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(-) Description

Title :  HUMAN DYNEIN LIGHT CHAIN (DYNLL2) IN COMPLEX WITH AN IN VITRO EVOLVED PEPTIDE (AC-SRGTQTE).
 
Authors :  P. Rapali, L. Radnai, D. Suveges, C. Hetenyi, V. Harmat, F. Tolgyesi, W. Y. Wahlgren, G. Katona, L. Nyitray, G. Pal
Date :  07 Sep 10  (Deposition) - 04 May 11  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.31
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,C,E,G  (1x)
Biol. Unit 2:  B (1x),D (1x),F (1x),H (1x)
Biol. Unit 3:  B (1x),D (1x),F (1x),H (1x)
Keywords :  Protein Transport, Dimer Interface (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

(-) Compounds

Molecule 1 - DYNEIN LIGHT CHAIN 2, CYTOPLASMIC
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDYNEIN LIGHT CHAIN LC8-TYPE 2,8 KDA DYNEIN LIGHT CHAIN B
 
Molecule 2 - SAC-ARG-GLY-THR-GLN-THR-GLU
    ChainsE, F, G, H
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)A C E G 
Biological Unit 2 (1x) B (1x) D (1x) F (1x) H (1x)
Biological Unit 3 (1x) B (1x) D (1x) F (1x) H (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SAC4Mod. Amino AcidN-ACETYL-SERINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2SAC2Mod. Amino AcidN-ACETYL-SERINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SAC1Mod. Amino AcidN-ACETYL-SERINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2SAC1Mod. Amino AcidN-ACETYL-SERINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:33 , GLU B:35 , ILE B:38BINDING SITE FOR RESIDUE ACT B1090

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Pro A:52 -Thr A:53
2Pro B:52 -Thr B:53
3Pro C:52 -Thr C:53
4Lys D:5 -Ala D:6
5Pro D:52 -Thr D:53

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DYNEIN_LIGHT_1PS01239 Dynein light chain type 1 signature.DYL2_HUMAN55-69
 
 
 
  4A:55-69
B:55-69
C:55-69
D:55-69
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DYNEIN_LIGHT_1PS01239 Dynein light chain type 1 signature.DYL2_HUMAN55-69
 
 
 
  2A:55-69
-
C:55-69
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DYNEIN_LIGHT_1PS01239 Dynein light chain type 1 signature.DYL2_HUMAN55-69
 
 
 
  2-
B:55-69
-
D:55-69
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DYNEIN_LIGHT_1PS01239 Dynein light chain type 1 signature.DYL2_HUMAN55-69
 
 
 
  2-
B:55-69
-
D:55-69

(-) Exons   (0, 0)

(no "Exon" information available for 2XQQ)

(-) 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: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 --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.....eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------DYNEIN_LIGHT_1 -------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  2xqq A  3 DRKAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG 89
                                    12        22        32        42        52        62        72        82       

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

    Alignment length:89
                                    10        20        30        40        50        60        70        80         
            DYL2_HUMAN    1 MSDRKAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG 89
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeee...eeee.....eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------DYNEIN_LIGHT_1 -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                  2xqq B  1 MSDRKAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG 89
                                    10        20        30        40        50        60        70        80         

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with DYL2_HUMAN | Q96FJ2 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:86
                                    13        23        33        43        53        63        73        83      
            DYL2_HUMAN    4 RKAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG 89
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.....eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------DYNEIN_LIGHT_1 -------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  2xqq C  4 RKAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG 89
                                    13        23        33        43        53        63        73        83      

Chain D from PDB  Type:PROTEIN  Length:85
 aligned with DYL2_HUMAN | Q96FJ2 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:85
                                    14        24        34        44        54        64        74        84     
            DYL2_HUMAN    5 KAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG 89
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Dynein_light-2xqqD01 D:5-89                                                           Pfam domains (1)
           Pfam domains (2) Dynein_light-2xqqD02 D:5-89                                                           Pfam domains (2)
           Pfam domains (3) Dynein_light-2xqqD03 D:5-89                                                           Pfam domains (3)
           Pfam domains (4) Dynein_light-2xqqD04 D:5-89                                                           Pfam domains (4)
         Sec.struct. author ..eeeeeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeee...eeee.....eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------DYNEIN_LIGHT_1 -------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  2xqq D  5 KAVIKNADMSEDMQQDAVDCATQAMEKYNIEKDIAAYIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG 89
                                    14        24        34        44        54        64        74        84     

Chain E from PDB  Type:PROTEIN  Length:7
                                      
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .eeee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                  2xqq E  1 sRGTQTE  7
                            |      
                            1-SAC  

Chain F from PDB  Type:PROTEIN  Length:7
                                      
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .eeee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                  2xqq F  1 sRGTQTE  7
                            |      
                            1-SAC  

Chain G from PDB  Type:PROTEIN  Length:7
                                      
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .eeee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                  2xqq G  1 sRGTQTE  7
                            |      
                            1-SAC  

Chain H from PDB  Type:PROTEIN  Length:7
                                      
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .eeee.. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                  2xqq H  1 sRGTQTE  7
                            |      
                            1-SAC  

   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  (0, 0)

(no "SCOP Domain" information available for 2XQQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DYL2_HUMAN | Q96FJ23p8m 4d07

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2XQQ)