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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DYNEIN LIGHT CHAIN DNLC2A
 
Authors :  J. -F. Liu, Z. -X. Wang, X. -Q. Wang, Q. Tang, X. -M. An, L. -L. Gui, D. -C. Li
Date :  08 Aug 06  (Deposition) - 14 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Dnlc2A, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. -F. Liu, Z. -X. Wang, X. -Q. Wang, Q. Tang, X. -M. An, L. -L. Gui, D. -C. Liang
Crystal Structure Of Human Dynein Light Chain Dnlc2A: Structural Insights Into The Interaction With Ic74
Biochem. Biophys. Res. Commun. V. 349 1125 2006
PubMed-ID: 16970917  |  Reference-DOI: 10.1016/J.BBRC.2006.08.161

(-) Compounds

Molecule 1 - DYNEIN LIGHT CHAIN 2A, CYTOPLASMIC
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainM15
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDNLC2A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDYNEIN-ASSOCIATED PROTEIN KM23, BITHORAXOID-LIKE PROTEIN, BLP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CS1Ligand/IonCESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CS-1Ligand/IonCESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CS-1Ligand/IonCESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:12 , SER A:13 , GLN A:14 , VAL A:17 , GLN B:12 , SER B:13 , GLN B:14 , VAL B:17BINDING SITE FOR RESIDUE CS B 1042

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HZ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HZ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049124S13RDLRB1_HUMANPolymorphism1063616A/BS13R
2UniProtVAR_049125I71FDLRB1_HUMANPolymorphism10036A/BI71F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049124S13RDLRB1_HUMANPolymorphism1063616A/BS13R
2UniProtVAR_049125I71FDLRB1_HUMANPolymorphism10036A/BI71F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049124S13RDLRB1_HUMANPolymorphism1063616A/BS13R
2UniProtVAR_049125I71FDLRB1_HUMANPolymorphism10036A/BI71F

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HZ5)

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003571561aENSE00001410108chr20:33104214-3310426653DLRB1_HUMAN1-110--
1.2ENST000003571562ENSE00001388289chr20:33114073-3311414876DLRB1_HUMAN2-27262A:5-27
B:8-27
23
20
1.4aENST000003571564aENSE00001384991chr20:33122432-33122599168DLRB1_HUMAN27-83572A:27-82
B:27-83
56
57
1.5ENST000003571565ENSE00001830464chr20:33128385-33128762378DLRB1_HUMAN83-96142A:86-94
B:83-95 (gaps)
9
13

(-) 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 DLRB1_HUMAN | Q9NP97 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:90
                                    14        24        34        44        54        64        74        84        94
           DLRB1_HUMAN    5 EETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNP 94
               SCOP domains d2hz5a_ A: automated matches                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh...eeeeeee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeee.---.eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------R---------------------------------------------------------F----------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:5-27  -------------------------------------------------------Exon 1.5     Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.4a  PDB: A:27-82 UniProt: 27-83 [INCOMPLETE]      ----------- Transcript 1 (2)
                  2hz5 A  5 EETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAP---YFLIVIQNP 94
                                    14        24        34        44        54        64        74       | - |      94
                                                                                                        82  86        

Chain B from PDB  Type:PROTEIN  Length:86
 aligned with DLRB1_HUMAN | Q9NP97 from UniProtKB/Swiss-Prot  Length:96

    Alignment length:88
                                    17        27        37        47        57        67        77        87        
           DLRB1_HUMAN    8 LKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNPT 95
               SCOP domains d2hz5b_ B: automated matches                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...eeeeeee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeee..--.eeeeee... Sec.struct. author
                 SAPs(SNPs) -----R---------------------------------------------------------F------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:8-2-------------------------------------------------------Exon 1.5      Transcript 1 (1)
           Transcript 1 (2) -------------------Exon 1.4a  PDB: B:27-83 UniProt: 27-83                   ------------ Transcript 1 (2)
                  2hz5 B  8 LKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAPD--YFLIVIQNPT 95
                                    17        27        37        47        57        67        77     |  87        
                                                                                                      83 86         

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HZ5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HZ5)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DLRB1_HUMAN | Q9NP97)
molecular function
    GO:0003777    microtubule motor activity    Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
    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: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: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.
    GO:0007632    visual behavior    The behavior of an organism in response to a visual stimulus.
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: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: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.

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        DLRB1_HUMAN | Q9NP971z09 2b95 2e8j

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