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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF MURINE GAMMA-HERPESVIRUS 68 BCL-2 HOMOLOG M11 AND A BECLIN 1 BH3 DOMAIN-DERIVED PEPTIDE
 
Authors :  M. Su, Y. Mei, S. Sinha
Date :  30 Aug 13  (Deposition) - 29 Jan 14  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A (2x),B (2x),C (2x),D (2x)
Keywords :  Bh3D, Bcl-2 Family, Anti-Apoptotic And Anti-Autophagic Activities, Viral Protein-Apoptosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Su, Y. Mei, R. Sanishvili, B. Levine, C. L. Colbert, S. Sinha
Targeting Gamma-Herpesvirus 68 Bcl-2-Mediated Down-Regulation Of Autophagy.
J. Biol. Chem. V. 289 8029 2014
PubMed-ID: 24443581  |  Reference-DOI: 10.1074/JBC.M113.515361

(-) Compounds

Molecule 1 - BCL-2 HOMOLOG (GENE 16?)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21(D+)
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-136
    Gene: GAMMAHV.M11, M11, V-BCL-2, V-BCL-2 GAMMAHV.M11
    Organism Common: MUHV-4
    Organism Scientific: MURID HERPESVIRUS 4
    Organism Taxid: 33708
    Synonym: M11, M11 PROTEIN, V-BCL-2
 
Molecule 2 - BECLIN-1
    Chains: C, D
    Engineered: YES
    Fragment: UNP RESIDUES 107-130
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: COILED-COIL MYOSIN-LIKE BCL2-INTERACTING PROTEIN, PROTEIN GT197
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D
Biological Unit 3 (2x): A (2x)B (2x)C (2x)D (2x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 3 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:57 , ALA A:58 , HOH A:325 , SO4 B:201 , ARG C:115 , ARG D:115BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWARESO4 A:201 , ARG B:57 , ALA B:58 , ARG C:115 , ARG D:115BINDING SITE FOR RESIDUE SO4 B 201
3AC3SOFTWAREHIS B:3 , LYS B:4BINDING SITE FOR RESIDUE SO4 B 202
4AC4SOFTWAREASN B:127 , ASN B:130 , HIS B:131BINDING SITE FOR RESIDUE SO4 B 203

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:29 -B:104

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MI8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MI8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MI8)

(-) Exons   (0, 0)

(no "Exon" information available for 4MI8)

(-) 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:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mi8 A   2 SHKKSGTYWATLITAFLKTVSKVEELDCVDSAVLVDVSKIITLTQEFRRHYDSVYRADYGPALKNWKRDLSKLFTSLFVDVINSGRIVGFFDVGRYVCEEVLCPGSWTEDHELLNDCMTHFFIENNLMNHFPLED 136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     


Chain B from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mi8 B   2 SHKKSGTYWATLITAFLKTVSKVEELDCVDSAVLVDVSKIITLTQEFRRHYDSVYRADYGPALKNWKRDLSKLFTSLFVDVINSGRIVGFFDVGRYVCEEVLCPGSWTEDHELLNDCMTHFFIENNLMNHFPLEDH 137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      


Chain C from PDB  Type:PROTEIN  Length:20
                                                    
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 4mi8 C 108 TMENLSRRLKVTEALFDIMS 127
                                   117       127


Chain D from PDB  Type:PROTEIN  Length:22
                                                      
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 4mi8 D 106 SGTMENLSRRLKVTEALFDIMS 127
                                   115       125
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 4MI8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MI8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MI8)

(-) Gene Ontology  (65, 66)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BECN1_HUMAN | Q14457: 2p1l 2pon 3dvu 4ddp 5efm 5hhe
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        P89884_MHV68 | P89884: 2abo 3bl2 3dvu

(-) Related Entries Specified in the PDB File

3dvu STRUCTURE OF GAMMA-HERPESVIRUS M11 BOUND TO THE BECLIN 1 BH3D