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(-) Description

Title :  MAPPING THE E2 GLYCOPROTEIN OF ALPHAVIRUSES
 
Authors :  S. Mukhopadhyay, W. Zhang, S. Gabler, P. R. Chipman, E. G. Strauss, J. H. Strauss, T. S. Baker, R. J. Kuhn, M. G. Rossmann
Date :  31 Mar 05  (Deposition) - 07 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  9.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
Biol. Unit 1:  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T  (60x)
Keywords :  Icosahedral Enveloped Virus, Cryo-Electron Microscopy, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mukhopadhyay, W. Zhang, S. Gabler, P. R. Chipman, E. G. Strauss, J. H. Strauss, T. S. Baker, R. J. Kuhn, M. G. Rossmann
Mapping The Structure And Function Of The E1 And E2 Glycoproteins In Alphaviruses.
Structure V. 14 63 2006
PubMed-ID: 16407066  |  Reference-DOI: 10.1016/J.STR.2005.07.025
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPIKE GLYCOPROTEIN E1
    Cell: BHK
    Chains: A, C, E, G
    Fragment: E1 ECTODOMAIN DOMAINS I+II, RESIDUES 1-290
    Organism Scientific: SINDBIS VIRUS
    Organism Taxid: 11034
    Strain: TE12
 
Molecule 2 - SPIKE GLYCOPROTEIN E1
    Cell: BHK
    Chains: B, D, F, H
    Fragment: E1 ECTODOMAIN DOMAIN III, RESIDUES 295-383
    Organism Scientific: SINDBIS VIRUS
    Organism Taxid: 11034
    Strain: TE12
 
Molecule 3 - SPIKE GLYCOPROTEIN E1
    Cell: BHK
    Chains: I, K, M, O
    Fragment: E1 TRANSMEMBRANE REGION, RESIDUES 409-439
    Organism Scientific: SINDBIS VIRUS
    Organism Taxid: 11034
    Strain: TE12
 
Molecule 4 - SPIKE GLYCOPROTEIN E2
    Cell: BHK
    Chains: J, L, N, P
    Fragment: E2 TRANSMEMBRANE REGION, RESIDUES 363-398
    Organism Scientific: SINDBIS VIRUS
    Organism Taxid: 11034
    Strain: TE12
 
Molecule 5 - CAPSID PROTEIN C
    Cell: BHK
    Chains: Q, R, S, T
    EC Number: 3.4.21.-
    Fragment: CAPSID PROTEIN, RESIDUES 114-264
    Organism Scientific: SINDBIS VIRUS
    Organism Taxid: 11034
    Strain: TE12
    Synonym: COAT PROTEIN C

 Structural Features

(-) Chains, Units

  1234567891011121314151617181920
Asymmetric Unit : ABCDEFGHIJKLMNOPQRST
Biological Unit 1 (60x): ABCDEFGHIJKLMNOPQRST

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1Z8Y)

(-) Sites  (0, 0)

(no "Site" information available for 1Z8Y)

(-) SS Bonds  (32, 32)

Asymmetric Unit
No.Residues
1A:49 -A:114
2A:62 -A:94
3A:63 -A:96
4A:68 -A:78
5A:259 -A:271
6B:301 -B:376
7B:306 -B:380
8B:328 -B:370
9C:49 -C:114
10C:62 -C:94
11C:63 -C:96
12C:68 -C:78
13C:259 -C:271
14D:301 -D:376
15D:306 -D:380
16D:328 -D:370
17E:49 -E:114
18E:62 -E:94
19E:63 -E:96
20E:68 -E:78
21E:259 -E:271
22F:301 -F:376
23F:306 -F:380
24F:328 -F:370
25G:49 -G:114
26G:62 -G:94
27G:63 -G:96
28G:68 -G:78
29G:259 -G:271
30H:301 -H:376
31H:306 -H:380
32H:328 -H:370

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z8Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 8)

Asymmetric Unit (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_POLS_SINDV_006 *K719LPOLS_SINDV  ---  ---J/L/N/PL29L
2UniProtVAR_POLS_SINDV_007 *D919VPOLS_SINDV  ---  ---A/C/E/GD113V
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 480)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_POLS_SINDV_006 *K719LPOLS_SINDV  ---  ---J/L/N/PL29L
2UniProtVAR_POLS_SINDV_007 *D919VPOLS_SINDV  ---  ---A/C/E/GD113V
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHAVIRUS_CPPS51690 Alphavirus core protein (CP) domain profile.POLS_SINDV114-264
 
 
 		  4Q:114-264
R:114-264
S:114-264
T:114-264
Biological Unit 1 (1, 240)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHAVIRUS_CPPS51690 Alphavirus core protein (CP) domain profile.POLS_SINDV114-264
 
 
 		  240Q:114-264
R:114-264
S:114-264
T:114-264

(-) Exons   (0, 0)

(no "Exon" information available for 1Z8Y)

(-) 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:290
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:290
                                   816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096
          POLS_SINDV    807 YEHATTVPNVPQIPYKALVERAGYAPLNLEITVMSSEVLPSTNQEYITCKFTTVVPSPKIKCCGSLECQPAAHADYTCKVFGGVYPFMWGGAQCFCDSENSQMSEAYVELSADCASDHAQAIKVHTAAMKVGLRIVYGNTTSFLDVYVNGVTPGTSKDLKVIAGPISASFTPFDHKVVIHRGLVYNYDFPEYGAMKPGAFGDIQATSLTSKDLIASTDIRLLKPSAKNVHVPYTQASSGFEMWKNNSGRPLQETAPFGCKIAVNPLRAVDCSYGNIPISIDIPNAAFIRT 1096
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee........eee.......eeeeee....eeeee....eee..eeee....eee...............eeeeee..................eeeeeeeeee.hhhh...eeeee.eeeee....eee..................ee..eee..............eeee....eee................ee.........ee....ee...........ee...hhhhhhhhh........hhhhheee....eee.....ee...ee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1z8y A    1 YEHATTVPNVPQIPYKALVERAGYAPLNLEITVMSSEVLPSTNQEYITCKFTTVVPSPKIKCCGSLECQPAAHADYTCKVFGGVYPFMWGGAQCFCDSENSQMSEAYVELSADCASDHAQAIKVHTAAMKVGLRIVYGNTTSFLDVYVNGVTPGTSKDLKVIAGPISASFTPFDHKVVIHRGLVYNYDFPEYGAMKPGAFGDIQATSLTSKDLIASTDIRLLKPSAKNVHVPYTQASSGFEMWKNNSGRPLQETAPFGCKIAVNPLRAVDCSYGNIPISIDIPNAAFIRT  290
                                    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


Chain B from PDB  Type:PROTEIN  Length:89
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:89
                                  1110      1120      1130      1140      1150      1160      1170      1180         
          POLS_SINDV   1101 LVSTVKCEVSECTYSADFGGMATLQYVSDREGQCPVHSHSSTATLQESTVHVLEKGAVTVHFSTASPQANFIVSLCGKKTTCNAECKPP 1189
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..............eeeeee....eee.............eee...................ee........ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                1z8y B  295 LVSTVKCEVSECTYSADFGGMATLQYVSDREGQCPVHSHSSTATLQESTVHVLEKGAVTVHFSTASPQANFIVSLCGKKTTCNAECKPP  383
                                   304       314       324       334       344       354       364       374         


Chain C from PDB  Type:PROTEIN  Length:290
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:290
                                   816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096
          POLS_SINDV    807 YEHATTVPNVPQIPYKALVERAGYAPLNLEITVMSSEVLPSTNQEYITCKFTTVVPSPKIKCCGSLECQPAAHADYTCKVFGGVYPFMWGGAQCFCDSENSQMSEAYVELSADCASDHAQAIKVHTAAMKVGLRIVYGNTTSFLDVYVNGVTPGTSKDLKVIAGPISASFTPFDHKVVIHRGLVYNYDFPEYGAMKPGAFGDIQATSLTSKDLIASTDIRLLKPSAKNVHVPYTQASSGFEMWKNNSGRPLQETAPFGCKIAVNPLRAVDCSYGNIPISIDIPNAAFIRT 1096
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee........eee.......eeeeee....eeeee....eee..eeee....eee...............eeeeee..................eeeeeeeeee.hhhh...eeeee.eeeee....eee..................ee..eee..............eeee....eee................ee.........ee....ee...........ee...hhhhhhhhh........hhhhheee....eee.....ee...ee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1z8y C    1 YEHATTVPNVPQIPYKALVERAGYAPLNLEITVMSSEVLPSTNQEYITCKFTTVVPSPKIKCCGSLECQPAAHADYTCKVFGGVYPFMWGGAQCFCDSENSQMSEAYVELSADCASDHAQAIKVHTAAMKVGLRIVYGNTTSFLDVYVNGVTPGTSKDLKVIAGPISASFTPFDHKVVIHRGLVYNYDFPEYGAMKPGAFGDIQATSLTSKDLIASTDIRLLKPSAKNVHVPYTQASSGFEMWKNNSGRPLQETAPFGCKIAVNPLRAVDCSYGNIPISIDIPNAAFIRT  290
                                    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


Chain D from PDB  Type:PROTEIN  Length:89
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:89
                                  1110      1120      1130      1140      1150      1160      1170      1180         
          POLS_SINDV   1101 LVSTVKCEVSECTYSADFGGMATLQYVSDREGQCPVHSHSSTATLQESTVHVLEKGAVTVHFSTASPQANFIVSLCGKKTTCNAECKPP 1189
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..............eeeeee....eee.............eee...................ee........ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                1z8y D  295 LVSTVKCEVSECTYSADFGGMATLQYVSDREGQCPVHSHSSTATLQESTVHVLEKGAVTVHFSTASPQANFIVSLCGKKTTCNAECKPP  383
                                   304       314       324       334       344       354       364       374         


Chain E from PDB  Type:PROTEIN  Length:290
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:290
                                   816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096
          POLS_SINDV    807 YEHATTVPNVPQIPYKALVERAGYAPLNLEITVMSSEVLPSTNQEYITCKFTTVVPSPKIKCCGSLECQPAAHADYTCKVFGGVYPFMWGGAQCFCDSENSQMSEAYVELSADCASDHAQAIKVHTAAMKVGLRIVYGNTTSFLDVYVNGVTPGTSKDLKVIAGPISASFTPFDHKVVIHRGLVYNYDFPEYGAMKPGAFGDIQATSLTSKDLIASTDIRLLKPSAKNVHVPYTQASSGFEMWKNNSGRPLQETAPFGCKIAVNPLRAVDCSYGNIPISIDIPNAAFIRT 1096
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee........eee.......eeeeee....eeeee....eee..eeee....eee...............eeeeee..................eeeeeeeeee.hhhh...eeeee.eeeee....eee..................ee..eee..............eeee....eee................ee.........ee....ee...........ee...hhhhhhhhh........hhhhheee....eee.....ee...ee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1z8y E    1 YEHATTVPNVPQIPYKALVERAGYAPLNLEITVMSSEVLPSTNQEYITCKFTTVVPSPKIKCCGSLECQPAAHADYTCKVFGGVYPFMWGGAQCFCDSENSQMSEAYVELSADCASDHAQAIKVHTAAMKVGLRIVYGNTTSFLDVYVNGVTPGTSKDLKVIAGPISASFTPFDHKVVIHRGLVYNYDFPEYGAMKPGAFGDIQATSLTSKDLIASTDIRLLKPSAKNVHVPYTQASSGFEMWKNNSGRPLQETAPFGCKIAVNPLRAVDCSYGNIPISIDIPNAAFIRT  290
                                    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


Chain F from PDB  Type:PROTEIN  Length:89
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:89
                                  1110      1120      1130      1140      1150      1160      1170      1180         
          POLS_SINDV   1101 LVSTVKCEVSECTYSADFGGMATLQYVSDREGQCPVHSHSSTATLQESTVHVLEKGAVTVHFSTASPQANFIVSLCGKKTTCNAECKPP 1189
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..............eeeeee....eee.............eee...................ee........ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                1z8y F  295 LVSTVKCEVSECTYSADFGGMATLQYVSDREGQCPVHSHSSTATLQESTVHVLEKGAVTVHFSTASPQANFIVSLCGKKTTCNAECKPP  383
                                   304       314       324       334       344       354       364       374         


Chain G from PDB  Type:PROTEIN  Length:290
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:290
                                   816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096
          POLS_SINDV    807 YEHATTVPNVPQIPYKALVERAGYAPLNLEITVMSSEVLPSTNQEYITCKFTTVVPSPKIKCCGSLECQPAAHADYTCKVFGGVYPFMWGGAQCFCDSENSQMSEAYVELSADCASDHAQAIKVHTAAMKVGLRIVYGNTTSFLDVYVNGVTPGTSKDLKVIAGPISASFTPFDHKVVIHRGLVYNYDFPEYGAMKPGAFGDIQATSLTSKDLIASTDIRLLKPSAKNVHVPYTQASSGFEMWKNNSGRPLQETAPFGCKIAVNPLRAVDCSYGNIPISIDIPNAAFIRT 1096
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee........eee.......eeeeee....eeeee....eee..eeee....eee...............eeeeee..................eeeeeeeeee.hhhh...eeeee.eeeee....eee..................ee..eee..............eeee....eee................ee.........ee....ee...........ee...hhhhhhhhh........hhhhheee....eee.....ee...ee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1z8y G    1 YEHATTVPNVPQIPYKALVERAGYAPLNLEITVMSSEVLPSTNQEYITCKFTTVVPSPKIKCCGSLECQPAAHADYTCKVFGGVYPFMWGGAQCFCDSENSQMSEAYVELSADCASDHAQAIKVHTAAMKVGLRIVYGNTTSFLDVYVNGVTPGTSKDLKVIAGPISASFTPFDHKVVIHRGLVYNYDFPEYGAMKPGAFGDIQATSLTSKDLIASTDIRLLKPSAKNVHVPYTQASSGFEMWKNNSGRPLQETAPFGCKIAVNPLRAVDCSYGNIPISIDIPNAAFIRT  290
                                    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


Chain H from PDB  Type:PROTEIN  Length:89
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:89
                                  1110      1120      1130      1140      1150      1160      1170      1180         
          POLS_SINDV   1101 LVSTVKCEVSECTYSADFGGMATLQYVSDREGQCPVHSHSSTATLQESTVHVLEKGAVTVHFSTASPQANFIVSLCGKKTTCNAECKPP 1189
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..............eeeeee....eee.............eee...................ee........ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                1z8y H  295 LVSTVKCEVSECTYSADFGGMATLQYVSDREGQCPVHSHSSTATLQESTVHVLEKGAVTVHFSTASPQANFIVSLCGKKTTCNAECKPP  383
                                   304       314       324       334       344       354       364       374         


Chain I from PDB  Type:PROTEIN  Length:31
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:31
                                  1224      1234      1244 
          POLS_SINDV   1215 WLFALFGGASSLLIIGLMIFACSMMLTSTRR 1245
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .................hhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                1z8y I    1 WLFALFGGASSLLIIGLMIFACSMMLTSTRR   31
                                    10        20        30 


Chain J from PDB  Type:PROTEIN  Length:36
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:36
                                   700       710       720      
          POLS_SINDV    691 HPVYTILAVASATVAMMIGVTVAVLCACKARRECLT  726
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------L------- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                1z8y J    1 HPVYTILAVASATVAMMIGVTVAVLCACLARRECLT   36
                                    10        20        30      


Chain K from PDB  Type:PROTEIN  Length:31
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:31
                                  1224      1234      1244 
          POLS_SINDV   1215 WLFALFGGASSLLIIGLMIFACSMMLTSTRR 1245
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .................hhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                1z8y K    1 WLFALFGGASSLLIIGLMIFACSMMLTSTRR   31
                                    10        20        30 


Chain L from PDB  Type:PROTEIN  Length:36
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:36
                                   700       710       720      
          POLS_SINDV    691 HPVYTILAVASATVAMMIGVTVAVLCACKARRECLT  726
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------L------- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                1z8y L    1 HPVYTILAVASATVAMMIGVTVAVLCACLARRECLT   36
                                    10        20        30      


Chain M from PDB  Type:PROTEIN  Length:31
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:31
                                  1224      1234      1244 
          POLS_SINDV   1215 WLFALFGGASSLLIIGLMIFACSMMLTSTRR 1245
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .................hhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                1z8y M    1 WLFALFGGASSLLIIGLMIFACSMMLTSTRR   31
                                    10        20        30 


Chain N from PDB  Type:PROTEIN  Length:36
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:36
                                   700       710       720      
          POLS_SINDV    691 HPVYTILAVASATVAMMIGVTVAVLCACKARRECLT  726
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------L------- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                1z8y N    1 HPVYTILAVASATVAMMIGVTVAVLCACLARRECLT   36
                                    10        20        30      


Chain O from PDB  Type:PROTEIN  Length:31
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:31
                                  1224      1234      1244 
          POLS_SINDV   1215 WLFALFGGASSLLIIGLMIFACSMMLTSTRR 1245
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
           Pfam domains (1) Alpha_E1_glycop-1z8yO01 O:1-30- Pfam domains (1)
           Pfam domains (2) Alpha_E1_glycop-1z8yO02 O:1-30- Pfam domains (2)
           Pfam domains (3) Alpha_E1_glycop-1z8yO03 O:1-30- Pfam domains (3)
           Pfam domains (4) Alpha_E1_glycop-1z8yO04 O:1-30- Pfam domains (4)
           Pfam domains (5) Alpha_E1_glycop-1z8yO05 O:1-30- Pfam domains (5)
           Pfam domains (6) Alpha_E1_glycop-1z8yO06 O:1-30- Pfam domains (6)
           Pfam domains (7) Alpha_E1_glycop-1z8yO07 O:1-30- Pfam domains (7)
           Pfam domains (8) Alpha_E1_glycop-1z8yO08 O:1-30- Pfam domains (8)
           Pfam domains (9) Alpha_E1_glycop-1z8yO09 O:1-30- Pfam domains (9)
          Pfam domains (10) Alpha_E1_glycop-1z8yO10 O:1-30- Pfam domains (10)
          Pfam domains (11) Alpha_E1_glycop-1z8yO11 O:1-30- Pfam domains (11)
          Pfam domains (12) Alpha_E1_glycop-1z8yO12 O:1-30- Pfam domains (12)
         Sec.struct. author .................hhhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                1z8y O    1 WLFALFGGASSLLIIGLMIFACSMMLTSTRR   31
                                    10        20        30 


Chain P from PDB  Type:PROTEIN  Length:36
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:36
                                   700       710       720      
          POLS_SINDV    691 HPVYTILAVASATVAMMIGVTVAVLCACKARRECLT  726
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
           Pfam domains (1) Alpha_E2_glycop-1z8yP01 P:1-36       Pfam domains (1)
           Pfam domains (2) Alpha_E2_glycop-1z8yP02 P:1-36       Pfam domains (2)
           Pfam domains (3) Alpha_E2_glycop-1z8yP03 P:1-36       Pfam domains (3)
           Pfam domains (4) Alpha_E2_glycop-1z8yP04 P:1-36       Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------L------- SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                1z8y P    1 HPVYTILAVASATVAMMIGVTVAVLCACLARRECLT   36
                                    10        20        30      


Chain Q from PDB  Type:PROTEIN  Length:151
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:151
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263 
          POLS_SINDV    114 RLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW  264
               SCOP domains d1z8yq1 Q:114-264 Viral capsid protein                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeeee..eeeee.....ee...hhhhh..eeehhh.eeeee.hhhhh............eeeee..eeeeee..eeeee...........eee.....eeeeeeeeee...eeeeeeeee.....eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ALPHAVIRUS_CP  PDB: Q:114-264 UniProt: 114-264                                                                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1z8y Q  114 RLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW  264
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263 


Chain R from PDB  Type:PROTEIN  Length:151
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:151
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263 
          POLS_SINDV    114 RLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW  264
               SCOP domains d1z8yr1 R:114-264 Viral capsid protein                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeeee..eeeee.....ee...hhhhh..eeehhh.eeeee.hhhhh............eeeee..eeeeee..eeeee...........eee.....eeeeeeeeee...eeeeeeeee.....eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ALPHAVIRUS_CP  PDB: R:114-264 UniProt: 114-264                                                                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1z8y R  114 RLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW  264
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263 


Chain S from PDB  Type:PROTEIN  Length:151
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:151
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263 
          POLS_SINDV    114 RLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW  264
               SCOP domains d1z8ys1 S:114-264 Viral capsid protein                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeeee..eeeee.....ee...hhhhh..eeehhh.eeeee.hhhhh............eeeee..eeeeee..eeeee...........eee.....eeeeeeeeee...eeeeeeeee.....eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ALPHAVIRUS_CP  PDB: S:114-264 UniProt: 114-264                                                                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1z8y S  114 RLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW  264
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263 


Chain T from PDB  Type:PROTEIN  Length:151
 aligned with POLS_SINDV | P03316 from UniProtKB/Swiss-Prot  Length:1245

    Alignment length:151
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263 
          POLS_SINDV    114 RLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW  264
               SCOP domains d1z8yt1 T:114-264 Viral capsid protein                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Peptidase_S3-1z8yT01 T:114-264                                                                                                                          Pfam domains (1)
           Pfam domains (2) Peptidase_S3-1z8yT02 T:114-264                                                                                                                          Pfam domains (2)
           Pfam domains (3) Peptidase_S3-1z8yT03 T:114-264                                                                                                                          Pfam domains (3)
           Pfam domains (4) Peptidase_S3-1z8yT04 T:114-264                                                                                                                          Pfam domains (4)
         Sec.struct. author .eeeee.....eeeeeeee..eeeee.....ee...hhhhh..eeehhh.eeeee.hhhhh............eeeee..eeeeee..eeeee...........eee.....eeeeeeeeee...eeeeeeeee.....eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ALPHAVIRUS_CP  PDB: T:114-264 UniProt: 114-264                                                                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1z8y T  114 RLFDVKNEDGDVIGHALAMEGKVMKPLHVKGTIDHPVLSKLKFTKSSAYDMEFAQLPVNMRSEAFTYTSEHPEGFYNWHHGAVQYSGGRFTIPRGVGGRGDSGRPIMDNSGRVVAIVLGGADEGTRTALSVVTWNSKGKTIKTTPEGTEEW  264
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
   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  (0, 0)

(no "CATH Domain" information available for 1Z8Y)

(-) Pfam Domains  (3, 20)

Asymmetric Unit
(-)
Clan: Peptidase_PA (797)
(-)
Clan: no clan defined [family: Alpha_E1_glycop] (11)
(-)
Clan: no clan defined [family: Alpha_E2_glycop] (9)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T   (POLS_SINDV | P03316)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    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.
    GO:0044389    ubiquitin-like protein ligase binding    Interacting selectively and non-covalently with a ubiquitin-like protein ligase, such as ubiquitin-ligase.
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0061025    membrane fusion    The membrane organization process that joins two lipid bilayers to form a single membrane.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0039619    T=4 icosahedral viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=4 symmetry. The T=4 capsid is composed of 12 pentameric and 30 hexameric capsomeres.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0098029    icosahedral viral capsid, spike    A short structure attached to an icosahedral virion capsid, and used for attachment to the host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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  1z8y
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLS_SINDV | P03316: 1kxa 1kxb 1kxc 1kxd 1kxe 1kxf 1ld4 1svp 2snv 2snw 3j0f 3muu 3muw

(-) Related Entries Specified in the PDB File

1ld4 FITTING OF STRUCTURAL PROTEINS INTO HIGHER RESOLUTION EM MAP RELATED ID: EMD-1121 RELATED DB: EMDB