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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GAMMA-TUBULIN BOUND TO GTPGAMMAS
 
Authors :  H. A. Aldaz, L. M. Rice, T. Stearns, D. A. Agard
Date :  20 Mar 05  (Deposition) - 31 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Aldaz, L. M. Rice, T. Stearns, D. A. Agard
Insights Into Microtubule Nucleation From The Crystal Structure Of Human Gamma-Tubulin.
Nature V. 435 523 2005
PubMed-ID: 15917813  |  Reference-DOI: 10.1038/NATURE03586
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TUBULIN GAMMA-1 CHAIN
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    GeneTUBG1, TUBG
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGAMMA-1 TUBULIN, GAMMA-TUBULIN COMPLEX COMPONENT 1, GCP-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GSP1Ligand/Ion5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGSP A:2466BINDING SITE FOR RESIDUE MG A 475
2AC2SOFTWAREGLY A:11 , GLN A:12 , CYS A:13 , GLN A:16 , ASN A:102 , SER A:140 , GLY A:144 , THR A:145 , GLY A:146 , VAL A:171 , PRO A:173 , GLN A:184 , ASN A:207 , PHE A:225 , ILE A:228 , ASN A:229 , MG A:475BINDING SITE FOR RESIDUE GSP A 2466

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z5V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z5V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070577Y92CTBG1_HUMANDisease (CDCBM4)398123046AY92C
2UniProtVAR_070578T331PTBG1_HUMANDisease (CDCBM4)398123047AT331P
3UniProtVAR_070579L387PTBG1_HUMANDisease (CDCBM4)398123045AL387P
4UniProtVAR_052674M413VTBG1_HUMANPolymorphism13663AM413V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TUBULINPS00227 Tubulin subunits alpha, beta, and gamma signature.TBG1_HUMAN142-148  1A:142-148

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002514131ENSE00001324148chr17:40761694-40761804111TBG1_HUMAN1-17171A:2-1716
1.2ENST000002514132ENSE00001679778chr17:40762126-40762238113TBG1_HUMAN17-54381A:17-54 (gaps)38
1.3ENST000002514133ENSE00001741503chr17:40762441-40762608168TBG1_HUMAN55-110561A:55-110 (gaps)56
1.4ENST000002514134ENSE00001793243chr17:40764093-4076416169TBG1_HUMAN111-133231A:111-13323
1.5ENST000002514135ENSE00001713232chr17:40764445-4076452480TBG1_HUMAN134-160271A:134-16027
1.6ENST000002514136ENSE00001798674chr17:40764965-40765091127TBG1_HUMAN160-202431A:160-202 (gaps)43
1.7ENST000002514137ENSE00001794531chr17:40765665-4076575187TBG1_HUMAN203-231291A:203-23129
1.8ENST000002514138ENSE00001670595chr17:40765867-40766016150TBG1_HUMAN232-281501A:232-28049
1.9ENST000002514139ENSE00001663179chr17:40766278-40766430153TBG1_HUMAN282-332511A:284-332 (gaps)49
1.10ENST0000025141310ENSE00001696623chr17:40766514-40766675162TBG1_HUMAN333-386541A:333-386 (gaps)54
1.11ENST0000025141311ENSE00001305412chr17:40766862-40767247386TBG1_HUMAN387-451651A:387-44054

(-) 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:412
 aligned with TBG1_HUMAN | P23258 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:439
                                    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       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431         
           TBG1_HUMAN     2 PREIITLQLGQCGNQIGFEFWKQLCAEHGISPEGIVEEFATEGTDRKDVFFYQADDEHYIPRAVLLDLEPRVIHSILNSPYAKLYNPENIYLSEHGGGAGNNWASGFSQGEKIHEDIFDIIDREADGSDSLEGFVLCHSIAGGTGSGLGSYLLERLNDRYPKKLVQTYSVFPNQDEMSDVVVQPYNSLLTLKRLTQNADCVVVLDNTALNRIATDRLHIQNPSFSQINQLVSTIMSASTTTLRYPGYMNNDLIGLIASLIPTPRLHFLMTGYTPLTTDQSVASVRKTTVLDVMRRLLQPKNVMVSTGRDRQTNHCYIAILNIIQGEVDPTQVHKSLQRIRERKLANFIPWGPASIQVALSRKSPYLPSAHRVSGLMMANHTSISSLFERTCRQYDKLRKREAFLEQFRKEDMFKDNFDEMDTSREIVQQLIDEYHAATR 440
               SCOP domains d1z5va1 A:2-246 automated matches                                                                                                                                                                                                                    d1z5va2 A:247-440 automated matche   s                                                                                                                                                             SCOP domains
               CATH domains 1z5vA01 A:2-269  [code=3.40.50.1440,        no name defined]                                                                                                                                                                                                                -----------   -------------------------    -------------------------------------------------------    --------------------------------------------------------------------- CATH domains
               Pfam domains --Tubulin-1z5vA01 A:4-227                                                                                                                                                                                                         ------------------------------------Tubulin_C-1z5vA02    A:264-393                                                                                                    ----------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhhh........-------.......eee.....eee.eeeee.hhhhhhhhhh.......hhh.eee.------..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeeee...---....hhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh......eeeeee.......---.....hhhhhhhhhhhhhhh.....----....eeeeeeeee.....hhhhhhhhhhhhh............eeeeee......----..eeeeeeee..hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------C----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P-------------------------------------------------------P-------------------------V--------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------TUBULIN---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1        -------------------------------------Exon 1.3  PDB: A:55-110 (gaps) UniProt: 55-110          Exon 1.4  PDB: A:111-13Exon 1.5  PDB: A:134-160   ------------------------------------------Exon 1.7  PDB: A:203-231     Exon 1.8  PDB: A:232-280 UniProt: 232-281         Exon 1.9  PDB: A:284-332 (gaps) UniProt: 282-332   Exon 1.10  PDB: A:333-386 (gaps) UniProt: 333-386     Exon 1.11  PDB: A:387-440 UniProt: 387-451             Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.2  PDB: A:17-54 (gaps)         ---------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:160-202 (gaps)            ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1z5v A   2 PREIITLQLGQCGNQIGFEFWKQLCAEHGISPEAIV-------TDRKDVFFYQADDEHYIPRAVLLDLEPRVIHSILNSPYAKLYNPENIYLS------GNNWASGFSQGEKIHEDIFDIIDREADGSDSLEGFVLCHSIAGGTGSGLGSYLLERLNDRYPKKLVQTYSVFPNQ---SDVVVQPYNSLLTLKRLTQNADCLVVLDNTALNRIATDRLHIQNPSFSQINQLVSTIMSASTTTLRYPGYMNNDLIGLIASLIPTPRLHFLMTGYTPLTTDQ---SVRKTTVLDVMRRLLQPKNVMVSTG----TNHCYIAILNIIQGEVDPTQVHKSLQRIRERKLANFIPWGPASIQVALSRKSPYL----RVSGLMMANHTSISSLFERTCRQYDKLRKREAFLEQFRKEDMFKDNFDEMDTSREIVQQLIDEYHAATR 440
                                    11        21        31     |   -   |    51        61        71        81        91  |    101       111       121       131       141       151       161       171   |   181       191       201       211       221       231       241       251       261       271        |-  |    291       301      |  - |     321       331       341       351       361     |   -|      381       391       401       411       421       431         
                                                              37      45                                               94    101                                                                       175 179                                                                                                  280 284                     308  313                                                   367  372                                                                    

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TBG1_HUMAN | P23258)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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).
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
biological process
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    GO:0031122    cytoplasmic microtubule organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell.
    GO:0000212    meiotic spindle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a meiotic cell cycle.
    GO:0000226    microtubule cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
    GO:0007020    microtubule nucleation    The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation).
    GO:0007017    microtubule-based process    Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
cellular component
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    GO:0031252    cell leading edge    The area of a motile cell closest to the direction of movement.
    GO:0005814    centriole    A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0036064    ciliary basal body    A membrane-tethered, short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium (also called flagellum) that is similar in structure to a centriole and derives from it. The cilium basal body is the site of assembly and remodelling of the cilium and serves as a nucleation site for axoneme growth. As well as anchoring the cilium, it is thought to provide a selective gateway regulating the entry of ciliary proteins and vesicles by intraflagellar transport.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
    GO:0000794    condensed nuclear chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005881    cytoplasmic microtubule    Any microtubule in the cytoplasm of a cell.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0000930    gamma-tubulin complex    A multiprotein complex composed of gamma-tubulin and other non-tubulin proteins. Gamma-tubulin complexes are localized to microtubule organizing centers, and play an important role in the nucleation of microtubules. The number and complexity of non-tubulin proteins associated with these complexes varies between species.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0000242    pericentriolar material    A network of small fibers that surrounds the centrioles in cells; contains the microtubule nucleating activity of the centrosome.
    GO:0005827    polar microtubule    Any of the spindle microtubules that come from each pole and overlap at the spindle midzone. This interdigitating structure consisting of antiparallel microtubules is responsible for pushing the poles of the spindle apart.
    GO:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.
    GO:0005876    spindle microtubule    Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TBG1_HUMAN | P232581z5w 3cb2

(-) Related Entries Specified in the PDB File

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