Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  4.3A RESOLUTION STRUCTURE OF A MIND-MINE(I24N) PROTEIN COMPLEX
 
Authors :  S. Lovell, K. P. Battaile, K. -T. Park, W. Wu, T. Holyoak, J. Lutkenhaus
Date :  25 Mar 11  (Deposition) - 17 Aug 11  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A (2x),B (2x),C (1x),D (1x)
Biol. Unit 2:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 3:  A,B  (1x)
Biol. Unit 4:  C,D  (1x)
Keywords :  Atpase, Protein Complex, Bacterial Cell Division Inhibitor, Mine, Cell Cycle, Hydrolase-Cell Cycle Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. T. Park, W. Wu, K. P. Battaile, S. Lovell, T. Holyoak, J. Lutkenhaus
The Min Oscillator Uses Mind-Dependent Conformational Changes In Mine To Spatially Regulate Cytokinesis.
Cell(Cambridge, Mass. ) V. 146 396 2011
PubMed-ID: 21816275  |  Reference-DOI: 10.1016/J.CELL.2011.06.042

(-) Compounds

Molecule 1 - SEPTUM SITE-DETERMINING PROTEIN MIND
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B1175, JW1164, MIND
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: CELL DIVISION INHIBITOR MIND
 
Molecule 2 - CELL DIVISION TOPOLOGICAL SPECIFICITY FACTOR
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJB216
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 12-88
    Gene: B1174, JW1163, MINE
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: MINE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): A (2x)B (2x)C (1x)D (1x)
Biological Unit 2 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 3 (1x): AB  
Biological Unit 4 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ADP-1Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ADP-1Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ADP-1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , THR A:17 , THR A:18 , ARG A:182 , ILE A:211 , PRO A:212 , GLU A:213 , ASP A:214 , VAL A:217 , LYS B:11 , GLU B:146BINDING SITE FOR RESIDUE ADP A 261
2AC2SOFTWARELYS A:11 , GLU A:146 , GLY B:13 , VAL B:14 , GLY B:15 , LYS B:16 , THR B:17 , THR B:18 , ARG B:182 , PRO B:212 , GLU B:213 , ASP B:214 , VAL B:217BINDING SITE FOR RESIDUE ADP B 261

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R9J)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro C:58 -Glu C:59
2Pro D:58 -Glu D:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R9J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R9J)

(-) Exons   (0, 0)

(no "Exon" information available for 3R9J)

(-) 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 MIND_ECOLI | P0AEZ3 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
           MIND_ECOLI     2 ARIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFDIGLRNLDLIMGCERRVVYDFVNVIQGDATLNQALIKDKRTENLYILPASQTRDKDALTREGVAKVLDDLKAMDFEFIVCDSPAGIETGALMALYFADEAIITTNPEVSSVRDSDRILGILASKSRRAENGEEPIKEHLLLTRYNPGRVSRGDMLSMEDVLEILRIKLVGVIPEDQSVLRASNQGEPVILDINADAGKAYADTVERLLGEERPFRFIEE 258
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhh........hhhhhhh...hhhhhhee......eeee...........hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh.-------.....eeeeeeeeehhhhhhh....hhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r9j A   2 ARIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFAIGLRNLDLIMGCERRVVYDFVNVIQGDATLNQALIKDKRTENLYILPASQTRDKDALTREGVAKVLDDLKAMDFEFIVCDSPAGIETGALMALYFADEAIITTNPEVSSVRDSDRILGILAS-------GEEPIKEHLLLTRYNPGRVSRGDMLSMEDVLEILRIKLVGVIPEDQSVLRASNQGEPVILDINADAGKAYADTVERLLGEERPFRFIEE 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161|      171       181       191       201       211       221       231       241       251       
                                                                                                                                                                                          162     170                                                                                        


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with MIND_ECOLI | P0AEZ3 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
           MIND_ECOLI     2 ARIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFDIGLRNLDLIMGCERRVVYDFVNVIQGDATLNQALIKDKRTENLYILPASQTRDKDALTREGVAKVLDDLKAMDFEFIVCDSPAGIETGALMALYFADEAIITTNPEVSSVRDSDRILGILASKSRRAENGEEPIKEHLLLTRYNPGRVSRGDMLSMEDVLEILRIKLVGVIPEDQSVLRASNQGEPVILDINADAGKAYADTVERLLGEERPFRFIEE 258
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhh...eeeee......hhhhhh........hhhhhhh...hhhhhhee......eeee...........hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...-------...eeeeeeeeehhhhhhh....hhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r9j B   2 ARIIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFAIGLRNLDLIMGCERRVVYDFVNVIQGDATLNQALIKDKRTENLYILPASQTRDKDALTREGVAKVLDDLKAMDFEFIVCDSPAGIETGALMALYFADEAIITTNPEVSSVRDSDRILGILASKS-------EPIKEHLLLTRYNPGRVSRGDMLSMEDVLEILRIKLVGVIPEDQSVLRASNQGEPVILDINADAGKAYADTVERLLGEERPFRFIEE 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161  |      -|      181       191       201       211       221       231       241       251       
                                                                                                                                                                                            164     172                                                                                      


Chain C from PDB  Type:PROTEIN  Length:70
 aligned with MINE_ECOLI | P0A734 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:70
                                    22        32        42        52        62        72        82
           MINE_ECOLI    13 NTANIAKERLQIIVAERRRSDAEPHYLPQLRKDILEVICKYVQIDPEMVTVQLEQKDGDISILELNVTLP  82
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...........eeeee...eeeee...ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 3r9j C  13 NTANIAKERLQNIVAERRRSDAEPHYLPQLRKDILEVICKYVQIDPEMVTVQLEQKDGDISILELNVTLP  82
                                    22        32        42        52        62        72        82


Chain D from PDB  Type:PROTEIN  Length:70
 aligned with MINE_ECOLI | P0A734 from UniProtKB/Swiss-Prot  Length:88

    Alignment length:70
                                    22        32        42        52        62        72        82
           MINE_ECOLI    13 NTANIAKERLQIIVAERRRSDAEPHYLPQLRKDILEVICKYVQIDPEMVTVQLEQKDGDISILELNVTLP  82
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..........eeeeee...eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 3r9j D  13 NTANIAKERLQNIVAERRRSDAEPHYLPQLRKDILEVICKYVQIDPEMVTVQLEQKDGDISILELNVTLP  82
                                    22        32        42        52        62        72        82
   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  (0, 0)

(no "SCOP Domain" information available for 3R9J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R9J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R9J)

(-) Gene Ontology  (18, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MIND_ECOLI | P0AEZ3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0051782    negative regulation of cell division    Any process that stops, prevents, or reduces the frequency, rate or extent of cell division.
cellular component
    GO:0060187    cell pole    Either of two different areas at opposite ends of an axis of a cell.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0031226    intrinsic component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C,D   (MINE_ECOLI | P0A734)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0000918    barrier septum site selection    The process of marking the site where a barrier septum will form.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0032955    regulation of barrier septum assembly    Any process that modulates the frequency, rate or extent of barrier septum formation. Barrier septum formation is the assembly and arrangement of a septum that spans the plasma membrane interface between progeny cells following cytokinesis.
    GO:0051302    regulation of cell division    Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro C:58 - Glu C:59   [ RasMol ]  
    Pro D:58 - Glu D:59   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3r9j
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MIND_ECOLI | P0AEZ3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MINE_ECOLI | P0A734
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    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
  MIND_ECOLI | P0AEZ3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MINE_ECOLI | P0A734
    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
        MIND_ECOLI | P0AEZ3: 3q9l 3r9i
        MINE_ECOLI | P0A734: 1ev0 3r9i

(-) Related Entries Specified in the PDB File

3q9l MIND-ATP COMPLEX
3r9i