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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ZINC-BOUND SHANK SAM DOMAIN
 
Authors :  M. K. Baron, J. U. Bowie, S. Faham
Date :  22 Nov 05  (Deposition) - 07 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Post-Synaptic Density, Sam Domain, Shank, Scaffolding Protein, Zinc, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Baron, T. M. Boeckers, B. Vaida, S. Faham, M. Gingery, M. R. Sawaya, D. Salyer, E. D. Gundelfinger, J. U. Bowie
An Architectural Framework That May Lie At The Core Of The Postsynaptic Density.
Science V. 311 531 2006
PubMed-ID: 16439662  |  Reference-DOI: 10.1126/SCIENCE.1118995
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SH3 AND MULTIPLE ANKYRIN REPEAT DOMAINS 3
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET3C
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: SAM DOMAIN
    Gene: SHANK3
    Mutation: YES
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: SHANK3, PROLINE-RICH SYNAPSE ASSOCIATED PROTEIN 2, PROSAP2, SPANK-2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:21 , HIS A:22 , HIS A:54 , CL A:256BINDING SITE FOR RESIDUE ZN A 255
2AC2SOFTWAREGLU B:21 , HIS B:22 , HIS B:54 , CL B:257BINDING SITE FOR RESIDUE ZN B 256
3AC3SOFTWAREGLU C:21 , HIS C:22 , HIS C:54 , CL C:258BINDING SITE FOR RESIDUE ZN C 257
4AC4SOFTWAREHIS A:22 , THR A:50 , ARG A:51 , HIS A:54 , ZN A:255BINDING SITE FOR RESIDUE CL A 256
5AC5SOFTWAREHIS B:22 , THR B:50 , ARG B:51 , HIS B:54 , ZN B:256BINDING SITE FOR RESIDUE CL B 257
6AC6SOFTWAREHIS C:22 , THR C:50 , ARG C:51 , HIS C:54 , ZN C:257BINDING SITE FOR RESIDUE CL C 258

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F44)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F44)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F44)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.SHAN3_RAT1677-1740
 
 		  3A:5-65
B:5-65
C:5-63
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.SHAN3_RAT1677-1740
 
 		  1A:5-65
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.SHAN3_RAT1677-1740
 
 		  1-
B:5-65
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.SHAN3_RAT1677-1740
 
 		  1-
-
C:5-63

(-) Exons   (0, 0)

(no "Exon" information available for 2F44)

(-) 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:65
 aligned with SHAN3_RAT | Q9JLU4 from UniProtKB/Swiss-Prot  Length:1740

    Alignment length:65
                                  1682      1692      1702      1712      1722      1732     
           SHAN3_RAT   1673 PLQLWSKFDVGDWLESIHLGEHRDRFEDHEIEGAHLPALTKEDFVELGVTRVGHRMNIERALRQL 1737
               SCOP domains d2f44a_ A: Sh3 and multiple ankyrin repeat domains 3 (Shank3)     SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SAM_DOMAIN  PDB: A:5-65 UniProt: 1677-1740                    PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                2f44 A    1 MLQLWSKFDVGDWLESIHLGEHRDRFEDHEIEGAHLPALTKEDFVELGVTRVGHRENIERALRQL   65
                                    10        20        30        40        50        60     


Chain B from PDB  Type:PROTEIN  Length:64
 aligned with SHAN3_RAT | Q9JLU4 from UniProtKB/Swiss-Prot  Length:1740

    Alignment length:64
                                  1683      1693      1703      1713      1723      1733    
           SHAN3_RAT   1674 LQLWSKFDVGDWLESIHLGEHRDRFEDHEIEGAHLPALTKEDFVELGVTRVGHRMNIERALRQL 1737
               SCOP domains d2f44b_ B: Sh3 and multiple ankyrin repeat domains 3 (Shank3)    SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SAM_DOMAIN  PDB: B:5-65 UniProt: 1677-1740                    PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                2f44 B    2 LQLWSKFDVGDWLESIHLGEHRDRFEDHEIEGAHLPALTKEDFVELGVTRVGHRENIERALRQL   65
                                    11        21        31        41        51        61    


Chain C from PDB  Type:PROTEIN  Length:62
 aligned with SHAN3_RAT | Q9JLU4 from UniProtKB/Swiss-Prot  Length:1740

    Alignment length:62
                                  1683      1693      1703      1713      1723      1733  
           SHAN3_RAT   1674 LQLWSKFDVGDWLESIHLGEHRDRFEDHEIEGAHLPALTKEDFVELGVTRVGHRMNIERALR 1735
               SCOP domains d2f44c_ C: Sh3 and multiple ankyrin repeat domains 3 (Shank3)  SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SAM_DOMAIN  PDB: C:5-63 UniProt: 1677-1740                  PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                2f44 C    2 LQLWSKFDVGDWLESIHLGEHRDRFEDHEIEGAHLPALTKEDFVELGVTRVGHRENIERALR   63
                                    11        21        31        41        51        61
   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, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F44)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F44)

(-) Gene Ontology  (53, 53)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SHAN3_RAT | Q9JLU4)
molecular function
    GO:0030160    GKAP/Homer scaffold activity    Functions as a physical support bridging the N-methyl-D-aspartate receptor-PSD-95-GKAP complex and the mGluR-Homer complex, which are involved in receptor signaling in synapses.
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0035255    ionotropic glutamate receptor binding    Interacting selectively and non-covalently with an ionotropic glutamate receptor. Ionotropic glutamate receptors bind glutamate and exert an effect through the regulation of ion channels.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    GO:0097110    scaffold protein binding    Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0097113    AMPA glutamate receptor clustering    The glutamate receptor clustering process in which alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptors are localized to distinct domains in the cell membrane.
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0097114    NMDA glutamate receptor clustering    The receptor clustering process in which N-methyl-D-aspartate (NMDA) receptors are localized to distinct domains in the cell membrane.
    GO:0048854    brain morphogenesis    The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0060997    dendritic spine morphogenesis    The process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0097117    guanylate kinase-associated protein clustering    The clustering process in which guanylate kinase-associated proteins (GKAPs) are localized to distinct domains in the cell membrane. GKAP facilitates assembly of the post synaptic density of neurons.
    GO:0007612    learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
    GO:0035641    locomotory exploration behavior    The specific movement from place to place of an organism in response to a novel environment.
    GO:0007613    memory    The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
    GO:0032232    negative regulation of actin filament bundle assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of actin filament bundles.
    GO:0045794    negative regulation of cell volume    Any process that decreases cell volume.
    GO:0050885    neuromuscular process controlling balance    Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors.
    GO:2000969    positive regulation of AMPA receptor activity    Any process that activates or increases the frequency, rate or extent of AMPA selective glutamate receptor activity.
    GO:0060999    positive regulation of dendritic spine development    Any process that increases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
    GO:2000463    positive regulation of excitatory postsynaptic potential    Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
    GO:1900451    positive regulation of glutamate receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of glutamate receptor signaling pathway.
    GO:0048170    positive regulation of long-term neuronal synaptic plasticity    A process that increases long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
    GO:1900273    positive regulation of long-term synaptic potentiation    Any process that activates or increases the frequency, rate or extent of long-term synaptic potentiation.
    GO:0051835    positive regulation of synapse structural plasticity    Any process that activates, maintains or increases the frequency, rate or extent of synaptic structural plasticity.
    GO:0051968    positive regulation of synaptic transmission, glutamatergic    Any process that activates, maintains or increases the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.
    GO:0097107    postsynaptic density assembly    The aggregation, arrangement and bonding together of a set of components to form a postsynaptic density, a region that lies adjacent to the cytoplasmic face of the postsynaptic membrane at excitatory synapse.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:2000822    regulation of behavioral fear response    Any process that modulates the frequency, rate or extent of behavioral fear response.
    GO:0061001    regulation of dendritic spine morphogenesis    Any process that modulates the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:2000821    regulation of grooming behavior    Any process that modulates the frequency, rate or extent of grooming behavior.
    GO:1900452    regulation of long term synaptic depression    Any process that modulates the frequency, rate or extent of long term synaptic depression.
    GO:1900271    regulation of long-term synaptic potentiation    Any process that modulates the frequency, rate or extent of long-term synaptic potentiation.
    GO:0035176    social behavior    Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
    GO:0021773    striatal medium spiny neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a medium spiny neuron residing in the striatum.
    GO:0007416    synapse assembly    The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
    GO:0071625    vocalization behavior    The behavior in which an organism produces sounds by a mechanism involving its respiratory system.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0060170    ciliary membrane    The portion of the plasma membrane surrounding a cilium.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    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:0044309    neuron spine    A small membranous protrusion, often ending in a bulbous head and attached to the neuron by a narrow stalk or neck.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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  2f44
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  SHAN3_RAT | Q9JLU4
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 Related Entries

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

UniProtKB/Swiss-Prot
        SHAN3_RAT | Q9JLU4: 2f3n 5g4x 5o99

(-) Related Entries Specified in the PDB File

2f3n NATIVE SHANK SAM DOMAIN