General Information

Database accession: MF2110004

Name: Coiled-coil trigger site of the rod domain of cortexillin I

PDB ID: 1d7m PDB

Experimental method: X-ray (2.70 Å)

Assembly: homodimer

Source organism: Dictyostelium discoideum

Primer publication of the structure:

Burkhard P, Kammerer RA, Steinmetz MO, Bourenkov GP, Aebi U
The coiled-coil trigger site of the rod domain of cortexillin I unveils a distinct network of interhelical and intrahelical salt bridges.
(2000) Structure 8: 223-30

PMID: 10745004 PubMed

Abstract:

CONCLUSIONS: The knowledge gained from the structure could be used in the de novo design of alpha-helical coiled coils for applications such as two-stage drug targeting and delivery systems, and in the design of coiled coils as templates for combinatorial helical libraries in drug discovery and as synthetic carrier molecules.
RESULTS: The X-ray crystal structure of the 18-heptad-repeat alpha-helical coiled-coil domain of the actin-bundling protein cortexillin I from Dictyostelium discoideum is a tightly packed parallel two-stranded alpha-helical coiled coil. It harbors a distinct 14-residue sequence motif that is essential for coiled-coil formation, and is a prerequisite for the assembly of cortexillin I. The atomic structure reveals novel types of ionic coiled-coil interactions. In particular, the structure shows that a characteristic interhelical and intrahelical salt-bridge pattern, in combination with the hydrophobic interactions occurring at the dimer interface, is the key structural feature of its coiled-coil trigger site.
BACKGROUND: The parallel two-stranded alpha-helical coiled coil is the most frequently encountered subunit-oligomerization motif in proteins. The simplicity and regularity of this motif have made it an attractive system to explore some of the fundamental principles of protein folding and stability and to test the principles of de novo design.

Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

protein homodimerization activity Interacting selectively and non-covalently with an identical protein to form a homodimer. GeneOntology

actin filament binding Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits. GeneOntology

Biological process:

cortical actin cytoskeleton organization A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of actin-based cytoskeletal structures in the cell cortex, i.e. just beneath the plasma membrane. GeneOntology

epithelial cell morphogenesis The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state. GeneOntology

sexual reproduction A reproduction process that creates a new organism by combining the genetic material of two organisms. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two different individuals (parents) join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny. GeneOntology

cellular protein localization Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell. GeneOntology

chemotaxis to cAMP The directed movement of a motile cell or organism in response to the presence of 3',5'-cAMP. GeneOntology

macropinocytosis An endocytosis process that results in the uptake of liquid material by cells from their external environment by the 'ruffling' of the cell membrane to form heterogeneously sized intracellular vesicles called macropinosomes, which can be up to 5 micrometers in size. GeneOntology

actin filament bundle assembly The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness. GeneOntology

sorocarp stalk morphogenesis The process in which the sorocarp stalk is generated and organized. The sorocarp stalk is a tubular structure that consists of cellulose-covered cells stacked on top of each other and surrounded by an acellular stalk tube composed of cellulose and glycoprotein. An example of this process is found in Dictyostelium discoideum. GeneOntology

positive regulation of gene expression Any process that increases 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 (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. GeneOntology

actomyosin contractile ring contraction The process of an actomyosin ring getting smaller in diameter, in the context of cytokinesis that takes place as part of a cell cycle. GeneOntology

regulation of myosin II filament assembly Any process that modulates the frequency, rate or extent of the formation of a bipolar filament composed of myosin II molecules. GeneOntology

positive regulation of cytoskeleton organization Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures. GeneOntology

establishment of protein localization The directed movement of a protein to a specific location. GeneOntology

regulation of GTPase activity Any process that modulates the rate of GTP hydrolysis by a GTPase. GeneOntology

cleavage furrow formation Generation of the cleavage furrow, a shallow groove in the cell surface near the old metaphase plate that marks the site of cytokinesis. This process includes the recruitment and localized activation of signals such as RhoA at the site of the future furrow to ensure that furrowing initiates at the correct site in the cell. GeneOntology

aggregation involved in sorocarp development The process whose specific outcome is the progression of the aggregate over time, from its formation to the point when a slug is formed. Aggregate development begins in response to starvation and continues by the chemoattractant-mediated movement of cells toward each other. The aggregate is a multicellular structure that gives rise to the slug. GeneOntology

positive regulation of protein phosphorylation Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein. GeneOntology

mitotic cytokinesis A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells. GeneOntology

response to bacterium Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium. GeneOntology

actin filament network formation The assembly of a network of actin filaments; actin filaments on different axes and with differing orientations are crosslinked together to form a mesh of filaments. GeneOntology

Cellular component:

basal cortex The region that lies just beneath the plasma membrane on the basal edge of a cell. GeneOntology

lateral part of motile cell The area of a motile cell perpendicular to the direction of movement. GeneOntology

cytosol The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GeneOntology

cell trailing edge The area of a motile cell opposite to the direction of movement. GeneOntology

actomyosin contractile ring A cytoskeletal structure composed of actin filaments and myosin that forms beneath the plasma membrane of many cells, including animal cells and yeast cells, in a plane perpendicular to the axis of the spindle, i.e. the cell division plane. Ring contraction is associated with centripetal growth of the membrane that divides the cytoplasm of the two daughter cells. In animal cells, the contractile ring is located inside the plasma membrane at the location of the cleavage furrow. In budding fungal cells, e.g. mitotic S. cerevisiae cells, the contractile ring forms beneath the plasma membrane at the mother-bud neck before mitosis. GeneOntology

cell leading edge The area of a motile cell closest to the direction of movement. GeneOntology

extracellular space That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. GeneOntology

plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GeneOntology

phagocytic vesicle A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis. GeneOntology

cleavage furrow In animal cells, the first sign of cleavage, or cytokinesis, is the appearance of a shallow groove in the cell surface near the old metaphase plate. A contractile ring containing actin and myosin is located just inside the plasma membrane at the location of the furrow. Ring contraction is associated with centripetal growth of the membrane that deepens the cleavage furrow and divides the cytoplasm of the two daughter cells. While the term 'cleavage furrow' was initially associated with animal cells, such a structure occurs in many other types of cells, including unicellular protists. GeneOntology

Structure Summary Structural annotations of the participating protein chains.

Entry contents: 2 distinct polypeptide molecules

Chains: A, B

Notes: No modifications of the original PDB file. Chain identifiers are identical with the PDB's identifiers.

Number of unique protein segments: 1

Chain A

Name: Cortexillin-1

Source organism: Dictyostelium discoideum

Length: 101 residues

Sequence:Sequence according to PDB SEQRESEMANRLAGLENSLESEKVSREQLIKQKDQLNSLLASLESEGAEREKRLRELEAKLDETLKNLELEKLARMELEARLAKTEKDRAILELKLAEAIDEKSKLE

UniProtKB AC: Q54HG2 (positions: 243-343) UniProt Coverage: 22.7%

UniRef90 AC: UniRef90_Q54HG2 (positions: 243-343) UniRef90

Chain B

Name: Cortexillin-1

Source organism: Dictyostelium discoideum

Length: 101 residues

Sequence:Sequence according to PDB SEQRESEMANRLAGLENSLESEKVSREQLIKQKDQLNSLLASLESEGAEREKRLRELEAKLDETLKNLELEKLARMELEARLAKTEKDRAILELKLAEAIDEKSKLE

UniProtKB AC: Q54HG2 (positions: 243-343) UniProt Coverage: 22.7%

UniRef90 AC: UniRef90_Q54HG2 (positions: 243-343) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Complex evidence:

The subunits in the structure are bound via coiled coil interactions (PMID: 10745004). Coiled coils are highly versatile folding units (PMID: 11166216), where the formation of the structure and the interaction between subunits is almost ubiquitously linked. This cooperative nature of binding and folding that results in a two-step process has been demonstrated for coiled coils with varying oligomeric state from dimers (PMID: 9811815) and trimers (PMID: 10933510) up to heptamers (PMID: 17030805). While the interaction and folding are linked, in certain cases there can be significant residual structure before association (PMID: 8401212). However, these residual structural elements usually encompass 1-2 turns of helices that serve as a 'nucleation site' driving interaction and helix formation (zipping up) (PMID: 17438295), thus even in these cases monomeric coiled coil subunits cannot be considered to have a stable structure.

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

No related structure was found in the Protein Data Bank.

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