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(-) Description

Title :  CRYSTAL STRUCTURE OF MONOMERIC HUMAN CYSTATIN C STABILIZED AGAINST AGGREGATION
 
Authors :  R. Kolodziejczyk, K. Michalska, A. Hernandez-Santoyo, M. Wahlbom, A. M. Jaskolski
Date :  18 Feb 09  (Deposition) - 23 Feb 10  (Release) - 28 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cysteine Protease Inhibitor, 3D Domain Swapping, Protein Aggregation, Amyloid, Protein Engineering, Twinning, Hereditary Cystatin C Amyloid Angiopathy, Amyloidosis, Disease Mutation, Polymorphism, Protease Inhibitor, Secreted, Thiol Protease Inhibitor, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Kolodziejczyk, K. Michalska, A. Hernandez-Santoyo, M. Wahlbom, A. Grubb, M. Jaskolski
Crystal Structure Of Human Cystatin C Stabilized Against Amyloid Formation.
Febs J. V. 277 1726 2010
PubMed-ID: 20175878  |  Reference-DOI: 10.1111/J.1742-4658.2010.07596.X

(-) Compounds

Molecule 1 - CYSTATIN-C
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHD 313
    Expression System StrainMC1061
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentHUMAN CYSTATIN C STAB1: UNP RESIDUES 27-146
    GeneCST3
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYSTATIN-3, NEUROENDOCRINE BASIC POLYPEPTIDE, GAMMA-TRACE, POST-GAMMA-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  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 3GAX)

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:47 -A:69
2A:73 -A:83
3A:97 -A:117
4B:47 -B:69
5B:73 -B:83
6B:97 -B:117

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_002207L94QCYTC_HUMANDisease (AMYL6)28939068A/BL68Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_002207L94QCYTC_HUMANDisease (AMYL6)28939068AL68Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_002207L94QCYTC_HUMANDisease (AMYL6)28939068BL68Q

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYSTATINPS00287 Cysteine proteases inhibitors signature.CYTC_HUMAN80-93
 
  2A:54-67
B:54-67
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYSTATINPS00287 Cysteine proteases inhibitors signature.CYTC_HUMAN80-93
 
  1A:54-67
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYSTATINPS00287 Cysteine proteases inhibitors signature.CYTC_HUMAN80-93
 
  1-
B:54-67

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003984112bENSE00001533104chr20:23618582-23618257326CYTC_HUMAN1-81812A:12-55
B:12-55
44
44
1.3ENST000003984113ENSE00000660936chr20:23616004-23615891114CYTC_HUMAN82-119382A:56-93 (gaps)
B:56-93 (gaps)
38
38
1.4aENST000003984114aENSE00001533102chr20:23614636-2361455186CYTC_HUMAN120-146272A:94-120
B:94-120
27
27
1.5ENST000003984115ENSE00001533100chr20:23610102-236085341569CYTC_HUMAN-00--

(-) 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:107
 aligned with CYTC_HUMAN | P01034 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:109
                                    47        57        67        77        87        97       107       117       127       137         
           CYTC_HUMAN    38 GPMDASVEEEGVRRALDFAVGEYNKASNDMYHSRALQVVRARKQIVAGVNYFLDVELGRTTCTKTQPNLDNCPFHDQPHLKRKAFCSFQIYAVPWQGTMTLSKSTCQDA 146
               SCOP domains d3gaxa_ A: Cystatin C                                                                                         SCOP domains
               CATH domains 3gaxA00 A:12-120  [code=3.10.450.10, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeee...eeeeeeeeeeeeeee...--........hhhhhh.eeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------Q---------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------CYSTATIN      ----------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2b  PDB: A:12-55 UniProt: 1-81       Exon 1.3  PDB: A:56-93 (gaps)         Exon 1.4a  PDB: A:94-120    Transcript 1
                 3gax A  12 GPMDASVEEEGVRRALDFAVGEYNKASNDMYHSRACQVVRARKQIVAGVNYFLDVELCRTTCTKTQ--LDNCPFHDQPHLKRKAFCSFQIYAVPWQGTMTLSKSTCQDA 120
                                    21        31        41        51        61        71     |  81        91       101       111         
                                                                                            77 80                                        

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with CYTC_HUMAN | P01034 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:109
                                    47        57        67        77        87        97       107       117       127       137         
           CYTC_HUMAN    38 GPMDASVEEEGVRRALDFAVGEYNKASNDMYHSRALQVVRARKQIVAGVNYFLDVELGRTTCTKTQPNLDNCPFHDQPHLKRKAFCSFQIYAVPWQGTMTLSKSTCQDA 146
               SCOP domains d3gaxb_ B: Cystatin C                                                                                         SCOP domains
               CATH domains 3gaxB00 B:12-120  [code=3.10.450.10, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....hhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeee...eeeeeeeeeeeeeee.....--......hhhhhh.eeeeeeeeeehhhheeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------Q---------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------CYSTATIN      ----------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2b  PDB: B:12-55 UniProt: 1-81       Exon 1.3  PDB: B:56-93 (gaps)         Exon 1.4a  PDB: B:94-120    Transcript 1
                 3gax B  12 GPMDASVEEEGVRRALDFAVGEYNKASNDMYHSRACQVVRARKQIVAGVNYFLDVELCRTTCTKTQPN--NCPFHDQPHLKRKAFCSFQIYAVPWQGTMTLSKSTCQDA 120
                                    21        31        41        51        61        71       | -|       91       101       111         
                                                                                              79 82                                      

   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  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CYTC_HUMAN | P01034)
molecular function
    GO:0001540    amyloid-beta binding    Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    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).
biological process
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0060313    negative regulation of blood vessel remodeling    Any process that decreases the rate, frequency or extent of blood vessel remodeling, the reorganization or renovation of existing blood vessels.
    GO:0010711    negative regulation of collagen catabolic process    Any process that decreases the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix.
    GO:0060311    negative regulation of elastin catabolic process    Any process that decreases the rate, frequency or extent of elastin catabolism, the chemical reactions and pathways resulting in the breakdown of elastin.
    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:0010716    negative regulation of extracellular matrix disassembly    Any process that decreases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix.
    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:0045861    negative regulation of proteolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0034103    regulation of tissue remodeling    Any process that modulates the frequency, rate, or extent of tissue remodeling.
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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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
        CYTC_HUMAN | P010341g96 1r4c 1tij 3nx0 3ps8 3qrd 3s67 3sva

(-) Related Entries Specified in the PDB File

1g96 DIMERIC FORM OF HUMAN CYSTATIN C
1r4c DIMERIC FORM OF N-TRUNCATED HUMAN CYSTATIN C
1tij DIMERIC FORM OF HUMAN CYSTATIN C