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Title :   CRYSTAL STRUCTURE OF DYNEIN LIGHT CHAIN LC8 IN COMPLEX WITH A PEPTIDE DERIVED FROM SWALLOW

Authors :   G. Benison, E. Barbar, P. A. Karplus

Date :   05 Aug 08 (Deposition) - 12 Aug 08 (Release) - 06 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,C
Biol. Unit 1: A,C  (2x)

Keywords :   Protein-Peptide Complex, Transport Protein, Cytoplasm, Dynein, Microtubule, Motor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Benison, P. A. Karplus, E. Barbar
The Interplay Of Ligand Binding And Quaternary Structure In The Diverse Interactions Of Dynein Light Chain Lc8.
J. Mol. Biol. V. 384 954 2008
PubMed-ID: 18948118 | Reference-DOI: 10.1016/J.JMB.2008.09.083
(for further references see the PDB file header)

Molecule 1 - DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET15DA
	Gene	:	CTP, CDLC1, DDLC1, CG6998
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	8 KDA DYNEIN LIGHT CHAIN, CUT UP PROTEIN

Molecule 2 - PROTEIN SWALLOW 16-RESIDUE PEPTIDE
	Chains	:	C
	Engineered	:	YES
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE CAN BE NATURALLY FOUND IN DROSOPHILA MELANOGASTER (FRUIT FLY).
	Synthetic	:	YES

		1	2
Asymmetric Unit	:	A	C
Biological Unit 1 (2x)	:	A	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:14 , GLU A:15 , ARG A:71	BINDING SITE FOR RESIDUE ACT A 91

(no "SS Bond" information available for 3E2B)

Asymmetric Unit

No.	Residues
1	Pro A:52	-	Thr A:53

(no "SAP(SNP)/Variant" information available for 3E2B)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DYNEIN_LIGHT_1	PS01239	Dynein light chain type 1 signature.	DYL1_DROME	55-69	1	A:55-69

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DYNEIN_LIGHT_1	PS01239	Dynein light chain type 1 signature.	DYL1_DROME	55-69	2	A:55-69

(no "Exon" information available for 3E2B)

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:87
 aligned with DYL1_DROME | Q24117 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:87
                                    12        22        32        42        52        62        72        82       
           DYL1_DROME     3 DRKAVIKNADMSEEMQQDAVDCATQALEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETRHFIYFYLGQVAILLFKSG  89
               SCOP domains d3e2ba_ A: Dynein light chain 1 (DLC1)                                                  SCOP domains
               CATH domains 3e2bA00 A:3-89 Protein Inhibitor Of Neuronal Nitric Oxide Synthase;                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeee...eeeeeee..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------DYNEIN_LIGHT_1 -------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3e2b A   3 DRKAVIKNADMSEEMQQDAVDCATQALEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETRHFIYFYLGQVAILLFKSG  89
                                    12        22        32        42        52        62        72        82

Chain C from PDB  Type:PROTEIN  Length:10
 aligned with SWA_DROME | P40688 from UniProtKB/Swiss-Prot  Length:548

    Alignment length:10
                                   296
            SWA_DROME   287 ATSAKATQTD 296
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 3e2b C 287 ATSAKATQTD 296
                                   296

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: DLC (20)

Superfamily: DLC (20)

Family: DLC (20)

Protein domain: Dynein light chain 1 (DLC1) (15)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (9)

d3e2ba_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Protein Inhibitor Of Neuronal Nitric Oxide Synthase (19)

Homologous Superfamily: Protein Inhibitor Of Neuronal Nitric Oxide Synthase; (19)

Fruit fly (Drosophila melanogaster) (11)

3e2bA00

A:3-89

(no "Pfam Domain" information available for 3E2B)

Asymmetric Unit(hide GO term definitions)

Chain A (DYL1_DROME | Q24117)

molecular function
	GO:0042623	ATPase activity, coupled	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane.
	GO:0045505	dynein intermediate chain binding	Interacting selectively and non-covalently with an intermediate chain of the dynein complex.
	GO:0051959	dynein light intermediate chain binding	Interacting selectively and non-covalently with a light intermediate chain of the dynein complex.
	GO:0003774	motor activity	Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0051017	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.
	GO:0006914	autophagy	The cellular catabolic process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0022416	chaeta development	The process whose specific outcome is the progression of a chaeta over time, from its formation to the mature structure. A chaeta is a sensory multicellular cuticular outgrowth of a specifically differentiated cell.
	GO:0008407	chaeta morphogenesis	The process in which the anatomical structures of the chaeta are generated and organized. A chaeta is a sensory multicellular cuticular outgrowth of a specifically differentiated cell.
	GO:0000132	establishment of mitotic spindle orientation	A cell cycle process that sets the alignment of mitotic spindle relative to other cellular structures.
	GO:0007476	imaginal disc-derived wing morphogenesis	The process in which the anatomical structures of the imaginal disc-derived wing are generated and organized. The wing is an appendage modified for flying.
	GO:0034454	microtubule anchoring at centrosome	Any process in which a microtubule is maintained in a specific location in a cell by attachment to a centrosome.
	GO:0007018	microtubule-based movement	A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
	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.
	GO:0022008	neurogenesis	Generation of cells within the nervous system.
	GO:0048477	oogenesis	The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
	GO:1904801	positive regulation of neuron remodeling	Any process that activates or increases the frequency, rate or extent of neuron remodeling.
	GO:0035071	salivary gland cell autophagic cell death	The stage-specific programmed cell death of salivary gland cells during salivary gland histolysis.
	GO:0019233	sensory perception of pain	The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
	GO:0007291	sperm individualization	The resolution of the male germline syncytium or cyst into individual gametes by packaging each spermatid into its own plasma membrane.
	GO:0007290	spermatid nucleus elongation	The change in shape of the spermatid nucleus from a spherical structure to an elongated organelle, during the latter part of spermatid differentiation.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0035220	wing disc development	Progression of the wing disc over time, from its initial formation through to its metamorphosis to form adult structures including the wing hinge, wing blade and pleura.
cellular component
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005868	cytoplasmic dynein complex	Any dynein complex with a homodimeric dynein heavy chain core that catalyzes movement along a microtubule. Cytoplasmic dynein complexes participate in many cytoplasmic transport activities in eukaryotes, such as mRNA localization, intermediate filament transport, nuclear envelope breakdown, apoptosis, transport of centrosomal proteins, mitotic spindle assembly, virus transport, kinetochore functions, and movement of signaling and spindle checkpoint proteins. Some complexes participate in intraflagellar transport. Subunits associated with the dynein heavy chain mediate association between dynein heavy chain and cargoes, and may include light chains and light intermediate chains.
	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:0030286	dynein complex	Any of several large complexes that contain two or three dynein heavy chains and several light chains, and have microtubule motor activity.
	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:0005875	microtubule associated complex	Any multimeric complex connected to a microtubule.

Chain C (SWA_DROME | P40688)

molecular function
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
biological process
	GO:0007015	actin filament 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 actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
	GO:0008595	anterior/posterior axis specification, embryo	The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote.
	GO:0045450	bicoid mRNA localization	Any process in which bicoid mRNA is transported to and maintained within the oocyte as part of the specification of the anterior/posterior axis.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0008298	intracellular mRNA localization	Any process in which mRNA is transported to, or maintained in, a specific location within the cell.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0019094	pole plasm mRNA localization	Any process in which mRNA is transported to, or maintained in, the oocyte pole plasm. An example of this is found in Drosophila melanogaster.
	GO:0007317	regulation of pole plasm oskar mRNA localization	Any process that modulates the frequency, rate or extent of the process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm.
cellular component
	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.

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UniProtKB/Swiss-Prot
	DYL1_DROME \| Q24117	:	1rhw 2p2t 2pg1 3bri 3brl 3dvh 3dvp 3dvt 3fm7 3glw 4qh7 4qh8 5e0l 5e0m
	SWA_DROME \| P40688	:	3brl

2p1k	REPLACES PDB.2P1K

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Ligands, Modified Residues, Ions (1, 1)

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