3P8M - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   HUMAN DYNEIN LIGHT CHAIN (DYNLL2) IN COMPLEX WITH AN IN VITRO EVOLVED PEPTIDE DIMERIZED BY LEUCINE ZIPPER

Authors :   P. Rapali, L. Radnai, D. Suveges, C. Hetenyi, V. Harmat, F. Tolgyesi, W. Y. Wahlgren, G. Katona, L. Nyitray, G. Pal

Date :   14 Oct 10 (Deposition) - 31 Aug 11 (Release) - 31 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Phage Display, Leucine Zipper, Hub Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Rapali, L. Radnai, D. Suveges, V. Harmat, F. Tolgyesi, W. Y. Wahlgren, G. Katona, L. Nyitray, G. Pal
Directed Evolution Reveals The Binding Motif Preference Of The Lc8/Dynll Hub Protein And Predicts Large Numbers Of Novel Binders In The Human Proteome.
Plos One V. 6 18818 2011
PubMed-ID: 21533121 | Reference-DOI: 10.1371/JOURNAL.PONE.0018818

Molecule 1 - DYNEIN LIGHT CHAIN 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21(DE3)STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DYNLL2, DLC2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	8 KDA DYNEIN LIGHT CHAIN B, DLC8B, DYNEIN LIGHT CHAIN LC8- TYPE 2

Molecule 2 - GENERAL CONTROL PROTEIN GCN4
	Chains	:	D, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MODIFIED PET
	Expression System Strain	:	BL21(DE3)STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GCN4, AAS3, ARG9, YEL009C
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3P8M)

(no "Site" information available for 3P8M)

(no "SS Bond" information available for 3P8M)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:52	-	Thr A:53
2	Pro B:52	-	Thr B:53
3	Gly C:140	-	Gly C:141

(no "SAP(SNP)/Variant" information available for 3P8M)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DYNEIN_LIGHT_1	PS01239	Dynein light chain type 1 signature.	DYL2_HUMAN	55-69	2	A:55-69 B:55-69
2	BZIP	PS50217	Basic-leucine zipper (bZIP) domain profile.	GCN4_YEAST	231-276	2	C:134-170 D:134-170
3	BZIP_BASIC	PS00036	Basic-leucine zipper (bZIP) domain signature.	GCN4_YEAST	231-245	2	C:134-142 D:134-142

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YEL009C	1	YEL009C.1	V:139763-138918	846	GCN4_YEAST	1-281	281	2	C:131-172 (gaps) D:130-172 (gaps)	50 51

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:87
 aligned with DYL2_HUMAN | Q96FJ2 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:87
                                    12        22        32        42        52        62        72        82       
           DYL2_HUMAN     3 DRKAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG  89
               SCOP domains d3p8ma_ A: automated matches                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------DYNEIN_LIGHT_1 -------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3p8m A   3 DRKAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG  89
                                    12        22        32        42        52        62        72        82

Chain B from PDB  Type:PROTEIN  Length:87
 aligned with DYL2_HUMAN | Q96FJ2 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:87
                                    12        22        32        42        52        62        72        82       
           DYL2_HUMAN     3 DRKAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG  89
               SCOP domains d3p8mb_ B: automated matches                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------DYNEIN_LIGHT_1 -------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 3p8m B   3 DRKAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG  89
                                    12        22        32        42        52        62        72        82

Chain C from PDB  Type:PROTEIN  Length:42
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:50
                                   238       248       258       268       278
           GCN4_YEAST   229 ALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLV 278
               SCOP domains -------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....--h------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --BZIP_BASIC     --------------------------------- PROSITE (1)
                PROSITE (2) --BZIP  PDB: C:134-170 UniProt: 231-276         -- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: C:131-172 (gaps) UniProt: 1-281     Transcript 1
                 3p8m C 131 SVSRGTQTEGG--S------GMKQLEDKVEELLSKNYHLENEVARLKKLV 172
                                   140|  |     -|      152       162       172
                                    141  |    143                             
                                       142

Chain D from PDB  Type:PROTEIN  Length:43
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:51
                                   237       247       257       267       277 
           GCN4_YEAST   228 AALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKLV 278
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....--.------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---BZIP_BASIC     --------------------------------- PROSITE (1)
                PROSITE (2) ---BZIP  PDB: D:134-170 UniProt: 231-276         -- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: D:130-172 (gaps) UniProt: 1-281      Transcript 1
                 3p8m D 130 GSVSRGTQTEGG--S------GMKQLEDKVEELLSKNYHLENEVARLKKLV 172
                                   139 |  |    - |     151       161       171 
                                     141  |    143                             
                                        142

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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

Fold: DLC (20)

Superfamily: DLC (20)

Family: DLC (20)

Protein domain: automated matches (4)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d3p8ma_	A:
1b	d3p8mb_	B:

(no "CATH Domain" information available for 3P8M)

(no "Pfam Domain" information available for 3P8M)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DYL2_HUMAN | Q96FJ2)

molecular function
	GO:0008092	cytoskeletal protein binding	Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
	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).
biological process
	GO:0006888	ER to Golgi vesicle-mediated transport	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
	GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	GO:0016236	macroautophagy	The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
	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:1900740	positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway.
	GO:0008039	synaptic target recognition	The process in which a neuronal cell in a multicellular organism interprets signals produced by potential target cells, with which it may form synapses.
	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:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0097542	ciliary tip	Part of the cilium where the axoneme ends. The ciliary tip has been implicated in ciliary assembly and disassembly, as well as signal transduction.
	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: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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.
	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:0016459	myosin complex	A protein complex, formed of one or more myosin heavy chains plus associated light chains and other proteins, that functions as a molecular motor; uses the energy of ATP hydrolysis to move actin filaments or to move vesicles or other cargo on fixed actin filaments; has magnesium-ATPase activity and binds actin. Myosin classes are distinguished based on sequence features of the motor, or head, domain, but also have distinct tail regions that are believed to bind specific cargoes.
	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: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.

Chain C,D (GCN4_YEAST | P03069)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0001135	transcription factor activity, RNA polymerase II transcription factor recruiting	The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II.
	GO:0001084	transcription factor activity, TFIID-class binding	Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0001190	transcriptional activator activity, RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
	GO:0001191	transcriptional repressor activity, RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0010691	negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels	Any process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0001080	nitrogen catabolite activation of transcription from RNA polymerase II promoter	A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
	GO:0045899	positive regulation of RNA polymerase II transcriptional preinitiation complex assembly	Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
	GO:1903833	positive regulation of cellular response to amino acid starvation	Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.
	GO:0060261	positive regulation of transcription initiation from RNA polymerase II promoter	Any process that increases the rate, frequency or extent of a process involved in starting transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	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:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3p8m)

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(no "Sites" information available for 3p8m)

	Cis Peptide Bonds
		Gly C:140 - Gly C:141	[ RasMol ]
		Pro A:52 - Thr A:53	[ RasMol ]
		Pro B:52 - Thr B:53	[ RasMol ]

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	3p8m
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