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(-) Description

Title :  X11 PTB DOMAIN-10MER PEPTIDE COMPLEX
 
Authors :  C. -H. Lee, Z. Zhang, J. Kuriyan
Date :  28 Jul 97  (Deposition) - 24 Dec 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Complex (Peptide Binding Module/Peptide), Peptide Binding Module, Ptb Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Zhang, C. H. Lee, V. Mandiyan, J. P. Borg, B. Margolis, J. Schlessinger, J. Kuriyan
Sequence-Specific Recognition Of The Internalization Motif Of The Alzheimer'S Amyloid Precursor Protein By The X11 Ptb Domain.
Embo J. V. 16 6141 1997
PubMed-ID: 9321393  |  Reference-DOI: 10.1093/EMBOJ/16.20.6141
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - X11
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentPTB DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - PEPTIDE
    ChainsC, D

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (1x)A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1AQC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIDPS01179 Phosphotyrosine interaction domain (PID) profile.APBA1_HUMAN457-643  1A:328-488
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIDPS01179 Phosphotyrosine interaction domain (PID) profile.APBA1_HUMAN457-643  1A:328-488
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PIDPS01179 Phosphotyrosine interaction domain (PID) profile.APBA1_HUMAN457-643  1A:328-488

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002653811ENSE00001228144chr9:72287222-72287069154APBA1_HUMAN-00--
1.2ENST000002653812ENSE00001089894chr9:72132195-721309271269APBA1_HUMAN1-4004000--
1.3ENST000002653813ENSE00001089895chr9:72091059-7209096496APBA1_HUMAN401-432320--
1.4ENST000002653814ENSE00001089892chr9:72086611-7208657240APBA1_HUMAN433-446140--
1.5aENST000002653815aENSE00000982740chr9:72082884-72082739146APBA1_HUMAN446-494492A:323-365
B:330-365 (gaps)
43
36
1.6ENST000002653816ENSE00001015445chr9:72073104-7207307233APBA1_HUMAN495-505112A:366-370
B:366-371
5
6
1.7ENST000002653817ENSE00000982741chr9:72072055-7207196987APBA1_HUMAN506-534292A:385-405
B:386-405
21
20
1.8bENST000002653818bENSE00000917481chr9:72071348-72071163186APBA1_HUMAN535-596622A:406-467 (gaps)
B:406-467 (gaps)
62
62
1.9ENST000002653819ENSE00000982742chr9:72067217-72067038180APBA1_HUMAN597-656602A:468-488
B:468-494
21
27
1.10ENST0000026538110ENSE00000982743chr9:72064712-72064500213APBA1_HUMAN657-727710--
1.11ENST0000026538111ENSE00000982744chr9:72056031-72055912120APBA1_HUMAN728-767400--
1.12ENST0000026538112ENSE00000982745chr9:72047592-72047452141APBA1_HUMAN768-814470--
1.13ENST0000026538113ENSE00001228156chr9:72046314-720452041111APBA1_HUMAN815-837230--

(-) 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:130
 aligned with APBA1_HUMAN | Q02410 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:166
                                   461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611      
          APBA1_HUMAN   452 PEDLIDGIIFAANYLGSTQLLSDKTPSKNVRMMQAQEAVSRIKMAQKLAKSRKKAPEGESQPMTEVDLFISTQRIKVLNADTQETMMDHPLRTISYIADIGNIVVLMARRRMPRSNSQENVEASHPSQDGKRQYKMICHVFESEDAQLIAQSIGQAFSVAYQEFLR 617
               SCOP domains d1aqca_ A: X11                                                                                                                                                         SCOP domains
               CATH domains -1aqcA00 A:324-488 Pleckstrin-homology domain (P              H domain)/Phosphotyrosine-binding domain (PTB)                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeeee......hhhhhhhhhhhhhhhhhhhh.--------------..eeeeee...eeeeee.....eeeeeehhheeeeeee..eeeeee...----------------------.eeeeeeee...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PID  PDB: A:328-488 UniProt: 457-643                                                                                                                              PROSITE
               Transcript 1 Exon 1.5a  PDB: A:323-365 UniProt: 446-494 Exon 1.6   Exon 1.7  PDB: A:385-405     Exon 1.8b  PDB: A:406-467 (gaps) UniProt: 535-596             Exon 1.9 [INCOMPLETE] Transcript 1
                 1aqc A 323 mEDLIDGIIFAANYLGSTQLLSDKTPSKNVRmmQAQEAVSRIKmAQKL--------------mTEVDLFILTQRIKVLNADTQETmmDHPLRTISYIADIGNIVVLmARRR----------------------YKmICHVFESEDAQLIAQSIGQAFSVAYQEFLR 488
                            |      332       342       352 ||    362   |   | -         -  |    392       402     ||412       422      |432|        -         -   | | 462       472       482      
                            |                            354-MSE     366-MSE            385-MSE                408-MSE              429-MSE                    456 |                              
                          323-MSE                         355-MSE                                               409-MSE                                          458-MSE                          

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with APBA1_HUMAN | Q02410 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:165
                                   468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618     
          APBA1_HUMAN   459 IIFAANYLGSTQLLSDKTPSKNVRMMQAQEAVSRIKMAQKLAKSRKKAPEGESQPMTEVDLFISTQRIKVLNADTQETMMDHPLRTISYIADIGNIVVLMARRRMPRSNSQENVEASHPSQDGKRQYKMICHVFESEDAQLIAQSIGQAFSVAYQEFLRANGINP 623
               SCOP domains d1aqcb_ B: X11                                                                                                                                                        SCOP domains
               CATH domains 1aqcB00 B:330-       494 Pleckstrin-homolo              gy domain (PH domain)/Phosphotyrosine-binding do                      main (PTB)                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.-------.hhhhhhhhhhhhhhhhhhh.--------------eeeeeee...eeeeee....eeeeeee...eeeeeee..eeeeeee..----------------------..eeeeeee...hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PID  PDB: - UniProt: 457-643                                                                                                                                          PROSITE
               Transcript 1 Exon 1.5a  PDB: B:330-365 (gaps)    Exon 1.6   Exon 1.7  PDB: B:386-405     Exon 1.8b  PDB: B:406-467 (gaps) UniProt: 535-596             Exon 1.9  PDB: B:468-494    Transcript 1
                 1aqc B 330 IIFAANYLGSTQLL-------NVRmmQAQEAVSRIKmAQKLA--------------TEVDLFILTQRIKVLNADTQETmmDHPLRTISYIADIGNIVVLmARRR----------------------YKmICHVFESEDAQLIAQSIGQAFSVAYQEFLRANGINP 494
                                   339   |     - |  || 359      |369 |       -      |389       399       409       419       429   |     -         -      |459       469       479       489     
                                       343     351  ||        366-MSE1            386                   408-MSE              429-MSE                    456 |                                    
                                                  354-MSE                                                409-MSE                                          458-MSE                                
                                                   355-MSE                                                                                                                                       

Chain C from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 1aqc C   3 GYENPTYKFF  12
                                    12

Chain D from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 1aqc D   3 GYENPTYKFF  12
                                    12

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AQC)

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (APBA1_HUMAN | Q02410)
molecular function
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0001540    amyloid-beta binding    Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0008088    axo-dendritic transport    The directed movement of organelles or molecules along microtubules in neuron projections.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0014051    gamma-aminobutyric acid secretion    The regulated release of gamma-aminobutyric acid by a cell or a tissue. The gamma-aminobutyric acid is the principal inhibitory neurotransmitter in the brain but is also found in several extraneural tissues.
    GO:0014047    glutamate secretion    The controlled release of glutamate by a cell. The glutamate is the most abundant excitatory neurotransmitter in the nervous system.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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: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.
    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.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        APBA1_HUMAN | Q024101u37 1u38 1u39 1u3b 1x11 1x45 1y7n

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1AQC)