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(-) Description

Title :  CRYSTAL STRUCTURE OF CALCINEURIN IN COMPLEX WITH THE CALCINEURIN-INHIBITING DOMAIN OF THE AFRICAN SWINE FEVER VIRUS PROTEIN A238L
 
Authors :  S. Grigoriu, W. Peti, R. Page
Date :  05 May 12  (Deposition) - 06 Mar 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ef-Hand, Phosphatase, Pxixit, Lxvp, Calcium Signaling, Transcription Regulation, T-Cell Activation, Calcineurin Inhibition, Calmodulin, Rcan, Nfat, Heart, Nucleus, Skeletal Muscle, Ion Channels, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Grigoriu, R. Bond, P. Cossio, J. A. Chen, N. Ly, G. Hummer, R. Page, M. S. Cyert, W. Peti
The Molecular Mechanism Of Substrate Engagement And Immunosuppressant Inhibition Of Calcineurin.
Plos Biol. V. 11 01492 2013
PubMed-ID: 23468591  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1001492

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT ALPHA ISOFORM
    Chains: A
    EC Number: 3.1.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P11
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CALCINEURIN A SUBUNIT
    Gene: PPP3CA, CALNA, CNA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CAM-PRP CATALYTIC SUBUNIT, CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT ALPHA ISOFORM
 
Molecule 2 - CALCINEURIN SUBUNIT B TYPE 1
    Chains: B
    EC Number: 3.1.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P11
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CALCINEURIN B SUBUNIT
    Gene: PPP3R1, CNA2, CNB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN PHOSPHATASE 2B REGULATORY SUBUNIT 1, PROTEIN PHOSPHATASE 3 REGULATORY SUBUNIT B ALPHA ISOFORM 1
 
Molecule 3 - ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN A238L
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-RP1B
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: A238L CID (UNP RESIDUES 200-239)
    Organism Common: ASFV
    Organism Scientific: AFRICAN SWINE FEVER VIRUS MALAWI LIL 20/1
    Organism Taxid: 10500
    Strain: MALAWI (LIL 20-1)
    Synonym: P28

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL8Ligand/IonGLYCEROL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:285 , ASN A:316 , HOH A:680 , HOH A:752 , ASP C:215 , ASN C:216BINDING SITE FOR RESIDUE GOL A 401
02AC2SOFTWAREHIS A:49 , LYS A:52 , GLU A:205 , TYR A:224 , GLY A:225 , PRO A:226 , HOH A:820BINDING SITE FOR RESIDUE GOL A 402
03AC3SOFTWAREASP A:90 , HIS A:92 , ARG A:254 , HIS A:281 , GLU A:282 , ALA A:283 , HOH A:533BINDING SITE FOR RESIDUE GOL A 403
04AC4SOFTWARELEU A:236 , ASP A:238 , GLU A:242 , LYS A:243 , THR A:244 , HOH A:701 , HOH A:769BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWAREASP B:62 , ASP B:64 , ASN B:66 , GLU B:68 , GLU B:73 , HOH B:320BINDING SITE FOR RESIDUE CA B 201
06AC6SOFTWAREASP B:30 , ASP B:32 , SER B:34 , SER B:36 , GLU B:41 , HOH B:332BINDING SITE FOR RESIDUE CA B 202
07AC7SOFTWAREASP B:99 , ASP B:101 , ASP B:103 , TYR B:105 , GLU B:110 , HOH B:309BINDING SITE FOR RESIDUE CA B 203
08AC8SOFTWAREASP B:140 , ASP B:142 , ASP B:144 , ARG B:146 , GLU B:151 , HOH B:303BINDING SITE FOR RESIDUE CA B 204
09AC9SOFTWAREGLU A:53 , ARG A:55 , HOH A:716 , ASN B:138 , HOH B:308BINDING SITE FOR RESIDUE GOL B 205
10BC1SOFTWARETYR B:105 , ASP B:142 , ASP B:144 , ARG B:146 , HOH B:391BINDING SITE FOR RESIDUE GOL B 206
11BC2SOFTWAREPHE B:81 , LYS B:90 , HOH B:383 , HOH B:384BINDING SITE FOR RESIDUE GOL B 207
12BC3SOFTWARETYR A:124 , THR A:161 , HOH A:613 , LEU C:234BINDING SITE FOR RESIDUE GOL C 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F0Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:83 -Pro A:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F0Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F0Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4F0Z)

(-) 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:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4f0za_ A: Protein phosphatase-2B (PP-2B, calcineurin A subunit)                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhh......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eeee...eeee.....hhhhhhhhhhhhh......eee.........hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee...eeee..........hhhhhh..........hhhhhhhhhee............eee.......eeehhhhhhhhhhhh...eeee........eee...........eeee....hhhhh....eeeeeee..eeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f0z A  14 TDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESVALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMDAFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFGNEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHEAQDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLN 370
                                    23        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       


Chain B from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains d4f0zb_ B: Calcineurin regulatory subunit (B-chain)                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh...hhhhhhhhhh......eehhhhhhhhhh.....hhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f0z B   6 YPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVDFKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISFEEFCAVVGGLD 160
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155     


Chain C from PDB  Type:PROTEIN  Length:30
                                                              
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..eeeee....................... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 4f0z C 205 KPKIIITGCEDNVYEKLPEQNSNFLCVKKL 234
                                   214       224       234
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F0Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F0Z)

(-) Gene Ontology  (57, 76)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:83 - Pro A:84   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        CANB1_HUMAN | P63098: 1aui 1m63 1mf8 2p6b 3ll8 4or9 4ora 4orc 5sve
        PP2BA_HUMAN | Q08209: 1aui 1m63 1mf8 2jog 2jzi 2p6b 2r28 2w73 3ll8 4q5u 5c1v 5sve

(-) Related Entries Specified in the PDB File

1aui CRYSTAL STRUCTURE OF HUMAN CALCINEURIN HETERODIMER
1m63 CRYSTAL STRUCTURE OF CALCINEURIN-CYCLOPHILIN-CYCLOSPORIN
1mf8 CRYSTAL STRUCTURE OF HUMAN CALCINEURIN COMPLEXED WITH CYCLOSPORIN A AND HUMAN CYCLOPHILIN
1tco TERNARY COMPLEX OF A CALCINEURIN A FRAGMENT, CALCINEURIN B, FKBP12 AND THE IMMUNOSUPPRESSANT DRUG FK506 (TACROLIMUS)
2p6b CRYSTAL STRUCTURE OF HUMAN CALCINEURIN IN COMPLEX WITH PVIVIT PEPTIDE
3ll8 CRYSTAL STRUCTURE OF CALCINEURIN IN COMPLEX WITH AKAP79 PEPTIDE