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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN FKBP52
 
Authors :  P. Li, Y. Ding, B. Wu, C. Shu, B. Shen, Z. Rao
Date :  16 Oct 02  (Deposition) - 30 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fkbp52, The N-Terminal Domain, Crystal Structure, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Li, Y. Ding, B. Wu, C. Shu, B. Shen, Z. Rao
Structure Of The N-Terminal Domain Of Human Fkbp52.
Acta Crystallogr. , Sect. D V. 59 16 2003
PubMed-ID: 12499534  |  Reference-DOI: 10.1107/S0907444902017523
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FKBP52
    ChainsA, B
    EC Number5.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A(+)
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentTHE N-TERMINAL FRAGMENT (1-140)
    GeneFKBP4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFK506-BINDING PROTEIN 4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1N1A)

(-) Sites  (0, 0)

(no "Site" information available for 1N1A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N1A)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:16 -Pro A:17
2Pro A:119 -Pro A:120
3Pro B:119 -Pro B:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N1A)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FKBP_PPIASEPS50059 FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.FKBP4_HUMAN50-138
 
167-253
  2A:50-138
B:50-138
-

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000000010081ENSE00000802791chr12:2904119-2904410292FKBP4_HUMAN1-35352A:16-35
B:16-35
20
20
1.2ENST000000010082ENSE00000713106chr12:2906304-2906448145FKBP4_HUMAN36-84492A:36-84 (gaps)
B:36-84 (gaps)
49
49
1.3ENST000000010083ENSE00000713108chr12:2906895-2907037143FKBP4_HUMAN84-131482A:84-131
B:84-131
48
48
1.4ENST000000010084ENSE00000713109chr12:2907872-2907992121FKBP4_HUMAN132-172412A:132-140
B:132-140
9
9
1.5ENST000000010085ENSE00000713111chr12:2908254-2908410157FKBP4_HUMAN172-224530--
1.6ENST000000010086ENSE00000713114chr12:2909016-290910691FKBP4_HUMAN224-254310--
1.7ENST000000010087ENSE00000713116chr12:2909205-290928884FKBP4_HUMAN255-282280--
1.8ENST000000010088ENSE00000713118chr12:2909558-2909743186FKBP4_HUMAN283-344620--
1.9ENST000000010089ENSE00000713120chr12:2910283-2910522240FKBP4_HUMAN345-424800--
1.10ENST0000000100810ENSE00000802792chr12:2912317-2913124808FKBP4_HUMAN425-459350--

(-) 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:121
 aligned with FKBP4_HUMAN | Q02790 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:125
                                    25        35        45        55        65        75        85        95       105       115       125       135     
          FKBP4_HUMAN    16 APLPMEGVDISPKQDEGVLKVIKREGTGTEMPMIGDRVFVHYTGWLLDGTKFDSSLDRKDKFSFDLGKGEVIKAWDIAIATMKVGEVCHITCKPEYAYGSAGSPPKIPPNATLVFEVELFEFKGE 140
               SCOP domains d1n1aa_ A: FKBP52, N-terminal domains                                                                                         SCOP domains
               CATH domains 1n1aA00 A:16-140  [code=3.10.50.40, no name defined]                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee........eeeeeee............eeeeeeeeee....eeee..----.eeee......hhhhhhhhh......eeeeee.hhhh...............eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------FKBP_PPIASE  PDB: A:50-138 UniProt: 50-138                                               -- PROSITE
           Transcript 1 (1) Exon 1.1            Exon 1.2  PDB: A:36-84 (gaps) UniProt: 36-84     -----------------------------------------------Exon 1.4  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.3  PDB: A:84-131 UniProt: 84-131         --------- Transcript 1 (2)
                 1n1a A  16 APLPMEGVDISPKQDEGVLKVIKREGTGTEMPMIGDRVFVHYTGWLLDGTKFDSSL----KFSFDLGKGEVIKAWDIAIATMKVGEVCHITCKPEYAYGSAGSPPKIPPNATLVFEVELFEFKGE 140
                                    25        35        45        55        65     |   -|       85        95       105       115       125       135     
                                                                                  71   76                                                                

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with FKBP4_HUMAN | Q02790 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:125
                                    25        35        45        55        65        75        85        95       105       115       125       135     
          FKBP4_HUMAN    16 APLPMEGVDISPKQDEGVLKVIKREGTGTEMPMIGDRVFVHYTGWLLDGTKFDSSLDRKDKFSFDLGKGEVIKAWDIAIATMKVGEVCHITCKPEYAYGSAGSPPKIPPNATLVFEVELFEFKGE 140
               SCOP domains d1n1ab_ B: FKBP52, N-terminal domains                                                                                         SCOP domains
               CATH domains 1n1aB00 B:16-140  [code=3.10.50.40, no name defined]                                                                          CATH domains
           Pfam domains (1) ---------------------------FKBP_C-1n1aB01 B:43-135                                                                      ----- Pfam domains (1)
           Pfam domains (2) ---------------------------FKBP_C-1n1aB02 B:43-135                                                                      ----- Pfam domains (2)
         Sec.struct. author ..hhhhhee........eeeeeee............eeeeeeeeee....eeee..----.eeee......hhhhhhhhh......eeeeee.hhhh...............eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------FKBP_PPIASE  PDB: B:50-138 UniProt: 50-138                                               -- PROSITE
           Transcript 1 (1) Exon 1.1            Exon 1.2  PDB: B:36-84 (gaps) UniProt: 36-84     -----------------------------------------------Exon 1.4  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.3  PDB: B:84-131 UniProt: 84-131         --------- Transcript 1 (2)
                 1n1a B  16 APLPMEGVDISPKQDEGVLKVIKREGTGTEMPMIGDRVFVHYTGWLLDGTKFDSSL----KFSFDLGKGEVIKAWDIAIATMKVGEVCHITCKPEYAYGSAGSPPKIPPNATLVFEVELFEFKGE 140
                                    25        35        45        55        65     |   -|       85        95       105       115       125       135     
                                                                                  71   76                                                                

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (43, 43)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FKBP4_HUMAN | Q02790)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005528    FK506 binding    Interacting selectively and non-covalently with the 23-membered macrolide lactone FK506.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0032767    copper-dependent 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), in the presence of copper.
    GO:0035259    glucocorticoid receptor binding    Interacting selectively and non-covalently with a glucocorticoid receptor.
    GO:0031072    heat shock protein binding    Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    GO:0051219    phosphoprotein binding    Interacting selectively and non-covalently with a phosphorylated protein.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0048156    tau protein binding    Interacting selectively and non-covalently with tau protein. tau is a microtubule-associated protein, implicated in Alzheimer's disease, Down Syndrome and ALS.
biological process
    GO:0030521    androgen receptor signaling pathway    Any series of molecular signals generated as a consequence of an androgen binding to its receptor.
    GO:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
    GO:0006825    copper ion transport    The directed movement of copper (Cu) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007566    embryo implantation    Attachment of the blastocyst to the uterine lining.
    GO:0046661    male sex differentiation    The establishment of the sex of a male organism by physical differentiation.
    GO:0031115    negative regulation of microtubule polymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization.
    GO:0031111    negative regulation of microtubule polymerization or depolymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization or depolymerization.
    GO:0010977    negative regulation of neuron projection development    Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0030850    prostate gland development    The process whose specific outcome is the progression of the prostate gland over time, from its formation to the mature structure. The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
    GO:0031503    protein complex localization    A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
    GO:1900034    regulation of cellular response to heat    Any process that modulates the frequency, rate or extent of cellular response to heat.
    GO:0048608    reproductive structure development    The reproductive developmental process whose specific outcome is the progression of structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures.
    GO:0006463    steroid hormone receptor complex assembly    The aggregation, arrangement and bonding together of a set of components to form a steroid hormone receptor complex, an intracellular receptor that binds steroid hormones. The complex is often a dimer, and forms after the steroid has bound the receptor.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0044295    axonal growth cone    The migrating motile tip of a growing nerve cell axon.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FKBP4_HUMAN | Q027901p5q 1q1c 1qz2 4drj 4lav 4law 4lax 4lay 4tw8

(-) Related Entries Specified in the PDB File

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