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(-) Description

Title :  SOLUTION NMR STRUCTURE OF CHIMERIC AVIDIN, CHIAVD(I117Y), IN THE BIOTIN BOUND FORM
 
Authors :  H. Tossavainen, S. Kukkurainen, J. A. E. Maatta, T. Pihlajamaa, V. P. Hy M. S. Kulomaa, P. Permi
Date :  07 Oct 13  (Deposition) - 06 Aug 14  (Release) - 06 Aug 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C,D  (15x)
NMR Structure *:  A,B,C,D  (1x)
Keywords :  Biotin Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Tossavainen, S. Kukkurainen, J. A. E. Maatta, N. Kahkonen, T. Pihlajamaa, V. P. Hytonen, M. S. Kulomaa, P. Permi
Chimeric Avidin - Nmr Structure And Dynamics Of A 56 Kda Homotetrameric Thermostable Protein
Plos One V. 9 00564 2014
PubMed-ID: 24959850  |  Reference-DOI: 10.1371/JOURNAL.PONE.0100564

(-) Compounds

Molecule 1 - AVIDIN, AVIDIN-RELATED PROTEIN 4/5
    ChainsA, D, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET101D
    Expression System Vector TypeVECTOR
    FragmentP02701 RESIDUES 25-61, 85-152 AND P56734 RESIDUES 62-82
    GeneAVD, AVR4, AVR5
    MutationYES
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    Other DetailsCHIMERA OF AVIDIN AND AVIDIN-RELATED PROTEIN 4/5

 Structural Features

(-) Chains, Units

  1234
NMR Structure (15x)ABCD
NMR Structure * (1x)ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2MF6)

(-) Sites  (0, 0)

(no "Site" information available for 2MF6)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:4 -A:83

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2MF6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 4)

NMR Structure (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_AVID_CHICK_001 *I58TAVID_CHICK  ---  ---A/B/C/DI34T
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_AVID_CHICK_001 *I58TAVID_CHICK  ---  ---A/B/C/DI34T
   * ID not provided by source

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

(-) PROSITE Motifs  (2, 12)

NMR Structure (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_2PS51326 Avidin-like domain profile.AVR4_CHICK26-147
 
 
 
  4A:2-125
B:2-125
C:2-125
D:2-125
AVID_CHICK26-149
 
 
 
  4A:2-125
B:2-125
C:2-125
D:2-125
2AVIDIN_1PS00577 Avidin-like domain signature.AVR4_CHICK130-144
 
 
 
  4A:109-122
B:109-122
C:109-122
D:109-122
AVID_CHICK132-146
 
 
 
  4A:108-122
B:108-122
C:108-122
D:108-122
NMR Structure * (2, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_2PS51326 Avidin-like domain profile.AVR4_CHICK26-147
 
 
 
  4A:2-125
B:2-125
C:2-125
D:2-125
AVID_CHICK26-149
 
 
 
  4A:2-125
B:2-125
C:2-125
D:2-125
2AVIDIN_1PS00577 Avidin-like domain signature.AVR4_CHICK130-144
 
 
 
  4A:109-122
B:109-122
C:109-122
D:109-122
AVID_CHICK132-146
 
 
 
  4A:108-122
B:108-122
C:108-122
D:108-122

(-) Exons   (0, 0)

(no "Exon" information available for 2MF6)

(-) Sequences/Alignments

NMR Structure
   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:129
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:131
                                    31        41        51        61        71        81        91       101       111       121       131       141       151 
           AVID_CHICK    22 GLSARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRTQKE 152
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeee.......eeeeeee............eeeeeee.--......eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhhheeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------T---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----AVIDIN_2  PDB: A:2-125 UniProt: 26-149                                                                                      --- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------AVIDIN_1       ------ PROSITE (4)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mf6 A  -3 QTVARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVADNPGNITLSPLLGIQH--KRASQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGYNIFTRLRTQKE 128
                              ||     7        17        27        37        47      | 57        67        77        87        97       107       117       127 
                             -1|                                                   54 57                                                                       
                               1                                                                                                                               

Chain A from PDB  Type:PROTEIN  Length:129
 aligned with AVR4_CHICK | P56734 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:129
                                    31        41        51        61        71        81        91       101       111       121       131       141         
           AVR4_CHICK    22 SLSARKCSLTGKWTNNLGSIMTIRAVNSRGEFTGTYLTAVADNPGNITLSPLLGIQHKRASQPTFGFTVHWNFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDISYDWKATRVGYNNFTRLCTVEE 150
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeee.......eeeeeee............eeeeeee.......eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhhheeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------T-------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----AVIDIN_2  PDB: A:2-125 UniProt: 26-147                                                                                    --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------AVIDIN_1       ------ PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mf6 A  -3 QTVARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVADNPGNITLSPLLGIQHKRASQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGYNIFTRLRTQKE 128
                              ||     7        17        27        37        47      ||59        69        79        89        99       109       119         
                             -1|                                                   54|                                                                       
                               1                                                    57                                                                       

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:131
                                    31        41        51        61        71        81        91       101       111       121       131       141       151 
           AVID_CHICK    22 GLSARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRTQKE 152
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeee.......eeeeeee............eeeeeee.--......eeeeeee......eeeeeeeeeee...eeeeeeeeeee....hhhhhhhheeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------T---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----AVIDIN_2  PDB: B:2-125 UniProt: 26-149                                                                                      --- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------AVIDIN_1       ------ PROSITE (4)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mf6 B  -3 QTVARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVADNPGNITLSPLLGIQH--KRASQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGYNIFTRLRTQKE 128
                              ||     7        17        27        37        47      | 57        67        77        87        97       107       117       127 
                             -1|                                                   54 57                                                                       
                               1                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:129
 aligned with AVR4_CHICK | P56734 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:129
                                    31        41        51        61        71        81        91       101       111       121       131       141         
           AVR4_CHICK    22 SLSARKCSLTGKWTNNLGSIMTIRAVNSRGEFTGTYLTAVADNPGNITLSPLLGIQHKRASQPTFGFTVHWNFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDISYDWKATRVGYNNFTRLCTVEE 150
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeee.......eeeeeee............eeeeeee.......eeeeeee......eeeeeeeeeee...eeeeeeeeeee....hhhhhhhheeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------T-------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----AVIDIN_2  PDB: B:2-125 UniProt: 26-147                                                                                    --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------AVIDIN_1       ------ PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mf6 B  -3 QTVARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVADNPGNITLSPLLGIQHKRASQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGYNIFTRLRTQKE 128
                              ||     7        17        27        37        47      ||59        69        79        89        99       109       119         
                             -1|                                                   54|                                                                       
                               1                                                    57                                                                       

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:131
                                    31        41        51        61        71        81        91       101       111       121       131       141       151 
           AVID_CHICK    22 GLSARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRTQKE 152
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeee.......eeeeeee............eeeeeee.--......eeeeeee......eeeeeeeeeee...eeeeeeeeeee....hhhhhhhheeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------T---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----AVIDIN_2  PDB: C:2-125 UniProt: 26-149                                                                                      --- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------AVIDIN_1       ------ PROSITE (4)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mf6 C  -3 QTVARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVADNPGNITLSPLLGIQH--KRASQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGYNIFTRLRTQKE 128
                              ||     7        17        27        37        47      | 57        67        77        87        97       107       117       127 
                             -1|                                                   54 57                                                                       
                               1                                                                                                                               

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with AVR4_CHICK | P56734 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:129
                                    31        41        51        61        71        81        91       101       111       121       131       141         
           AVR4_CHICK    22 SLSARKCSLTGKWTNNLGSIMTIRAVNSRGEFTGTYLTAVADNPGNITLSPLLGIQHKRASQPTFGFTVHWNFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDISYDWKATRVGYNNFTRLCTVEE 150
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeee.......eeeeeee............eeeeeee.......eeeeeee......eeeeeeeeeee...eeeeeeeeeee....hhhhhhhheeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------T-------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----AVIDIN_2  PDB: C:2-125 UniProt: 26-147                                                                                    --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------AVIDIN_1       ------ PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mf6 C  -3 QTVARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVADNPGNITLSPLLGIQHKRASQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGYNIFTRLRTQKE 128
                              ||     7        17        27        37        47      ||59        69        79        89        99       109       119         
                             -1|                                                   54|                                                                       
                               1                                                    57                                                                       

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with AVID_CHICK | P02701 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:131
                                    31        41        51        61        71        81        91       101       111       121       131       141       151 
           AVID_CHICK    22 GLSARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRTQKE 152
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeee.......eeeeeee............eeeeeee.--......eeeeeee......eeeeeeeeeee...eeeeeeeeeee....hhhhhhhheeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------T---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----AVIDIN_2  PDB: D:2-125 UniProt: 26-149                                                                                      --- PROSITE (2)
                PROSITE (3) ----------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) --------------------------------------------------------------------------------------------------------------AVIDIN_1       ------ PROSITE (4)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mf6 D  -3 QTVARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVADNPGNITLSPLLGIQH--KRASQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGYNIFTRLRTQKE 128
                              ||     7        17        27        37        47      | 57        67        77        87        97       107       117       127 
                             -1|                                                   54 57                                                                       
                               1                                                                                                                               

Chain D from PDB  Type:PROTEIN  Length:129
 aligned with AVR4_CHICK | P56734 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:129
                                    31        41        51        61        71        81        91       101       111       121       131       141         
           AVR4_CHICK    22 SLSARKCSLTGKWTNNLGSIMTIRAVNSRGEFTGTYLTAVADNPGNITLSPLLGIQHKRASQPTFGFTVHWNFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDISYDWKATRVGYNNFTRLCTVEE 150
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeee.......eeeeeee............eeeeeee.......eeeeeee......eeeeeeeeeee...eeeeeeeeeee....hhhhhhhheeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------T-------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----AVIDIN_2  PDB: D:2-125 UniProt: 26-147                                                                                    --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------AVIDIN_1       ------ PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mf6 D  -3 QTVARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVADNPGNITLSPLLGIQHKRASQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGYNIFTRLRTQKE 128
                              ||     7        17        27        37        47      ||59        69        79        89        99       109       119         
                             -1|                                                   54|                                                                       
                               1                                                    57                                                                       

   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  (0, 0)

(no "SCOP Domain" information available for 2MF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2MF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2MF6)

(-) Gene Ontology  (1, 2)

NMR Structure(hide GO term definitions)
Chain A,B,C,D   (AVR4_CHICK | P56734)
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.

Chain A,B,C,D   (AVID_CHICK | P02701)
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.

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  AVR4_CHICK | P56734
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 Related Entries

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

UniProtKB/Swiss-Prot
        AVID_CHICK | P027011avd 1ave 1ij8 1ldo 1ldq 1lel 1nqn 1rav 1vyo 2a5b 2a5c 2a8g 2avi 2c4i 2cam 2jgs 3fdc 3mm0 3vgw 3vhh 3vhi 3vhm 4i60 4jhq 4u46 5chk 5hlm 5iru 5irw
        AVR4_CHICK | P567341y52 1y53 1y55 2fhl 2fhn 2of8 2of9 2ofa 2ofb 3mm0 4bcs

(-) Related Entries Specified in the PDB File

3mm0 X-RAY CRYSTALLOGRAPHIC STRUCTURE OF CHIMERIC AVIDIN IN THE BIOTIN-FREE FORM RELATED ID: 18125 RELATED DB: BMRB