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

(-) Description

Title :  TOG2:ALPHA/BETA-TUBULIN COMPLEX
 
Authors :  P. Ayaz, L. M. Rice
Date :  22 Jul 14  (Deposition) - 20 Aug 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Complex, Structural Protein-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Ayaz, S. Munyoki, E. A. Geyer, F. A. Piedra, E. S. Vu, R. Bromberg, Z. Otwinowski, N. V. Grishin, C. A. Brautigam, L. M. Rice
A Tethered Delivery Mechanism Explains The Catalytic Action Of A Microtubule Polymerase.
Elife V. 3 03069 2014
PubMed-ID: 25097237  |  Reference-DOI: 10.7554/ELIFE.03069

(-) Compounds

Molecule 1 - TUBULIN ALPHA-1 CHAIN
    Chains: A
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Strain: JEL1
    Expression System Taxid: 4932
    Gene: TUB1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 2 - TUBULIN BETA CHAIN
    Chains: B
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Strain: JEL1
    Expression System Taxid: 4932
    Gene: TUB2
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: BETA-TUBULIN
 
Molecule 3 - PROTEIN STU2
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-29B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: TOG2 DOMAIN (UNP RESIDUES 318-560)
    Gene: STU2
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SUPPRESSOR OF TUBULIN 2

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:11 , GLU A:72 , GTP A:502 , HOH A:604 , HOH A:606 , HOH A:607binding site for residue MG A 501
2AC2SOFTWAREGLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , ALA A:101 , ASN A:102 , SER A:141 , GLY A:144 , GLY A:145 , THR A:146 , GLY A:147 , VAL A:178 , THR A:180 , GLU A:184 , ASN A:207 , PHE A:225 , ASN A:229 , ILE A:232 , MG A:501 , HOH A:604 , HOH A:606 , HOH A:607 , HOH A:609 , LYS B:252binding site for residue GTP A 502
3AC3SOFTWAREGTP B:502 , HOH B:608binding site for residue MG B 501
4AC4SOFTWAREGLY B:10 , GLN B:11 , CYS B:12 , GLN B:15 , ALA B:97 , ASN B:99 , SER B:138 , GLY B:141 , GLY B:142 , THR B:143 , GLY B:144 , GLU B:181 , ASN B:204 , TYR B:222 , ASN B:226 , MG B:501 , HOH B:608binding site for residue GTP B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U3J)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Gly A:46 -Glu A:47
2Ser A:274 -Pro A:275
3Val A:342 -Gln A:343
4Pro B:243 -Gly B:244
5Ala B:271 -Pro B:272
6Gln B:359 -Gly B:360
7Thr C:405 -Pro C:406

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U3J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U3J)

(-) Exons   (0, 0)

(no "Exon" information available for 4U3J)

(-) Sequences/Alignments

Asymmetric/Biological 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:431
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhhhhhhhhhhhhhh.........................eee.....eee.eeeee.hhhhhhhhhhh..........eee.......hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeeeee......hhhhhhhhhhhhhhh...eeeeeeee.hhhhh...hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh........eeeee.......hhhhhhhhhhhhhh..........eeeeeeeeee..hhhhhhhhhhhhhhh............eeeeee................eeeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u3j A   1 MREVISINVGQAGCQIGNACWELYSLEHGIKPDGHLEDGLSKPKGGEEGFSTFFHETGYGKFVPRAIYVDLEPNVIDEVRNGPYKDLFHPEQLISGKEDAANNYARGHYTVGREILGDVLDRIRKLADQCDGLQGFLFTHSLGGGTGSGLGSLLLEELSAEYGKKSKLEFAVYPAPQVSTSVVEPYNTVLTTHTTLEHADCTFMVDNEAIYDMCKRNLDIPRPSFANLNNLIAQVVSSVTASLRFDGSLNVDLNEFQTNLVPYPRIHFPLVSYSPVLSKSSVSEITNACFEPGNQMVKCDPRDGKYMATCLLYRGDVVTRDVQRAVEQVKNKKTVQLVDWCPTGFKIGICYEPPTATPNSQLATVDRAVCMLSNTTSIAEAWKRIDRKFDLMYAKRAFVHWYVGEGMEEGEFTEAREDLAALERDYIEVGA 438
                                    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|      297       307       317       327       337       347       357       367       377       387       397       407       417       427       437 
                                                                                                                                                                                                                                                                                                                 280|                                                                                                                                                      
                                                                                                                                                                                                                                                                                                                  288                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhhhhhhhhhhhhhh............hhhhhhhhh.eee.....eee.eeeee.hhhhhhhhhh.......hhh.eee.......hhhhhhh.....hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhh....hhhhh.eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh.......eeeeee........eeeeeeeee..hhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u3j B   1 MREIIHISTGQCGNQIGAAFWETICGEHGLDFNGTYHGHDDIQKERLNVYFNEASSGKWVPRSINVDLEPGTIDAVRNSAIGNLFRPDNYIFGQSSAGNVWAKGHYTEGAELVDSVMDVIRREAEGCDSLQGFQITHSLGGGTGSGMGTLLISKIREEFPDRMMATFSVLPSPKTRVEPYNATLSVHQLVEHSDETFCIDNEALYDICQLKQPSYGDLNNLVSSVMSGVTTSLRYPGQLNSDLRKLAVNLVPFPRLHFFMVGYAPLTARSLTVPELTQQMFDAKNMMAAADPRNGRYLTVAAFFRGKVSVKEVEDEMHKVQSKNSDYFVEWIPNNVQTAVCSVAPQGLDMAATFIANSTSIQELFKRVGDQFSAMFKRKAFLHWYTSEGMDELEFSEAESNMNDLVSEYQQYQEATV 430
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   ||  183       193       203       215||     227       237       247       257       267       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       
                                                                                                                                                                                                       174|                               212|||                                                     275|                                                                                                                                                    
                                                                                                                                                                                                        178                                215||                                                      282                                                                                                                                                    
                                                                                                                                                                                                                                            216|                                                                                                                                                                                                             
                                                                                                                                                                                                                                             219                                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...hhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u3j C 319 LPEETILDKLPKDFQERITSSKWKDRVEALEEFWDSVLSQTKKLKSTSQNYSNLLGIYGHIIQKDANIQAVALAAQSVELICDKLKTPGFSKDYVSLVFTPLLDRTKEKKPSVIEAIRKALLTICKYYDPLASSGRNEDMLKDILEHMKHKTPQIRMECTQLFNASMKEEKDGYSTLQRYLKDEVVPIVIQIVNDTQPAIRTIGFESFAILIKIFGMNTFVKTLEHLDNLKRKKIEETVKT 559
                                   328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558
   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 4U3J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U3J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U3J)

(-) Gene Ontology  (29, 50)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    GTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala B:271 - Pro B:272   [ RasMol ]  
    Gln B:359 - Gly B:360   [ RasMol ]  
    Gly A:46 - Glu A:47   [ RasMol ]  
    Pro B:243 - Gly B:244   [ RasMol ]  
    Ser A:274 - Pro A:275   [ RasMol ]  
    Thr C:405 - Pro C:406   [ RasMol ]  
    Val A:342 - Gln A:343   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4u3j
    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
  STU2_YEAST | P46675
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TBA1_YEAST | P09733
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TBB_YEAST | P02557
    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
  STU2_YEAST | P46675
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TBA1_YEAST | P09733
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TBB_YEAST | P02557
    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
        STU2_YEAST | P46675: 2qk1 4ffb
        TBA1_YEAST | P09733: 4ffb
        TBB_YEAST | P02557: 4ffb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4U3J)