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(-) Description

Title :  VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVIRUS 68
 
Authors :  J. M. Alexander, D. H. Fremont, Midwest Center For Structural Genomics (Mcsg)
Date :  29 Aug 02  (Deposition) - 13 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Herpesvirus, Viral Immune Evasion, Chemokine Binding Protein, Decoy Receptor, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Alexander, C. A. Nelson, V. Van Berkel, E. K. Lau, J. M. Studts, T. J. Brett, S. H. Speck, T. M. Handel, H. W. Virgin, D. H. Fremont
Structural Basis Of Chemokine Sequestration By A Herpesvirus Decoy Receptor
Cell(Cambridge, Mass. ) V. 111 343 2002
PubMed-ID: 12419245  |  Reference-DOI: 10.1016/S0092-8674(02)01007-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - M3
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFB-1
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: M3
    Organism Common: MURINE HERPESVIRUS 68
    Organism Scientific: MURID HERPESVIRUS 4
    Organism Taxid: 33708

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1MKF)

(-) Sites  (0, 0)

(no "Site" information available for 1MKF)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:36 -A:47
2A:66 -A:195
3A:218 -A:264
4A:235 -A:262
5A:318 -A:337
6B:36 -B:47
7B:66 -B:195
8B:218 -B:264
9B:235 -B:262
10B:318 -B:337

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MKF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MKF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MKF)

(-) Exons   (0, 0)

(no "Exon" information available for 1MKF)

(-) 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:371
 aligned with O41925_MHV68 | O41925 from UniProtKB/TrEMBL  Length:406

    Alignment length:371
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405 
         O41925_MHV68    36 HSSGVSTQSVDLSQIKRGDEIQAHCLTPAETEVTECAGILKDVLSKNLHELQGLCNVKNKMGVPWVSVEELGQEIITGRLPFPSVGGTPVNDLVRVLVVAESNTPEETPEEEFYAYVELQTELYTFGLSDDNVVFTSDYMTVWMIDIPKSYVDVGMLTRATFLEQWPGAKVTVMIPYSSTFTWCGELGAISEESAPQPSLSARSPVCKNSARYSTSKFCEVDGCTAETGMEKMSLLTPFGGPPQQAKMNTCPCYYKYSVSPLPAMDHLILADLAGLDSLTSPVYVMAAYFDSTHENPVRPSSKLYHCALQMTSHDGVWTSTSSEQCPIRLVEGQSQNVLQVRVAPTSMPNLVGVSLMLEGQQYRLEYFGDH 406
               SCOP domains d1mkfa_ A: Viral chemokine binding protein m3                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1mkfA01 A:12-210  [code=2.60.40.1330, no name defined]                                                                                                                                                 1mkfA02 A:211-382  [code=2.60.40.1340, no name defined]                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.........hhhhhhhhhh......hhhhhhhhhhhhhhh.hhhhhhh.eeeeeeee.eeehhhheeeeee..............eeeeeeeee.............eeeeee....eeeehhh.eeeee..eeeeeeeee.hhh....eeeeee.......eeeeeeeee..eeeeeeeeee..........eeeee...hhhhhh..........hhhhh...eee..........eeee.hhhhhhhh.........eeeeeee.hhhh...eeeeeeee.............eeeeeeeeeee..eeee.......eeeee.....eeeeee.hhhhh.eeeeeeee..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mkf A  12 HSSGVSTQSVDLSQIKRGDEIQAHCLTPAETEVTECAGILKDVLSKNLHELQGLCNVKNKMGVPWVSVEELGQEIITGRLPFPSVGGTPVNDLVRVLVVAESNTPEETPEEEFYAYVELQTELYTFGLSDDNVVFTSDYMTVWMIDIPKSYVDVGMLTRATFLEQWPGAKVTVMIPYSSTFTWCGELGAISEESAPQPSLSARSPVCKNSARYSTSKFCEVDGCTAETGMEKMSLLTPFGGPPQQAKMNTCPCYYKYSVSPLPAMDHLILADLAGLDSLTSPVYVMAAYFDSTHENPVRPSSKLYHCALQMTSHDGVWTSTSSEQCPIRLVEGQSQNVLQVRVAPTSMPNLVGVSLMLEGQQYRLEYFGDH 382
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381 


Chain B from PDB  Type:PROTEIN  Length:371
 aligned with O41925_MHV68 | O41925 from UniProtKB/TrEMBL  Length:406

    Alignment length:371
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405 
         O41925_MHV68    36 HSSGVSTQSVDLSQIKRGDEIQAHCLTPAETEVTECAGILKDVLSKNLHELQGLCNVKNKMGVPWVSVEELGQEIITGRLPFPSVGGTPVNDLVRVLVVAESNTPEETPEEEFYAYVELQTELYTFGLSDDNVVFTSDYMTVWMIDIPKSYVDVGMLTRATFLEQWPGAKVTVMIPYSSTFTWCGELGAISEESAPQPSLSARSPVCKNSARYSTSKFCEVDGCTAETGMEKMSLLTPFGGPPQQAKMNTCPCYYKYSVSPLPAMDHLILADLAGLDSLTSPVYVMAAYFDSTHENPVRPSSKLYHCALQMTSHDGVWTSTSSEQCPIRLVEGQSQNVLQVRVAPTSMPNLVGVSLMLEGQQYRLEYFGDH 406
               SCOP domains d1mkfb_ B: Viral chemokine binding protein m3                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1mkfB01 B:12-210  [code=2.60.40.1330, no name defined]                                                                                                                                                 1mkfB02 B:211-382  [code=2.60.40.1340, no name defined]                                                                                                                      CATH domains
           Pfam domains (1) --M3-1mkfB01 B:14-380                                                                                                                                                                                                                                                                                                                                                            -- Pfam domains (1)
           Pfam domains (2) --M3-1mkfB02 B:14-380                                                                                                                                                                                                                                                                                                                                                            -- Pfam domains (2)
         Sec.struct. author ...eeee.........hhhhhhhhh.......hhhhhhhhhhhh....hhhhhhh.eeeeeeee.eeehhhheeeeee..............eeeeeeeee.............eeeeeee..eeeeehhh.eeeee..eeeeeeeee.hhh....eeeeee.......eeeeeeeee..eeeeeeeeee..........eeeee.........hhhhh.............eee.........eeeee.hhhhhhhh.........eeeeeee........eeeeeeee.............eeeeeeeeeee..eeee.......eeeee.....eeeeee...hhh.eeeeeeee..eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mkf B  12 HSSGVSTQSVDLSQIKRGDEIQAHCLTPAETEVTECAGILKDVLSKNLHELQGLCNVKNKMGVPWVSVEELGQEIITGRLPFPSVGGTPVNDLVRVLVVAESNTPEETPEEEFYAYVELQTELYTFGLSDDNVVFTSDYMTVWMIDIPKSYVDVGMLTRATFLEQWPGAKVTVMIPYSSTFTWCGELGAISEESAPQPSLSARSPVCKNSARYSTSKFCEVDGCTAETGMEKMSLLTPFGGPPQQAKMNTCPCYYKYSVSPLPAMDHLILADLAGLDSLTSPVYVMAAYFDSTHENPVRPSSKLYHCALQMTSHDGVWTSTSSEQCPIRLVEGQSQNVLQVRVAPTSMPNLVGVSLMLEGQQYRLEYFGDH 382
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: M3] (3)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O41925_MHV68 | O41925)
molecular function
    GO:0019956    chemokine binding    Interacting selectively and non-covalently with a chemokine. Chemokines are a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.

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  1mkf
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  O41925_MHV68 | O41925
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 Related Entries

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

UniProtKB/TrEMBL
        O41925_MHV68 | O41925: 1ml0 2nyz 2nz1

(-) Related Entries Specified in the PDB File

1dok MONOCYTE CHEMOATTRACTANT PROTEIN 1, P-FORM
1ml0 VIRAL CHEMOKINE BINDING PROTEIN M3 FROM MURINE GAMMAHERPESVI IN COMPLEX WITH THE P8A VARIANT OF CC- CHEMOKINE MCP-1 RELATED ID: APC35040 RELATED DB: TARGETDB