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(-) Description

Title :  BACTERIOPHAGE T4 BASEPLATE STRUCTURAL PROTEIN GP8
 
Authors :  P. G. Leiman, M. M. Shneider, V. A. Kostyuchenko, P. R. Chipman, V. V. Mesyanzhinov, M. G. Rossmann
Date :  20 Nov 02  (Deposition) - 10 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Bacteriophage T4, Baseplate, Dimer, Beta Sandwich, Halide Binding, Br, Bromine, Bromide, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. G. Leiman, M. M. Shneider, V. A. Kostyuchenko, P. R. Chipman, V. V. Mesyanzhinov, M. G. Rossmann
Structure And Location Of Gene Product 8 In The Bacteriophage T4 Baseplate
J. Mol. Biol. V. 328 821 2003
PubMed-ID: 12729757  |  Reference-DOI: 10.1016/S0022-2836(03)00366-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BASEPLATE STRUCTURAL PROTEIN GP8
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-22B(+)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GENE 8
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: BASEPLATE WEDGE PROTEIN 8

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 40)

Asymmetric Unit (1, 40)
No.NameCountTypeFull Name
1BR40Ligand/IonBROMIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION

(-) Sites  (38, 38)

Asymmetric Unit (38, 38)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:103 , TYR A:104 , THR A:105BINDING SITE FOR RESIDUE BR A 335
02AC2SOFTWAREHOH A:346 , ARG B:92BINDING SITE FOR RESIDUE BR A 336
03AC3SOFTWARELEU A:22 , ASN A:23 , ASN A:26 , ASN B:35BINDING SITE FOR RESIDUE BR A 337
04AC4SOFTWAREVAL A:65 , ASN B:109BINDING SITE FOR RESIDUE BR B 335
05AC5SOFTWAREPRO A:213 , GLU A:214 , HOH A:349BINDING SITE FOR RESIDUE BR A 338
06AC6SOFTWARELYS B:15BINDING SITE FOR RESIDUE BR B 336
07AC7SOFTWAREASN A:201 , ARG A:202 , LYS A:250BINDING SITE FOR RESIDUE BR A 339
08AC8SOFTWARESER A:84BINDING SITE FOR RESIDUE BR A 340
09AC9SOFTWARELYS A:282BINDING SITE FOR RESIDUE BR A 341
10BC1SOFTWAREARG A:17BINDING SITE FOR RESIDUE BR A 342
11BC2SOFTWARETYR A:25BINDING SITE FOR RESIDUE BR A 343
12BC3SOFTWAREASP B:102 , PRO B:103 , TYR B:104 , THR B:105 , ARG B:165 , TYR D:60BINDING SITE FOR RESIDUE BR B 337
13BC4SOFTWAREPRO B:213 , GLU B:214 , HOH B:357BINDING SITE FOR RESIDUE BR B 339
14BC5SOFTWAREVAL B:68BINDING SITE FOR RESIDUE BR B 340
15BC6SOFTWARESER A:124 , HOH B:386BINDING SITE FOR RESIDUE BR B 341
16BC7SOFTWARESER B:84BINDING SITE FOR RESIDUE BR B 342
17BC8SOFTWAREALA B:281 , LYS B:282 , MET B:303BINDING SITE FOR RESIDUE BR B 343
18BC9SOFTWARETYR B:25 , GLU B:214 , GLU B:215BINDING SITE FOR RESIDUE BR B 344
19CC1SOFTWARESER B:30 , HOH B:350BINDING SITE FOR RESIDUE BR B 345
20CC2SOFTWAREILE B:7BINDING SITE FOR RESIDUE BR B 346
21CC3SOFTWAREASP C:102 , PRO C:103 , TYR C:104 , THR C:105BINDING SITE FOR RESIDUE BR C 335
22CC4SOFTWAREPRO C:118 , HOH C:344 , ARG D:92 , ASN D:205BINDING SITE FOR RESIDUE BR C 336
23CC5SOFTWAREASN C:23 , ASN C:26BINDING SITE FOR RESIDUE BR C 337
24CC6SOFTWAREHOH C:368 , ASN D:109BINDING SITE FOR RESIDUE BR C 338
25CC7SOFTWAREASN C:26 , PRO C:213 , GLU C:214 , HOH C:357BINDING SITE FOR RESIDUE BR C 339
26CC8SOFTWAREHOH C:351 , LYS D:15BINDING SITE FOR RESIDUE BR D 335
27CC9SOFTWAREPRO C:83 , SER C:84 , HOH C:376BINDING SITE FOR RESIDUE BR C 341
28DC1SOFTWARELYS C:282BINDING SITE FOR RESIDUE BR C 342
29DC2SOFTWARETRP C:160BINDING SITE FOR RESIDUE BR C 343
30DC3SOFTWAREASP D:102 , TYR D:104 , THR D:105BINDING SITE FOR RESIDUE BR D 336
31DC4SOFTWAREASN C:35 , LEU D:22 , ASN D:23 , ASN D:26BINDING SITE FOR RESIDUE BR D 337
32DC5SOFTWAREHOH C:418BINDING SITE FOR RESIDUE BR D 338
33DC6SOFTWAREASN D:26 , PRO D:213 , GLU D:214 , HOH D:349BINDING SITE FOR RESIDUE BR D 339
34DC7SOFTWAREHOH C:413 , HOH D:367 , HOH D:369 , HOH D:407BINDING SITE FOR RESIDUE BR D 340
35DC8SOFTWARESER C:124BINDING SITE FOR RESIDUE BR D 341
36DC9SOFTWARESER D:84BINDING SITE FOR RESIDUE BR D 342
37EC1SOFTWAREMET D:303BINDING SITE FOR RESIDUE BR D 343
38EC2SOFTWARELEU D:82 , PRO D:83BINDING SITE FOR RESIDUE BR D 344

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:142 -A:153
2B:142 -B:153
3C:142 -C:153
4D:142 -D:153

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N8B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N8B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N8B)

(-) Exons   (0, 0)

(no "Exon" information available for 1N8B)

(-) 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:328
 aligned with BP08_BPT4 | P19062 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:328
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        
            BP08_BPT4     7 IYRAIVTSKFRTEKMLNFYNSIGSGPDKNTIFITFGRSEPWSSNENEVGFAPPYPTDSVLGVTDMWTHMMGTVKVLPSMLDAVIPRRDWGDTRYPDPYTFRINDIVVCNSAPYNATESGAGWLVYRCLDVPDTGMCSIASLTDKDECLKLGGKWTPSARSMTPPEGRGDAEGTIEPGDGYVWEYLFEIPPDVSINRCTNEYIVVPWPEELKEDPTRWGYEDNLTWQQDDFGLIYRVKANTIRFKAYLDSVYFPEAALPGNKGFRQISIITNPLEAKAHPNDPNVKAEKDYYDPEDLMRHSGEMIYMENRPPIIMAMDQTEEINILFTF 334
               SCOP domains d1n8ba_ A: Baseplate structural protein gp8                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----1n8bA01 A:12-87,A:246-334 baseplate structural protein gp8, domain 1        1n8bA02 A:88-245 baseplate structural protein gp8, domain 2                                                                                                   1n8bA01 A:12-87,A:246-334 baseplate structural protein gp8, domain 1                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhh........eeeeee.....hhhhhh..........hhhhhhhhhhheeeeeeehhh.eeeeee...................eeee..hhhhh......eeeeeeee....eee......hhhhhhhh...eee................ee......eeeeeeeehhhhhhhh....eeee.hhhhhhhhhhhhh....hhhhh...hhhhhh...eeeeeeeee.hhh..........eeeeeeee...................eehhhhh.....eeeeeeeeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n8b A   7 IYRAIVTSKFRTEKMLNFYNSIGSGPDKNTIFITFGRSEPWSSNENEVGFAPPYPTDSVLGVTDMWTHMMGTVKVLPSMLDAVIPRRDWGDTRYPDPYTFRINDIVVCNSAPYNATESGAGWLVYRCLDVPDTGMCSIASLTDKDECLKLGGKWTPSARSMTPPEGRGDAEGTIEPGDGYVWEYLFEIPPDVSINRCTNEYIVVPWPEELKEDPTRWGYEDNLTWQQDDFGLIYRVKANTIRFKAYLDSVYFPEAALPGNKGFRQISIITNPLEAKAHPNDPNVKAEKDYYDPEDLMRHSGEMIYMENRPPIIMAMDQTEEINILFTF 334
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        


Chain B from PDB  Type:PROTEIN  Length:328
 aligned with BP08_BPT4 | P19062 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:328
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        
            BP08_BPT4     7 IYRAIVTSKFRTEKMLNFYNSIGSGPDKNTIFITFGRSEPWSSNENEVGFAPPYPTDSVLGVTDMWTHMMGTVKVLPSMLDAVIPRRDWGDTRYPDPYTFRINDIVVCNSAPYNATESGAGWLVYRCLDVPDTGMCSIASLTDKDECLKLGGKWTPSARSMTPPEGRGDAEGTIEPGDGYVWEYLFEIPPDVSINRCTNEYIVVPWPEELKEDPTRWGYEDNLTWQQDDFGLIYRVKANTIRFKAYLDSVYFPEAALPGNKGFRQISIITNPLEAKAHPNDPNVKAEKDYYDPEDLMRHSGEMIYMENRPPIIMAMDQTEEINILFTF 334
               SCOP domains d1n8bb_ B: Baseplate structural protein gp8                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----1n8bB01 B:12-87,B:246-334 baseplate structural protein gp8, domain 1        1n8bB02 B:88-245 baseplate structural protein gp8, domain 2                                                                                                   1n8bB01 B:12-87,B:246-334 baseplate structural protein gp8, domain 1                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhh........eeeeee.....hhhhh...........hhhhhhhhhh.eeeeeeehhhhheeeee...................eeee..............eeeeeee....ee...................ee................ee......eeeeeee.hhhhhhhh....eeee.hhhhhhhhhhhhh.....hhhhhh.hhhhhh...eee..eeee..............eeeeeeee..ee.........ee....eehhhhh.....eeeeeeeeeee......eeee..eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n8b B   7 IYRAIVTSKFRTEKMLNFYNSIGSGPDKNTIFITFGRSEPWSSNENEVGFAPPYPTDSVLGVTDMWTHMMGTVKVLPSMLDAVIPRRDWGDTRYPDPYTFRINDIVVCNSAPYNATESGAGWLVYRCLDVPDTGMCSIASLTDKDECLKLGGKWTPSARSMTPPEGRGDAEGTIEPGDGYVWEYLFEIPPDVSINRCTNEYIVVPWPEELKEDPTRWGYEDNLTWQQDDFGLIYRVKANTIRFKAYLDSVYFPEAALPGNKGFRQISIITNPLEAKAHPNDPNVKAEKDYYDPEDLMRHSGEMIYMENRPPIIMAMDQTEEINILFTF 334
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        


Chain C from PDB  Type:PROTEIN  Length:328
 aligned with BP08_BPT4 | P19062 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:328
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        
            BP08_BPT4     7 IYRAIVTSKFRTEKMLNFYNSIGSGPDKNTIFITFGRSEPWSSNENEVGFAPPYPTDSVLGVTDMWTHMMGTVKVLPSMLDAVIPRRDWGDTRYPDPYTFRINDIVVCNSAPYNATESGAGWLVYRCLDVPDTGMCSIASLTDKDECLKLGGKWTPSARSMTPPEGRGDAEGTIEPGDGYVWEYLFEIPPDVSINRCTNEYIVVPWPEELKEDPTRWGYEDNLTWQQDDFGLIYRVKANTIRFKAYLDSVYFPEAALPGNKGFRQISIITNPLEAKAHPNDPNVKAEKDYYDPEDLMRHSGEMIYMENRPPIIMAMDQTEEINILFTF 334
               SCOP domains d1n8bc_ C: Baseplate structural protein gp8                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----1n8bC01 C:12-87,C:246-334 baseplate structural protein gp8, domain 1        1n8bC02 C:88-245 baseplate structural protein gp8, domain 2                                                                                                   1n8bC01 C:12-87,C:246-334 baseplate structural protein gp8, domain 1                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhhhh........eeeeee.....................hhhhhhhhhhheeeeee.hhh.eeeeee...................eeee.............eeeee.......eee......hhhhhhhh...eee................ee.......eeeeeeehhhhhhhh....eeee.hhhhhhhh..........hhhhhh.hhhhhh...eeeeeeeee.hhh..........eeeeeeee...................eehhhhh.....eeeeeeeeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n8b C   7 IYRAIVTSKFRTEKMLNFYNSIGSGPDKNTIFITFGRSEPWSSNENEVGFAPPYPTDSVLGVTDMWTHMMGTVKVLPSMLDAVIPRRDWGDTRYPDPYTFRINDIVVCNSAPYNATESGAGWLVYRCLDVPDTGMCSIASLTDKDECLKLGGKWTPSARSMTPPEGRGDAEGTIEPGDGYVWEYLFEIPPDVSINRCTNEYIVVPWPEELKEDPTRWGYEDNLTWQQDDFGLIYRVKANTIRFKAYLDSVYFPEAALPGNKGFRQISIITNPLEAKAHPNDPNVKAEKDYYDPEDLMRHSGEMIYMENRPPIIMAMDQTEEINILFTF 334
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        


Chain D from PDB  Type:PROTEIN  Length:328
 aligned with BP08_BPT4 | P19062 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:328
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326        
            BP08_BPT4     7 IYRAIVTSKFRTEKMLNFYNSIGSGPDKNTIFITFGRSEPWSSNENEVGFAPPYPTDSVLGVTDMWTHMMGTVKVLPSMLDAVIPRRDWGDTRYPDPYTFRINDIVVCNSAPYNATESGAGWLVYRCLDVPDTGMCSIASLTDKDECLKLGGKWTPSARSMTPPEGRGDAEGTIEPGDGYVWEYLFEIPPDVSINRCTNEYIVVPWPEELKEDPTRWGYEDNLTWQQDDFGLIYRVKANTIRFKAYLDSVYFPEAALPGNKGFRQISIITNPLEAKAHPNDPNVKAEKDYYDPEDLMRHSGEMIYMENRPPIIMAMDQTEEINILFTF 334
               SCOP domains d1n8bd_ D: Baseplate structural protein gp8                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----1n8bD01 D:12-87,D:246-334 baseplate structural protein gp8, domain 1        1n8bD02 D:88-245 baseplate structural protein gp8, domain 2                                                                                                   1n8bD01 D:12-87,D:246-334 baseplate structural protein gp8, domain 1                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhhh........eeeeee.....hhhhh...........hhhhhhhhhhheeeeeeehhh.eeeeee...................eeee.............eeeeee......eee......hhhhhhh....eee................ee.......eeeeeeehhhhhhhh....eeee.hhhhhhh.hhhhh.....hhhhhh.hhhhhh...eeeeeeeee.hhh..........eeeeeeee...................eehhhhh.....eeeeeeeeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n8b D   7 IYRAIVTSKFRTEKMLNFYNSIGSGPDKNTIFITFGRSEPWSSNENEVGFAPPYPTDSVLGVTDMWTHMMGTVKVLPSMLDAVIPRRDWGDTRYPDPYTFRINDIVVCNSAPYNATESGAGWLVYRCLDVPDTGMCSIASLTDKDECLKLGGKWTPSARSMTPPEGRGDAEGTIEPGDGYVWEYLFEIPPDVSINRCTNEYIVVPWPEELKEDPTRWGYEDNLTWQQDDFGLIYRVKANTIRFKAYLDSVYFPEAALPGNKGFRQISIITNPLEAKAHPNDPNVKAEKDYYDPEDLMRHSGEMIYMENRPPIIMAMDQTEEINILFTF 334
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326
   Legend:   → Mismatch (orange background)
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  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, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1N8B)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (BP08_BPT4 | P19062)
biological process
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  BP08_BPT4 | P19062
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BP08_BPT4 | P19062: 1n7z 1n80 1pdm 1tja 5hx2 5iv5 5iv7

(-) Related Entries Specified in the PDB File

1n7z SEMET DERIVATIVE, CRYSTAL FORM II
1n80 NATIVE PROTEIN, CRYSTAL FORM I