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(-) Description

Title :  2.1A BACTERIOPHAGE PHI-29 CONNECTOR
 
Authors :  A. Guasch, J. Pous, B. Ibarra, F. X. Gomis-Ruth, J. M. Valpuesta, N. Sous J. L. Carrascosa, M. Coll
Date :  28 May 01  (Deposition) - 13 Feb 02  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (4x)
Keywords :  Virus, Connector, Portal, Sh3-Like, Helix Bundle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Guasch, J. Pous, B. Ibarra, F. X. Gomis-Ruth, J. M. Valpuesta, N. Sousa, J. L. Carrascosa, M. Coll
Detailed Architecture Of A Dna Translocating Machine: The High-Resolution Structure Of The Bacteriophage Phi29 Connector Particle.
J. Mol. Biol. V. 315 663 2002
PubMed-ID: 11812138  |  Reference-DOI: 10.1006/JMBI.2001.5278

(-) Compounds

Molecule 1 - UPPER COLLAR PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACTERIOPHAGE PHI-29
    Organism Taxid: 10756
    Synonym: CONNECTOR PROTEIN, LATE PROTEIN GP10

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (4x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MPD16Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:214 , ASN A:215 , TRP A:218 , GLU C:220binding site for residue MPD A 401
2AC2SOFTWAREGLU A:220 , LYS B:214 , ASN B:215 , TRP B:218binding site for residue MPD B 401
3AC3SOFTWAREASN A:29 , PHE C:128 , PRO C:129 , PRO C:132binding site for residue MPD C 401
4AC4SOFTWAREGLU B:220 , HOH B:610 , LYS C:214 , ASN C:215 , TRP C:218binding site for residue MPD C 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H5W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H5W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H5W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H5W)

(-) Exons   (0, 0)

(no "Exon" information available for 1H5W)

(-) 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:250
 aligned with PORTL_BPPH2 | P04332 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:269
                                    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         
          PORTL_BPPH2    17 RQKRNRWFIHYLNYLQSLAYQLFEWENLPPTINPSFLEKSIHQFGYVGFYKDPVISYIACNGALSGQRDVYNQATVFRAASPVYQKEFKLYNYRDMKEEDMGVVIYNNDMAFPTTPTLELFAAELAELKEIISVNQNAQKTPVLIRANDNNQLSLKQVYNQYEGNAPVIFAHEALDSDSIEVFKTDAPYVVDKLNAQKNAVWNEMMTFLGIKNANLEKKERMVTDEVSSNDEQIESSGTVFLKSREEACEKINELYGLNVKVKFRYDIV 285
               SCOP domains d1h5wa_ A: Upper collar protein gp10 (connector protein)                                                                                                                                                                                                                      SCOP domains
               CATH domains 1h5wA01            ----------------------------------------------------------------------------------------------1h5wA01                     1h5wA03     A:158-202                        1h5wA01                 ---               ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhheeeeeee...eeeee.eeee..........eeeee....eeeee.............eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..----.hhhhhhh..................eeeee.....hhhhhhhhhhhhhhhhhhhh....---------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h5w A  17 RQKRNRWFIHYLNYLQSLAYQLFEWENLPPTINPSFLEKSIHQFGYVGFYKDPVISYIACNGALSGQRDVYNQATVFRAASPVYQKEFKLYNYRDMKEEDMGVVIYNNDMAFPTTPTLELFAAELAELKEIISVNQNAQKTPVLIRAND----SLKQVYNQYEGNAPVIFAHEALDSDSIEVFKTDAPYVVDKLNAQKNAVWNEMMTFLGIKN---------------SNDEQIESSGTVFLKSREEACEKINELYGLNVKVKFRYDIV 285
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156        |-   |   176       186       196       206       216       226  |      -       246       256       266       276         
                                                                                                                                                                              165  170                                                        229             245                                        


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with PORTL_BPPH2 | P04332 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:270
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
          PORTL_BPPH2    16 QRQKRNRWFIHYLNYLQSLAYQLFEWENLPPTINPSFLEKSIHQFGYVGFYKDPVISYIACNGALSGQRDVYNQATVFRAASPVYQKEFKLYNYRDMKEEDMGVVIYNNDMAFPTTPTLELFAAELAELKEIISVNQNAQKTPVLIRANDNNQLSLKQVYNQYEGNAPVIFAHEALDSDSIEVFKTDAPYVVDKLNAQKNAVWNEMMTFLGIKNANLEKKERMVTDEVSSNDEQIESSGTVFLKSREEACEKINELYGLNVKVKFRYDIV 285
               SCOP domains d1h5wb_ B: Upper collar protein gp10 (connector protein)                                                                                                                                                                                                                       SCOP domains
               CATH domains 1h5wB01             ----------------------------------------------------------------------------------------------1h5wB01                     1h5wB03 B:158-202                            1h5wB01                 ----------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhheeeeeee...eeeee.eee...........eeeee....eeeee.............eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh.....eeee........eeeee.....hhhhhhhhhhhhhhhhhhhh.....--------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h5w B  16 QRQKRNRWFIHYLNYLQSLAYQLFEWENLPPTINPSFLEKSIHQFGYVGFYKDPVISYIACNGALSGQRDVYNQATVFRAASPVYQKEFKLYNYRDMKEEDMGVVIYNNDMAFPTTPTLELFAAELAELKEIISVNQNAQKTPVLIRANDNNQLSLKQVYNQYEGNAPVIFAHEALDSDSIEVFKTDAPYVVDKLNAQKNAVWNEMMTFLGIKNA--------------SNDEQIESSGTVFLKSREEACEKINELYGLNVKVKFRYDIV 285
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225    |    -       245       255       265       275       285
                                                                                                                                                                                                                                                230            245                                        


Chain C from PDB  Type:PROTEIN  Length:252
 aligned with PORTL_BPPH2 | P04332 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:267
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       
          PORTL_BPPH2    18 QKRNRWFIHYLNYLQSLAYQLFEWENLPPTINPSFLEKSIHQFGYVGFYKDPVISYIACNGALSGQRDVYNQATVFRAASPVYQKEFKLYNYRDMKEEDMGVVIYNNDMAFPTTPTLELFAAELAELKEIISVNQNAQKTPVLIRANDNNQLSLKQVYNQYEGNAPVIFAHEALDSDSIEVFKTDAPYVVDKLNAQKNAVWNEMMTFLGIKNANLEKKERMVTDEVSSNDEQIESSGTVFLKSREEACEKINELYGLNVKVKFRYDI 284
               SCOP domains d1h5wc_ C: Upper collar protein gp10 (connector protein)                                                                                                                                                                                                                    SCOP domains
               CATH domains 1h5wC01           ----------------------------------------------------------------------------------------------1h5wC01                     1h5wC03 C:158-202                            1h5wC01                 ---------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhheeeeeee...eeeee.eeee..........eeeee....eeeeee..........eeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhh.....eeee........eeeee.....hhhhhhhhhhhhhhhhhhhh.....---------------.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h5w C  18 QKRNRWFIHYLNYLQSLAYQLFEWENLPPTINPSFLEKSIHQFGYVGFYKDPVISYIACNGALSGQRDVYNQATVFRAASPVYQKEFKLYNYRDMKEEDMGVVIYNNDMAFPTTPTLELFAAELAELKEIISVNQNAQKTPVLIRANDNNQLSLKQVYNQYEGNAPVIFAHEALDSDSIEVFKTDAPYVVDKLNAQKNAVWNEMMTFLGIKNA---------------NDEQIESSGTVFLKSREEACEKINELYGLNVKVKFRYDI 284
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227  |      -       247       257       267       277       
                                                                                                                                                                                                                                              230             246
   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, 3)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H5W)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PORTL_BPPH2 | P04332)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
    GO:0019073    viral DNA genome packaging    The packing of viral DNA into a capsid.
    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: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:0046798    viral portal complex    A multimeric ring of proteins through which the DNA enters and exits the viral capsid.
    GO:0046729    viral procapsid    A stable empty viral capsid produced during the assembly of viruses.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PORTL_BPPH2 | P04332: 1fou 1ijg 1jnb 1l4p 1vri 1vrj 1ywe

(-) Related Entries Specified in the PDB File

1fou CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29
1ijg STRUCTURE OF THE BACTERIOPHAGE PHI29 HEAD- TAIL CONNECTORPROTEIN