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(-) Description

Title :  THE STRUCTURE AND EVOLUTION OF THE MAJOR CAPSID PROTEIN OF A LARGE, LIPID-CONTAINING, DNA VIRUS.
 
Authors :  N. Nandhagopal, A. A. Simpson, J. R. Gurnon, X. Yan, T. S. Baker, M. V. Gra J. L. Van Etten, M. G. Rossmann
Date :  27 Jun 02  (Deposition) - 20 Nov 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  A  (3x)
Biol. Unit 3:  B  (3x)
Keywords :  Pbcv-1, Major Capsid Protein Of Large Dna Virus, Vp54, Chlorella Virus, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Nandhagopal, A. A. Simpson, J. R. Gurnon, X. Yan, T. S. Baker, M. V. Graves, J. L. Van Etten, M. G. Rossmann
The Structure And Evolution Of The Major Capsid Protein Of Large, Lipid-Containing Dna Virus
Proc. Natl. Acad. Sci. Usa V. 99 14758 2002
PubMed-ID: 12411581  |  Reference-DOI: 10.1073/PNAS.232580699

(-) Compounds

Molecule 1 - MAJOR CAPSID PROTEIN
    Chains: A, B
    Organism Scientific: PARAMECIUM BURSARIA CHLORELLA VIRUS 1
    Organism Taxid: 10506
    Synonym: VP54

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB
Biological Unit 2 (3x): A 
Biological Unit 3 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 38)

Asymmetric Unit (4, 38)
No.NameCountTypeFull Name
1HG4Ligand/IonMERCURY (II) ION
2MAN24Ligand/IonALPHA-D-MANNOSE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG4Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 1 (3, 102)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2MAN72Ligand/IonALPHA-D-MANNOSE
3NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG12Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 2 (3, 51)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2MAN36Ligand/IonALPHA-D-MANNOSE
3NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG6Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 3 (3, 51)
No.NameCountTypeFull Name
1HG-1Ligand/IonMERCURY (II) ION
2MAN36Ligand/IonALPHA-D-MANNOSE
3NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG6Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (38, 38)

Asymmetric Unit (38, 38)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:280 , GLY A:289 , THR A:290 , ALA A:293 , PRO A:393 , MAN A:439 , MAN A:440 , MAN A:441 , MAN A:452BINDING SITE FOR RESIDUE NAG A 438
02AC2SOFTWARETHR A:391 , NAG A:438 , MAN A:441 , MAN A:442 , NAG A:450BINDING SITE FOR RESIDUE MAN A 439
03AC3SOFTWARENAG A:438 , MAN A:441 , MAN A:442BINDING SITE FOR RESIDUE MAN A 440
04AC4SOFTWARENAG A:438 , MAN A:439 , MAN A:440 , MAN A:442BINDING SITE FOR RESIDUE MAN A 441
05AC5SOFTWAREMAN A:439 , MAN A:440 , MAN A:441BINDING SITE FOR RESIDUE MAN A 442
06AC6SOFTWAREASN A:81 , GLY A:82 , ASN A:138 , LEU A:140 , NAG A:444 , MAN A:445 , MAN A:447 , MAN A:448 , MAN A:452BINDING SITE FOR RESIDUE MAN A 443
07AC7SOFTWAREGLY A:287 , ASP A:299 , MAN A:443 , NDG A:446 , MAN A:447 , MAN A:448BINDING SITE FOR RESIDUE NAG A 444
08AC8SOFTWAREMAN A:443 , MAN A:447 , MAN A:448 , MAN A:452BINDING SITE FOR RESIDUE MAN A 445
09AC9SOFTWAREGLY A:83 , ASP A:299 , ASN A:302 , NAG A:444BINDING SITE FOR RESIDUE NDG A 446
10BC1SOFTWAREMAN A:443 , NAG A:444 , MAN A:445 , MAN A:448BINDING SITE FOR RESIDUE MAN A 447
11BC2SOFTWAREMAN A:443 , NAG A:444 , MAN A:445 , MAN A:447BINDING SITE FOR RESIDUE MAN A 448
12BC3SOFTWAREILE A:388 , ASP A:389 , ALA A:395 , GLY A:398 , ASN A:399 , MAN A:453 , MAN A:454BINDING SITE FOR RESIDUE NDG A 449
13BC4SOFTWAREASP A:389 , THR A:391 , ASN A:406 , MAN A:439 , MAN A:451BINDING SITE FOR RESIDUE NAG A 450
14BC5SOFTWARENAG A:450BINDING SITE FOR RESIDUE MAN A 451
15BC6SOFTWARENAG A:438 , MAN A:443 , MAN A:445BINDING SITE FOR RESIDUE MAN A 452
16BC7SOFTWAREVAL A:141 , ALA A:394 , NDG A:449BINDING SITE FOR RESIDUE MAN A 453
17BC8SOFTWARENDG A:449BINDING SITE FOR RESIDUE MAN A 454
18BC9SOFTWAREASN B:280 , GLY B:289 , THR B:290 , ALA B:293 , THR B:391 , MAN B:539 , MAN B:540 , MAN B:541 , MAN B:552BINDING SITE FOR RESIDUE NAG B 538
19CC1SOFTWARENAG B:538 , MAN B:541 , MAN B:542 , NDG B:550BINDING SITE FOR RESIDUE MAN B 539
20CC2SOFTWARENAG B:538 , MAN B:541BINDING SITE FOR RESIDUE MAN B 540
21CC3SOFTWAREALA B:291 , NAG B:538 , MAN B:539 , MAN B:540 , MAN B:542BINDING SITE FOR RESIDUE MAN B 541
22CC4SOFTWAREMAN B:539 , MAN B:541BINDING SITE FOR RESIDUE MAN B 542
23CC5SOFTWAREASN B:81 , GLY B:82 , ASN B:138 , LEU B:140 , NDG B:544 , MAN B:545 , MAN B:547 , MAN B:552BINDING SITE FOR RESIDUE MAN B 543
24CC6SOFTWAREGLY B:82 , MAN B:543 , NAG B:546 , MAN B:547BINDING SITE FOR RESIDUE NDG B 544
25CC7SOFTWAREMAN B:543 , MAN B:548 , MAN B:552BINDING SITE FOR RESIDUE MAN B 545
26CC8SOFTWAREASP B:299 , ASN B:302 , NDG B:544BINDING SITE FOR RESIDUE NAG B 546
27CC9SOFTWAREMAN B:543 , NDG B:544 , MAN B:548BINDING SITE FOR RESIDUE MAN B 547
28DC1SOFTWAREALA B:292 , MAN B:545 , MAN B:547BINDING SITE FOR RESIDUE MAN B 548
29DC2SOFTWARESER B:387 , ILE B:388 , ASP B:389 , ALA B:395 , GLY B:398 , ASN B:399 , MAN B:553 , MAN B:554BINDING SITE FOR RESIDUE NAG B 549
30DC3SOFTWAREASP B:389 , ALA B:390 , ASN B:406 , MAN B:539 , MAN B:551BINDING SITE FOR RESIDUE NDG B 550
31DC4SOFTWARENDG B:550BINDING SITE FOR RESIDUE MAN B 551
32DC5SOFTWARENAG B:538 , MAN B:543 , MAN B:545BINDING SITE FOR RESIDUE MAN B 552
33DC6SOFTWAREVAL B:141 , ALA B:394 , GLY B:398 , NAG B:549BINDING SITE FOR RESIDUE MAN B 553
34DC7SOFTWARENAG B:549BINDING SITE FOR RESIDUE MAN B 554
35DC8SOFTWARELEU A:320 , CYS A:369 , PHE A:371 , ILE A:374BINDING SITE FOR RESIDUE HG A 455
36DC9SOFTWARECYS A:386 , THR A:409BINDING SITE FOR RESIDUE HG A 456
37EC1SOFTWARECYS B:386 , ASN B:406 , THR B:409BINDING SITE FOR RESIDUE HG B 457
38EC2SOFTWARELEU B:320 , PHE B:356 , CYS B:369 , PHE B:371 , ILE B:374BINDING SITE FOR RESIDUE HG B 458

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J5Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J5Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J5Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J5Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1J5Q)

(-) 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:413
 aligned with MCP_PBCV1 | P30328 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:413
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
            MCP_PBCV1    25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
               SCOP domains d1j5qa1 A:25-221 Major capsid protein vp54                                                                                                                                                           d1j5qa2 A:222-437 Major capsid protein vp54                                                                                                                                                                              SCOP domains
               CATH domains 1j5qA01 A:25-222 Adenovirus Type 2 Hexon, domain 4                                                                                                                                                    1j5qA02 A:223-437 Major capsid protein Vp54                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeee..........eeeee......eeeeeeeeeeee.........hhhhhheeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..hhhhhhhhhh.hhhhh....eeeeeee........ee..ee.......eeeeeeeeeeehhhhhhhhhhh.eeeeeeeeeeeeee..........eeeeee....eeeeeeeeee...............................hhhhh...hhhhh.eeeeeeee........eehhhhhhhhhhhhh.......eeeee.............ee.hhh..eeeeeee.eeee...hhhhhh.....eee.hhhhh.eeeeeeeeeeeeeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j5q A  25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   


Chain B from PDB  Type:PROTEIN  Length:413
 aligned with MCP_PBCV1 | P30328 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:413
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
            MCP_PBCV1    25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
               SCOP domains d1j5qb1 B:25-221 Major capsid protein vp54                                                                                                                                                           d1j5qb2 B:222-437 Major capsid protein vp54                                                                                                                                                                              SCOP domains
               CATH domains 1j5qB01 B:25-222 Adenovirus Type 2 Hexon, domain 4                                                                                                                                                    1j5qB02 B:223-437 Major capsid protein Vp54                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeee...........eeeee......eeeeeeeeeeee.........hhhhhheeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..hhhhhhhhhhee.hhh....eeeeeee........ee..ee.......eeeeeeeeeeehhhhhhhhhhh.eeeeeeeeeeeeee..........eeeee.....eeeeeeeeee...............................hhhhh...hhhhh.eeeeeeee..ee....eehhhhhhhhhhhhh.......eeeee.............ee.hhh..eeeeeee.eeee...hhhhhh.....eee.hhhhh.eeeeeeeeeeeeeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j5q B  25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J5Q)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MCP_PBCV1 | P30328)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  1j5q
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  MCP_PBCV1 | P30328
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 Related Entries

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

UniProtKB/Swiss-Prot
        MCP_PBCV1 | P30328: 1m3y 1m4x 3kk5

(-) Related Entries Specified in the PDB File

1m3y THE SAME PROTEIN IN DIFFERENT SPACE GROUP
1m4x THE SAME PROTEIN STUDIES BY CRYO-ELECTRON MICROSCOPY