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(-) Description

Title :  CRYSTAL STRUCTURE OF A FIVE SITE MUTATED CYANOVIRIN-N WITH A MANNOSE DIMER BOUND AT 1.8 A RESOLUTION
 
Authors :  R. Fromme, Z. Katilene, P. Fromme, G. Ghirlanda
Date :  16 May 07  (Deposition) - 31 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C#,D#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Cyanovirin-N, Sugar Binding Protein, Anti Hiv (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Fromme, Z. Katiliene, B. Giomarelli, F. Bogani, J. M. Mahon, T. Mori, P. Fromme, G. Ghirlanda
A Monovalent Mutant Of Cyanovirin-N Provides Insight Into The Role Of Multiple Interactions With Gp120 For Antiviral Activity.
Biochemistry V. 46 9199 2007
PubMed-ID: 17636873  |  Reference-DOI: 10.1021/BI700666M
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYANOVIRIN-N
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M51
    Expression System Taxid: 562
    Gene: CYANOVIRN-N
    Mutation: YES
    Organism Scientific: NOSTOC ELLIPSOSPORUM
    Organism Taxid: 45916
    Synonym: CV-N

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABC#D#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MAN4Ligand/IonALPHA-D-MANNOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:42 , VAL A:43 , ASP A:44 , THR A:57 , LYS A:74 , THR A:75 , ARG A:76 , GLN A:78 , HOH B:162 , HOH C:102 , HOH C:116 , MAN C:601BINDING SITE FOR RESIDUE MAN C 600
2AC2SOFTWAREGLU A:41 , ASN A:42 , SER A:52 , ASN A:53 , PHE A:54 , GLU A:56 , THR A:57 , HOH C:116 , HOH C:220 , MAN C:600BINDING SITE FOR RESIDUE MAN C 601
3AC3SOFTWAREASN B:42 , VAL B:43 , ASP B:44 , THR B:57 , LYS B:74 , THR B:75 , ARG B:76 , GLN B:78 , HOH D:216 , MAN D:601BINDING SITE FOR RESIDUE MAN D 600
4AC4SOFTWAREGLU B:41 , ASN B:42 , SER B:52 , ASN B:53 , PHE B:54 , GLU B:56 , THR B:57 , HOH D:404 , MAN D:600BINDING SITE FOR RESIDUE MAN D 601

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:8 -A:22
2A:58 -A:73
3B:8 -B:22
4B:58 -B:73

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PYS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PYS)

(-) Exons   (0, 0)

(no "Exon" information available for 2PYS)

(-) 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:101
 aligned with CVN_NOSEL | P81180 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                                                                                                             101 
                                    11        21        31        41        51        61        71        81        91       101 
            CVN_NOSEL     2 GKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIANIDGTLKYE-   -
               SCOP domains d2pysa_ A: automated matches                                                                          SCOP domains
               CATH domains 2pysA00 A:2-102 HIV-inactivating Protein,Cyanovirin-n;                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeeeeee..eeeeeee.....eeeeeee....eeee..eeee...hhhh.eeeeeee...eeeeeee.....eeeeeee....eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2pys A   2 GNFSQACYNSAIQGSVLTSTCIRTNGGYNTSSIDLNSVIENVDGSLKWQGSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIAAIDGTLKYEL 102
                                    11        21        31        41        51        61        71        81        91       101 


Chain B from PDB  Type:PROTEIN  Length:103
 aligned with CVN_NOSEL | P81180 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:103
                                                                                                                             101   
                                    11        21        31        41        51        61        71        81        91       101   
            CVN_NOSEL     2 GKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIANIDGTLKYE---   -
               SCOP domains d2pysb_ B: automated matches                                                                            SCOP domains
               CATH domains 2pysB00 B:2-104 HIV-inactivating Protein,Cyanovirin-n;                                                  CATH domains
           Pfam domains (1) -CVNH-2pysB01 B:3-100                                                                              ---- Pfam domains (1)
           Pfam domains (2) -CVNH-2pysB02 B:3-100                                                                              ---- Pfam domains (2)
         Sec.struct. author .hhhh.eeeeeee..eeeeeee.....eeeeeee....eeee..eeee...hhhh.eeeeeee...eeeeeee.....eeeeeee....eeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2pys B   2 GNFSQACYNSAIQGSVLTSTCIRTNGGYNTSSIDLNSVIENVDGSLKWQGSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIAAIDGTLKYELEH 104
                                    11        21        31        41        51        61        71        81        91       101
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CVNH] (11)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CVN_NOSEL | P81180)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    GO:0050688    regulation of defense response to virus    Any process that modulates the frequency, rate or extent of the antiviral response of a cell or organism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CVN_NOSEL | P81180: 1iiy 1j4v 1l5b 1l5e 1lom 1n02 2ezm 2ezn 2rdk 2rp3 2z21 3czz 3ezm 3gxy 3gxz 3lhc 3s3y 3s3z 4j4c 4j4d 4j4e 4j4f 4j4g

(-) Related Entries Specified in the PDB File

1iiy NMR WITH MANNOSE MONOMER
1l5e NMR
1lom DOMAIN-SWAP-DIMER
1m5m MAN-9 RES 2.5 A
2ezm NMR
2pyv
2z21
3ezm WILD-TYPE 1.5 A WITHOUT LIGAND