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(-) Description

Title :  STRUCTURE OF THE L-A VIRUS
 
Authors :  H. Naitow, J. Tang, M. Canady, R. B. Wickner, J. E. Johnson
Date :  18 Jun 02  (Deposition) - 02 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (60x)
Keywords :  Dsrna Virus Structure; Rna-Protein Interaction; Mrna Decapping; L-A Virus; Quai-Equivalence, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Naitow, J. Tang, M. Canady, R. B. Wickner, J. E. Johnson
L-A Virus At 3. 4 A Resolution Reveals Particle Architecture And Mrna Decapping Mechanism.
Nat. Struct. Biol. V. 9 725 2002
PubMed-ID: 12244300  |  Reference-DOI: 10.1038/NSB844
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAJOR COAT PROTEIN
    Chains: A, B
    Organism Scientific: SACCHAROMYCES CEREVISIAE VIRUS L-A (L1)
    Organism Taxid: 11008
    Synonym: GAG PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (60x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1M1C)

(-) Sites  (0, 0)

(no "Site" information available for 1M1C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M1C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M1C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M1C)

(-) Exons   (0, 0)

(no "Exon" information available for 1M1C)

(-) 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:651
 aligned with GAG_SCVLA | P32503 from UniProtKB/Swiss-Prot  Length:680

    Alignment length:651
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650 
            GAG_SCVLA     1 MLRFVTKNSQDKSSDLFSICSDRGTFVAHNRVRTDFKFDNLVFNRVYGVSQKFTLVGNPTVCFNEGSSYLEGIAKKYLTLDGGLAIDNVLNELRSTCGIPGNAVASHAYNITSWRWYDNHVALLMNMLRAYHLQVLTEQGQYSAGDIPMYHDGHVKIKLPVTIDDTAGPTQFAWPSDRSTDSYPDWAQFSESFPSIDVPYLDVRPLTVTEVNFVLMMMSKWHRRTNLAIDYEAPQLADKFAYRHALTVQDADEWIEGDRTDDQFRPPSSKVMLSALRKYVNHNRLYNQFYTAAQLLAQIMMKPVPNCAEGYAWLMHDALVNIPKFGSIRGRYPFLLSGDAALIQATALEDWSAIMAKPELVFTYAMQVSVALNTGLYLRRVKKTGFGTTIDDSYEDGAFLQPETFVQAALACCTGQDAPLNGMSDVYVTYPDLLEFDAVTQVPITVIEPAGYNIVDDHLVVVGVPVACSPYMIFPVAAFDTANPYCGNFVIKAANKYLRKGAVYDKLEAWKLAWALRVAGYDTHFKVYGDTHGLTKFYADNGDTWTHIPEFVTDGDVMEVFVTAIERRARHFVELPRLNSPAFFRSVEVSTTIYDTHVQAGAHAVYHASRINLDYVKPVSTGIQVINAGELKNYWGSVRRTQQGLGVVGLT 651
               SCOP domains d1m1ca_ A: L-A virus major coat protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh........ee.........eeeeeeeeeeeee..eeeeeeeeeeeeee.....eeeee.........hhhhh......hhhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..........ee...eee..............................ee..........eee....hhhhhhhhhhhh........hhhhh.........eee.......hhhhhhh..........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..ee....hhhhhh.....eeeee................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh.ee........eeehhhhh....eeeee.ee...........eeeee.........................eeee....ee...eeeeehhhhhhhhhhhhhh.eeeee.......................hhhhhh....eeeeeeeee...................eeeeeeeeeeeeee...eee..ee............eeee...........ee......ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m1c A   1 MLRFVTKNSQDKSSDLFSICSDRGTFVAHNRVRTDFKFDNLVFNRVYGVSQKFTLVGNPTVCFNEGSSYLEGIAKKYLTLDGGLAIDNVLNELRSTCGIPGNAVASHAYNITSWRWYDNHVALLMNMLRAYHLQVLTEQGQYSAGDIPMYHDGHVKIKLPVTIDDTAGPTQFAWPSDRSTDSYPDWAQFSESFPSIDVPYLDVRPLTVTEVNFVLMMMSKWHRRTNLAIDYEAPQLADKFAYRHALTVQDADEWIEGDRTDDQFRPPSSKVMLSALRKYVNHNRLYNQFYTAAQLLAQIMMKPVPNCAEGYAWLMHDALVNIPKFGSIRGRYPFLLSGDAALIQATALEDWSAIMAKPELVFTYAMQVSVALNTGLYLRRVKKTGFGTTIDDSYEDGAFLQPETFVQAALACCTGQDAPLNGMSDVYVTYPDLLEFDAVTQVPITVIEPAGYNIVDDHLVVVGVPVACSPYMIFPVAAFDTANPYCGNFVIKAANKYLRKGAVYDKLEAWKLAWALRVAGYDTHFKVYGDTHGLTKFYADNGDTWTHIPEFVTDGDVMEVFVTAIERRARHFVELPRLNSPAFFRSVEVSTTIYDTHVQAGAHAVYHASRINLDYVKPVSTGIQVINAGELKNYWGSVRRTQQGLGVVGLT 651
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650 


Chain B from PDB  Type:PROTEIN  Length:651
 aligned with GAG_SCVLA | P32503 from UniProtKB/Swiss-Prot  Length:680

    Alignment length:651
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650 
            GAG_SCVLA     1 MLRFVTKNSQDKSSDLFSICSDRGTFVAHNRVRTDFKFDNLVFNRVYGVSQKFTLVGNPTVCFNEGSSYLEGIAKKYLTLDGGLAIDNVLNELRSTCGIPGNAVASHAYNITSWRWYDNHVALLMNMLRAYHLQVLTEQGQYSAGDIPMYHDGHVKIKLPVTIDDTAGPTQFAWPSDRSTDSYPDWAQFSESFPSIDVPYLDVRPLTVTEVNFVLMMMSKWHRRTNLAIDYEAPQLADKFAYRHALTVQDADEWIEGDRTDDQFRPPSSKVMLSALRKYVNHNRLYNQFYTAAQLLAQIMMKPVPNCAEGYAWLMHDALVNIPKFGSIRGRYPFLLSGDAALIQATALEDWSAIMAKPELVFTYAMQVSVALNTGLYLRRVKKTGFGTTIDDSYEDGAFLQPETFVQAALACCTGQDAPLNGMSDVYVTYPDLLEFDAVTQVPITVIEPAGYNIVDDHLVVVGVPVACSPYMIFPVAAFDTANPYCGNFVIKAANKYLRKGAVYDKLEAWKLAWALRVAGYDTHFKVYGDTHGLTKFYADNGDTWTHIPEFVTDGDVMEVFVTAIERRARHFVELPRLNSPAFFRSVEVSTTIYDTHVQAGAHAVYHASRINLDYVKPVSTGIQVINAGELKNYWGSVRRTQQGLGVVGLT 651
               SCOP domains d1m1cb_ B: L-A virus major coat protein                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) LA-virus_coat-1m1cB01 B:1-436                                                                                                                                                                                                                                                                                                                                                                                                                       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) LA-virus_coat-1m1cB02 B:1-436                                                                                                                                                                                                                                                                                                                                                                                                                       ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhh.......ee........eeeeeeeeeeeeee..eeeeeeeee..eee......eee.....................hhhhhhhhhhhh.....hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh..........ee....ee...........................eeeee..........eee....hhhhhhhhhhhhh.......hhhhh.......eeeee.....hhhhhhh.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee...hhhhh.......eeee.........hhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh...ee.......eeehhhhh....ee....................ee.......hhhhh.............eee.............eehhhhhhhhhhhhhhheeee........................hhhhh.....ee...eeee....................eeeeeeeeeee..........ee............eeee.........eeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m1c B   1 MLRFVTKNSQDKSSDLFSICSDRGTFVAHNRVRTDFKFDNLVFNRVYGVSQKFTLVGNPTVCFNEGSSYLEGIAKKYLTLDGGLAIDNVLNELRSTCGIPGNAVASHAYNITSWRWYDNHVALLMNMLRAYHLQVLTEQGQYSAGDIPMYHDGHVKIKLPVTIDDTAGPTQFAWPSDRSTDSYPDWAQFSESFPSIDVPYLDVRPLTVTEVNFVLMMMSKWHRRTNLAIDYEAPQLADKFAYRHALTVQDADEWIEGDRTDDQFRPPSSKVMLSALRKYVNHNRLYNQFYTAAQLLAQIMMKPVPNCAEGYAWLMHDALVNIPKFGSIRGRYPFLLSGDAALIQATALEDWSAIMAKPELVFTYAMQVSVALNTGLYLRRVKKTGFGTTIDDSYEDGAFLQPETFVQAALACCTGQDAPLNGMSDVYVTYPDLLEFDAVTQVPITVIEPAGYNIVDDHLVVVGVPVACSPYMIFPVAAFDTANPYCGNFVIKAANKYLRKGAVYDKLEAWKLAWALRVAGYDTHFKVYGDTHGLTKFYADNGDTWTHIPEFVTDGDVMEVFVTAIERRARHFVELPRLNSPAFFRSVEVSTTIYDTHVQAGAHAVYHASRINLDYVKPVSTGIQVINAGELKNYWGSVRRTQQGLGVVGLT 651
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650
   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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1M1C)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: LA-virus_coat] (1)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GAG_SCVLA | P32503)
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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 Related Entries

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