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(-) Description

Title :  2.2 ANGSTROM CRYSTAL STRUCTURE OF THR114PHE ALPHA1-ANTITRYPSIN
 
Authors :  B. Gooptu, I. Nobeli, A. Purkiss, R. L. Phillips, M. Mallya, D. A. Lomas, T. E. Barrett
Date :  11 Jul 08  (Deposition) - 31 Mar 09  (Release) - 14 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Serpin, Serine Proteinase Inhibitor, Alpha1-Antitrypsin, Polymerisation, Rational Drug Design, Conformational Disease, Emphysema, Cirrhosis, Acute Phase, Alternative Splicing, Blood Coagulation, Disease Mutation, Glycoprotein, Hydrolase, Polymorphism, Protease, Protease Inhibitor, Secreted, Serine Protease Inhibitor, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Gooptu, E. Miranda, I. Nobeli, M. Mallya, A. Purkiss, S. C. Brown, C. Summers, R. L. Phillips, D. A. Lomas, T. E. Barrett
Crystallographic And Cellular Characterisation Of Two Mechanisms Stabilising The Native Fold Of Alpha1-Antitrypsin: Implications For Disease And Drug Design.
J. Mol. Biol. V. 387 857 2009
PubMed-ID: 19232354  |  Reference-DOI: 10.1016/J.JMB.2009.01.069
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-1-ANTITRYPSIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE31
    Expression System StrainXL-1BLUE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSERPINA1, AAT, PI, PRO0684, PRO2209
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALPHA-1 PROTEASE INHIBITOR, ALPHA-1- ANTIPROTEINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3DRM)

(-) Sites  (0, 0)

(no "Site" information available for 3DRM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DRM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DRM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (32, 32)

Asymmetric/Biological Unit (32, 32)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_006980A58TA1AT_HUMANPolymorphism149319176AA34T
02UniProtVAR_006981R63CA1AT_HUMANPolymorphism28931570AR39C
03UniProtVAR_006982L65PA1AT_HUMANPolymorphism28931569AL41P
04UniProtVAR_006983S69FA1AT_HUMANPolymorphism199687431AS45F
05UniProtVAR_006985S77FA1AT_HUMANPolymorphism55819880AS53F
06UniProtVAR_006986A84TA1AT_HUMANPolymorphism111850950AA60T
07UniProtVAR_006987G91EA1AT_HUMANPolymorphism28931568AG67E
08UniProtVAR_006988T92IA1AT_HUMANUnclassified  ---AT68I
09UniProtVAR_011620T109MA1AT_HUMANPolymorphism199422213AT85M
10UniProtVAR_006989P112TA1AT_HUMANUnclassified  ---AP88T
11UniProtVAR_006990I116NA1AT_HUMANPolymorphism28931572AI92N
12UniProtVAR_006991R125HA1AT_HUMANPolymorphism709932AR101H
13UniProtVAR_006992G139SA1AT_HUMANPolymorphism11558261AG115S
14UniProtVAR_006993G172RA1AT_HUMANPolymorphism112030253AG148R
15UniProtVAR_006994G172WA1AT_HUMANPolymorphism112030253AG148W
16UniProtVAR_006995Q180EA1AT_HUMANUnclassified  ---AQ156E
17UniProtVAR_006996E228KA1AT_HUMANPolymorphism199422208AE204K
18UniProtVAR_006997V237AA1AT_HUMANPolymorphism6647AV213A
19UniProtVAR_006998R247CA1AT_HUMANPolymorphism28929470AR223C
20UniProtVAR_006999D280VA1AT_HUMANPolymorphism28929472AD256V
21UniProtVAR_007000E288VA1AT_HUMANPolymorphism17580AE264V
22UniProtVAR_007001S354FA1AT_HUMANPolymorphism201788603AS330F
23UniProtVAR_007002A360TA1AT_HUMANPolymorphism1802959AA336T
24UniProtVAR_007003D365NA1AT_HUMANPolymorphism143370956AD341N
25UniProtVAR_007004E366KA1AT_HUMANPolymorphism28929474AE342K
26UniProtVAR_007005M382RA1AT_HUMANPolymorphism121912713AM358R
27UniProtVAR_007006P386HA1AT_HUMANUnclassified  ---AP362H
28UniProtVAR_007007P386TA1AT_HUMANPolymorphism12233AP362T
29UniProtVAR_007008E387KA1AT_HUMANPolymorphism121912712AE363K
30UniProtVAR_007009P393LA1AT_HUMANPolymorphism199422209AP369L
31UniProtVAR_007010E400DA1AT_HUMANPolymorphism1303AE376D
32UniProtVAR_007011P415HA1AT_HUMANUnclassified  ---AP391H

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.A1AT_HUMAN388-398  1A:364-374

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1dENST000003930881dENSE00001561696chr14:94856974-94856794181A1AT_HUMAN-00--
1.2bENST000003930882bENSE00001514164chr14:94855347-94855138210A1AT_HUMAN-00--
1.2dENST000003930882dENSE00001514163chr14:94855000-94854897104A1AT_HUMAN-00--
1.3bENST000003930883bENSE00001302079chr14:94849578-94848929650A1AT_HUMAN1-2162161A:24-192169
1.4aENST000003930884aENSE00001310159chr14:94847478-94847208271A1AT_HUMAN216-306911A:192-28291
1.5aENST000003930885aENSE00001226898chr14:94845948-94845801148A1AT_HUMAN306-355501A:282-33150
1.6bENST000003930886bENSE00001854348chr14:94844977-94844713265A1AT_HUMAN356-418631A:332-393 (gaps)62

(-) Sequences/Alignments

Asymmetric/Biological 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:362
 aligned with A1AT_HUMAN | P01009 from UniProtKB/Swiss-Prot  Length:418

    Alignment length:370
                                    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       407       417
           A1AT_HUMAN    48 NKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSSWVLLMKYLGNATAIFFLPDEGKLQHLENELTHDIITKFLENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFSNGADLSGVTEEAPLKLSKAVHKAVLTIDEKGTEAAGAMFLEAIPMSIPPEVKFNKPFVFLMIEQNTKSPLFMGKVVNPTQ 417
               SCOP domains d3drma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3drmA01 A:24-194,A:290-343 Antithrombin, subunit I, domain 2                                                                                                               3drmA02 A:195-289,A:352-393 Alpha-1-antitrypsin, domain 1                                      3drmA01 A:24-194,A:290-343                            --------3drmA02 A:195-289,A:352-393                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhh..hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.......eeeeeeeeee.....hhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh................eeeeeeeee........hhhhheeeeee.....eeeeeeeeeeeeeeeeee....eeeeeeee...eeeeeeee...hhhhhhhhhhhhhhhhhhhh...eeeeeeee.eeeeeeeehhhhhhh...hhhhh.................eeeeeeeeee...--------...........eee....eeeeeee.....eeeeeee..... Sec.struct. author
             SAPs(SNPs) (1) ----------T----C-P---F-------F------T------EI----------------M--T---N--------H-------------S--------------------------------R-------E-----------------------------------------------K--------A---------C--------------------------------V-------V-----------------------------------------------------------------F-----T----NK---------------R---HK-----L------D--------------H-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------W---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:24-192 UniProt: 1-216 [INCOMPLETE]                                                                                                                     -----------------------------------------------------------------------------------------Exon 1.5a  PDB: A:282-331 UniProt: 306-355        Exon 1.6b  PDB: A:332-393 (gaps) UniProt: 356-418 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.4a  PDB: A:192-282 UniProt: 216-306                                                 --------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3drm A  24 NKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIATAFAMLSLGTKADTHDEILEGLNFNLTEIPEAQIHEGFQELLRTLNQPDSQLQLTFGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIVDLVKELDRDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSSWVLLMKYLGNATAIFFLPDEGKLQHLENELTHDIITKFLENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFSNGADLSGVTEEAPLKLSKAVHKAVLTIDEK--------FLEAIPMSIPPEVKFNKPFVFLMIEQNTKSPLFMGKVVNPTQ 393
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
                                                                                                                                                                                                                                                                                                                                                         343      352                                         

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DRM)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A1AT_HUMAN | P01009)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or 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:0048208    COPII vesicle coating    The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0006953    acute-phase response    An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    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.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
cellular component
    GO:0030134    COPII-coated ER to Golgi transport vesicle    A vesicle with a coat formed of the COPII coat complex proteins. The COPII coat complex is formed by the Sec23p/Sec24p and the Sec13p/Sec31p heterodimers. COPII-associated vesicles transport proteins from the rough endoplasmic reticulum to the Golgi apparatus (anterograde transport).
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0033116    endoplasmic reticulum-Golgi intermediate compartment membrane    The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
    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.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        A1AT_HUMAN | P010091atu 1d5s 1ezx 1hp7 1iz2 1kct 1oo8 1oph 1psi 1qlp 1qmb 2d26 2qug 3cwl 3cwm 3dru 3ndd 3ndf 3ne4 3t1p 4pyw 5io1 7api 8api 9api

(-) Related Entries Specified in the PDB File

3dru