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 :  CRYSTAL STRUCTURE OF THE SAC DOMAIN OF CPAP IN A COMPLEX WITH TUBULIN AND DARPIN
 
Authors :  A. Sharma, M. O. Steinmetz
Date :  17 Mar 16  (Deposition) - 01 Jun 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,D,F
Keywords :  Tubulin, Cpap, Centriole, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Sharma, A. Aher, N. J. Dynes, D. Frey, E. A. Katrukha, R. Jaussi, I. Grigoriev, M. Croisier, R. A. Kammerer, A. Akhmanova, P. Gonczy, M. O. Steinmetz
Centriolar Cpap/Sas-4 Imparts Slow Processive Microtubule Growth.
Dev. Cell V. 37 362 2016
PubMed-ID: 27219064  |  Reference-DOI: 10.1016/J.DEVCEL.2016.04.024

(-) Compounds

Molecule 1 - TUBULIN ALPHA-1B CHAIN
    Chains: A
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: ALPHA-TUBULIN UBIQUITOUS,TUBULIN K-ALPHA-1,TUBULIN ALPHA- UBIQUITOUS CHAIN
 
Molecule 2 - TUBULIN BETA-2B CHAIN
    Chains: B
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
 
Molecule 3 - CENTROMERE PROTEIN J
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: CENPJ, CPAP, LAP, LIP1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CENP-J,CENTROSOMAL P4.1-ASSOCIATED PROTEIN,LAG-3-ASSOCIATED PROTEIN,LYST-INTERACTING PROTEIN 1
 
Molecule 4 - DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D1
    Chains: F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3LOC1Ligand/IonN-[(7S)-1,2,3,10-TETRAMETHOXY-9-OXO-6,7-DIHYDRO-5H-BENZO[D]HEPTALEN-7-YL]ETHANAMIDE
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , GLN A:11 , ALA A:12 , GLN A:15 , ASP A:98 , ALA A:99 , ALA A:100 , ASN A:101 , SER A:140 , GLY A:143 , GLY A:144 , THR A:145 , GLY A:146 , VAL A:177 , SER A:178 , GLU A:183 , ASN A:206 , TYR A:224 , ASN A:228 , ILE A:231 , MG A:502 , HOH A:636 , HOH A:641 , HOH A:644 , HOH A:714 , HOH A:730 , HOH A:762 , HOH A:780 , LYS B:254binding site for residue GTP A 501
2AC2SOFTWAREGTP A:501 , HOH A:636 , HOH A:641 , HOH A:644 , HOH A:780binding site for residue MG A 502
3AC3SOFTWAREGLY B:10 , GLN B:11 , CYS B:12 , GLN B:15 , SER B:140 , GLY B:143 , GLY B:144 , THR B:145 , GLY B:146 , VAL B:177 , SER B:178 , GLU B:183 , ASN B:206 , TYR B:224 , ASN B:228 , HOH B:612 , HOH B:618 , HOH B:621 , HOH B:680binding site for residue GDP B 501
4AC4SOFTWARETHR A:179 , ALA A:180 , VAL A:181 , CYS B:241 , LEU B:242 , ALA B:250 , LYS B:254 , LEU B:255 , ASN B:258 , MET B:259 , THR B:314 , VAL B:315 , ALA B:316 , ILE B:318 , ASN B:350 , LYS B:352 , ILE B:378 , HOH B:631 , HOH B:663binding site for residue LOC B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ITZ)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:273 -Pro A:274
2Gly B:246 -Gln B:247
3Ala B:273 -Pro B:274

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ITZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ITZ)

(-) Exons   (0, 0)

(no "Exon" information available for 5ITZ)

(-) 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:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhhhhhhhhhhhhhhh.........hhhhh.eee.....eee.eeeee..hhhhhhhhhh......hhh.eee.......hhhhhhh.hhhhhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh........eeeee.............hhhhhhhhhhhhhhh..........eeeeeeeeee..hhhhhhhhhhhhhhhh............eeeee................eeeeeeeee..hhhhhhhhhhhhhhhhh...hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itz A   1 MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVD 438
                                    10        20        30      ||48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438
                                                               37|                                                                                                                                                                                                                                                                                                                                                                                                        
                                                                46                                                                                                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhee...ee.eeeee..hhhhhhhhh.......hhh.eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh......eeeeeee.......hhhhhhhhhhhhhhh....hhhhh.eeeeeeeee...hhhhhhhhhhhhhhhhhhhh.......eeeeee.........eeeeeeee..hhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5itz B   1 MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNAKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATA 440
                                    10        20        30        40 ||     52  ||    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276||     292       302       312       322       332       342       352       370       380       390       400       410       420       430       440
                                                                    42|        55|                                                                                                                                                                                                                      277|                                                                         360|                                                                       
                                                                     45         60                                                                                                                                                                                                                       284                                                                          369                                                                       


Chain D from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ......hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5itz D 373 QPFLKRGEGLARF 385
                                   382   


Chain F from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itz F  13 DLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLAAIMGHLEIVEVLLKHGADV 139
                                    22        32        42        52        62        72        82        92       102       112       122       132
   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 5ITZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ITZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ITZ)

(-) Gene Ontology  (33, 44)

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
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LOC  [ 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 A:273 - Pro A:274   [ RasMol ]  
    Ala B:273 - Pro B:274   [ RasMol ]  
    Gly B:246 - Gln B:247   [ 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
  5itz
    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
  CENPJ_HUMAN | Q9HC77
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TBA1B_BOVIN | P81947
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TBB2B_BOVIN | Q6B856
    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
  CENPJ_HUMAN | Q9HC77
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TBA1B_BOVIN | P81947
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TBB2B_BOVIN | Q6B856
    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
        CENPJ_HUMAN | Q9HC77: 5eib
        TBA1B_BOVIN | P81947: 3dco 3edl 3iz0 3j1t 3j1u 3j2u 4i4t 4i50 4i55 4ihj 4iij 4o2a 4o2b 4o4h 4o4i 4o4j 4o4l 4tuy 4tv8 4tv9 4uxo 4uxp 4uxr 4uxs 4uxt 4uxy 4uy0 4wbn 4yj2 4yj3 5bmv 5eib 5gon 5hnw 5hnx 5hny 5hnz 5iyz 5j2t 5j2u 5jh7 5jvd 5la6 5lov 5lp6 5lxt 5lyj 5m7e 5m7g 5m8d 5m8g 5njh 5o7a
        TBB2B_BOVIN | Q6B856: 1sa0 1sa1 1tvk 1z2b 2p4n 2wbe 2xrp 3dco 3du7 3e22 3iz0 3j1t 3j1u 3j2u 4aqv 4aqw 4atu 4atx 4ck5 4ck6 4ck7 4i4t 4i50 4i55 4ihj 4iij 4o2a 4o2b 4o4h 4o4i 4o4j 4o4l 4tuy 4tv8 4tv9 4uxo 4uxp 4uxr 4uxs 4uxt 4uxy 4uy0 4wbn 4yj2 4yj3 5eib 5ezy 5gon 5hnw 5hnx 5hny 5hnz 5iyz 5j2t 5j2u 5jh7 5jvd 5la6 5lov 5lp6 5lxt 5lyj 5m5i 5m5l 5m5m 5m5n 5m5o 5m7e 5m7g 5m8d 5m8g 5njh 5o7a

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5ITZ)