOT0000000946734ENSRNOE00000066471chr4:165506877-165506775103A1M_RAT1446-1480352A:87-121
B:87-121		35
35
1.35ENSRNOT0000000946735ENSRNOE00000066623chr4:165505970-16550592942A1M_RAT1480-1494152A:121-135
B:121-132		15
12
1.36ENSRNOT0000000946736ENSRNOE00000332012chr4:165505230-165505085146A1M_RAT1494-150071A:135-136
-		2
-

(-) 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:134
 aligned with A1M_RAT | Q63041 from UniProtKB/Swiss-Prot  Length:1500

    Alignment length:134
                                  1371      1381      1391      1401      1411      1421      1431      1441      1451      1461      1471      1481      1491    
             A1M_RAT   1362 EAPFTLKVNTLPLNFDKAEHHRKFQIHINVSYIGERPNSNMVIVDVKMVSGFIPVKPSVKKLQDQSNIQRTEVNTNHVLIYIEKLTNQTMGFSFAVEQDIPVKNLKPAPVKVYDYYETDEFAIEEYSAPFSSDS 1495
               SCOP domains d1edya_ A: alpha-1-macroglobulin                                                                                                       SCOP domains
               CATH domains 1edyA00 A:3-136  [code=2.60.40.690, no name defined]                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..........eeeeeeeeee.........eeeeee....eeehhhhhhhhhhh..eeeeeee..eeeeee.......eeeeeeeee.........eeeeeee......eeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.31  PDB: A:3-33         ------------------------------Exon 1.33  PDB: A:64-86Exon 1.34  PDB: A:87-121           -------------1. Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.32  PDB: A:33-63        ---------------------------------------------------------Exon 1.35      - Transcript 1 (2)
                1edy A    3 EAPFTLKVNTLPLNFDKAEHHRKFQIHINVSYIGERPNSNMVIVDVKMVSGFIPVKPSVKKLQDQSNIQRTEVNTNHVLIYIEKLTNQTMGFSFAVEQDIPVKNLKPAPVKVYDYYETDEFAIEEYSAPFSSDS  136
                                    12        22        32        42        52        62        72        82        92       102       112       122       132    


Chain B from PDB  Type:PROTEIN  Length:130
 aligned with A1M_RAT | Q63041 from UniProtKB/Swiss-Prot  Length:1500

    Alignment length:130
                                  1371      1381      1391      1401      1411      1421      1431      1441      1451      1461      1471      1481      1491
             A1M_RAT   1362 EAPFTLKVNTLPLNFDKAEHHRKFQIHINVSYIGERPNSNMVIVDVKMVSGFIPVKPSVKKLQDQSNIQRTEVNTNHVLIYIEKLTNQTMGFSFAVEQDIPVKNLKPAPVKVYDYYETDEFAIEEYSAPF 1491
               SCOP domains d1edyb_ B: alpha-1-macroglobulin                                                                                                   SCOP domains
               CATH domains 1edyB00 B:3-132  [code=2.60.40.690, no name defined]                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.........eeeeeeeeee.........eeeeee....eeehhhhhhhhhhh..eeeeeee..eeeeee.......eeeeeeeee.........eeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.31  PDB: B:3-33         ------------------------------Exon 1.33  PDB: B:64-86Exon 1.34  PDB: B:87-121           ----------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.32  PDB: B:33-63        ---------------------------------------------------------Exon 1.35    Transcript 1 (2)
                1edy B    3 EAPFTLKVNTLPLNFDKAEHHRKFQIHINVSYIGERPNSNMVIVDVKMVSGFIPVKPSVKKLQDQSNIQRTEVNTNHVLIYIEKLTNQTMGFSFAVEQDIPVKNLKPAPVKVYDYYETDEFAIEEYSAPF  132
                                    12        22        32        42        52        62        72        82        92       102       112       122       132
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EDY)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A1M_RAT | Q63041)
molecular function
    GO:0048403    brain-derived neurotrophic factor binding    Interacting selectively and non-covalently with brain-derived neurotrophic factor.
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    GO:0048406    nerve growth factor binding    Interacting selectively and non-covalently with nerve growth factor (NGF).
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
biological process
    GO:0007566    embryo implantation    Attachment of the blastocyst to the uterine lining.
    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:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
cellular component
    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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