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(-) Description

Title :  SOLUTION STRUCTURE OF THE N-TERMINAL PAPD-LIKE DOMAIN OF HYDIN PROTEIN FROM HUMAN
 
Authors :  H. Li, T. Tomizawa, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  03 Apr 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Hydin, Papd-Like, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Li, T. Tomizawa, S. Koshiba, S. Watanabe, T. Harada, T. Kigawa, S. Yokoyama
Solution Structure Of The N-Terminal Papd-Like Domain Of Hydin Protein From Human
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYDROCEPHALUS-INDUCING PROTEIN HOMOLOG
    Chains: A
    Engineered: YES
    Expression System Plasmid: P060327-16
    Expression System Vector Type: PLASMID
    Fragment: PAPD-LIKE, UNP RESIDUES 182-296
    Gene: HYDIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2YS4)

(-) Sites  (0, 0)

(no "Site" information available for 2YS4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YS4)

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Arg A:65 -Pro A:66
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Glu A:70 -Pro A:71

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YS4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YS4)

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003935671aENSE00001424414chr16:71264569-71264465105HYDIN_HUMAN-00--
1.2aENST000003935672aENSE00002182352chr16:71220821-71220664158HYDIN_HUMAN1-45450--
1.3ENST000003935673ENSE00001651606chr16:71218893-71218768126HYDIN_HUMAN46-87420--
1.4ENST000003935674ENSE00001660436chr16:71212950-71212831120HYDIN_HUMAN88-127400--
1.5ENST000003935675ENSE00001638010chr16:71209644-71209510135HYDIN_HUMAN128-172451A:1-77
1.6ENST000003935676ENSE00001801312chr16:71196633-71196434200HYDIN_HUMAN173-239671A:8-6558
1.7ENST000003935677ENSE00001631444chr16:71186686-71186562125HYDIN_HUMAN239-281431A:65-10743
1.8ENST000003935678ENSE00001732065chr16:71171255-71171054202HYDIN_HUMAN281-348681A:107-12216
1.9ENST000003935679ENSE00001728099chr16:71163726-71163543184HYDIN_HUMAN348-409620--
1.10ENST0000039356710ENSE00001734156chr16:71149698-71149599100HYDIN_HUMAN410-443340--
1.11ENST0000039356711ENSE00001675420chr16:71127838-71127720119HYDIN_HUMAN443-482400--
1.12ENST0000039356712ENSE00001772928chr16:71122427-71122204224HYDIN_HUMAN483-557750--
1.13ENST0000039356713ENSE00001802008chr16:71113855-7111378868HYDIN_HUMAN557-580240--
1.15ENST0000039356715ENSE00001712559chr16:71103405-71103170236HYDIN_HUMAN580-658790--
1.16aENST0000039356716aENSE00001593787chr16:71101293-71101193101HYDIN_HUMAN659-692340--
1.18ENST0000039356718ENSE00001716764chr16:71098743-71098608136HYDIN_HUMAN692-737460--
1.19ENST0000039356719ENSE00001802215chr16:71096236-71096072165HYDIN_HUMAN738-792550--
1.20ENST0000039356720ENSE00001648371chr16:71094559-71094407153HYDIN_HUMAN793-843510--
1.21ENST0000039356721ENSE00001611924chr16:71065820-71065582239HYDIN_HUMAN844-923800--
1.22aENST0000039356722aENSE00001627183chr16:71061778-71061505274HYDIN_HUMAN923-1014920--
1.23ENST0000039356723ENSE00001725055chr16:71059429-71059286144HYDIN_HUMAN1015-1062480--
1.24ENST0000039356724ENSE00001628409chr16:71054220-71054077144HYDIN_HUMAN1063-1110480--
1.25ENST0000039356725ENSE00001726216chr16:71052345-71052032314HYDIN_HUMAN1111-12151050--
1.26ENST0000039356726ENSE00001801574chr16:71026113-71025973141HYDIN_HUMAN1215-1262480--
1.28ENST0000039356728ENSE00001718838chr16:71025299-71025196104HYDIN_HUMAN1262-1297360--
1.29ENST0000039356729ENSE00001798169chr16:71022387-7102229692HYDIN_HUMAN1297-1327310--
1.30ENST0000039356730ENSE00001728486chr16:71022036-71021827210HYDIN_HUMAN1328-1397700--
1.31ENST0000039356731ENSE00001651369chr16:71019225-71019088138HYDIN_HUMAN1398-1443460--
1.32ENST0000039356732ENSE00001778279chr16:71015471-71015294178HYDIN_HUMAN1444-1503600--
1.33ENST0000039356733ENSE00001776704chr16:71012944-71012817128HYDIN_HUMAN1503-1545430--
1.34ENST0000039356734ENSE00001658163chr16:71009172-71009039134HYDIN_HUMAN1546-1590450--
1.35ENST0000039356735ENSE00001761790chr16:71008573-71008437137HYDIN_HUMAN1590-1636470--
1.36ENST0000039356736ENSE00001602071chr16:71008203-71008076128HYDIN_HUMAN1636-1678430--
1.37ENST0000039356737ENSE00001802516chr16:71007923-71007732192HYDIN_HUMAN1679-1742640--
1.38ENST0000039356738ENSE00001798133chr16:71007395-71007246150HYDIN_HUMAN1743-1792500--
1.39ENST0000039356739ENSE00001650132chr16:71004662-71004423240HYDIN_HUMAN1793-1872800--
1.40ENST0000039356740ENSE00001752615chr16:70998799-70998631169HYDIN_HUMAN1873-1929570--
1.41ENST0000039356741ENSE00001664276chr16:70996041-70995862180HYDIN_HUMAN1929-1989610--
1.42ENST0000039356742ENSE00001754440chr16:70993723-70993550174HYDIN_HUMAN1989-2047590--
1.43ENST0000039356743ENSE00001596174chr16:70989451-70989278174HYDIN_HUMAN2047-2105590--
1.44ENST0000039356744ENSE00001677810chr16:70986538-70986324215HYDIN_HUMAN2105-2176720--
1.45ENST0000039356745ENSE00001612712chr16:70977852-70977715138HYDIN_HUMAN2177-2222460--
1.46ENST0000039356746ENSE00001708730chr16:70975722-70975539184HYDIN_HUMAN2223-2284620--
1.47ENST0000039356747ENSE00001731801chr16:70972658-70972517142HYDIN_HUMAN2284-2331480--
1.48ENST0000039356748ENSE00001713971chr16:70970017-70969855163HYDIN_HUMAN2331-2385550--
1.50ENST0000039356750ENSE00001647778chr16:70955120-70954494627HYDIN_HUMAN2386-25942090--
1.51ENST0000039356751ENSE00001666169chr16:70952332-70952114219HYDIN_HUMAN2595-2667730--
1.52ENST0000039356752ENSE00001671417chr16:70942764-70942556209HYDIN_HUMAN2668-2737700--
1.53ENST0000039356753ENSE00001631729chr16:70942337-70942155183HYDIN_HUMAN2737-2798620--
1.54ENST0000039356754ENSE00001700685chr16:70941394-70941275120HYDIN_HUMAN2798-2838410--
1.55ENST0000039356755ENSE00001626424chr16:70937967-70937808160HYDIN_HUMAN2838-2891540--
1.56ENST0000039356756ENSE00001618694chr16:70937700-70937528173HYDIN_HUMAN2892-2949580--
1.57ENST0000039356757ENSE00001717295chr16:70935105-70934907199HYDIN_HUMAN2949-3015670--
1.58ENST0000039356758ENSE00001679064chr16:70929983-70929884100HYDIN_HUMAN3016-3049340--
1.59ENST0000039356759ENSE00001601749chr16:70928451-70928352100HYDIN_HUMAN3049-3082340--
1.60ENST0000039356760ENSE00001759763chr16:70926432-70926264169HYDIN_HUMAN3082-3138570--
1.61ENST0000039356761ENSE00001710477chr16:70925787-70925549239HYDIN_HUMAN3139-3218800--
1.62ENST0000039356762ENSE00001693090chr16:70923607-70923490118HYDIN_HUMAN3218-3257400--
1.63ENST0000039356763ENSE00001662106chr16:70918027-70917823205HYDIN_HUMAN3258-3326690--
1.64ENST0000039356764ENSE00001723887chr16:70916798-70916563236HYDIN_HUMAN3326-3404790--
1.65ENST0000039356765ENSE00001714394chr16:70913659-70913508152HYDIN_HUMAN3405-3455510--
1.66ENST0000039356766ENSE00001608400chr16:70913389-70913200190HYDIN_HUMAN3455-3518640--
1.67ENST0000039356767ENSE00001597666chr16:70908822-70908720103HYDIN_HUMAN3519-3553350--
1.68ENST0000039356768ENSE00001634608chr16:70908495-70908208288HYDIN_HUMAN3553-3649970--
1.69ENST0000039356769ENSE00001629130chr16:70906082-70905940143HYDIN_HUMAN3649-3696480--
1.70ENST0000039356770ENSE00001645065chr16:70902691-70902473219HYDIN_HUMAN3697-3769730--
1.71ENST0000039356771ENSE00001684009chr16:70900232-70900072161HYDIN_HUMAN3770-3823540--
1.72ENST0000039356772ENSE00001780376chr16:70897085-7089698898HYDIN_HUMAN3823-3856340--
1.73ENST0000039356773ENSE00001697576chr16:70896158-70895951208HYDIN_HUMAN3856-3925700--
1.74ENST0000039356774ENSE00001762282chr16:70894804-70894592213HYDIN_HUMAN3925-3996720--
1.75ENST0000039356775ENSE00001639910chr16:70894109-70893971139HYDIN_HUMAN3996-4042470--
1.76ENST0000039356776ENSE00001604884chr16:70891773-70891608166HYDIN_HUMAN4043-4098560--
1.77ENST0000039356777ENSE00001637593chr16:70889178-70889031148HYDIN_HUMAN4098-4147500--
1.78ENST0000039356778ENSE00001767953chr16:70884558-70884351208HYDIN_HUMAN4147-4216700--
1.79ENST0000039356779ENSE00001772664chr16:70883850-70883629222HYDIN_HUMAN4217-4290740--
1.80ENST0000039356780ENSE00001734034chr16:70874136-70873967170HYDIN_HUMAN4291-4347570--
1.81ENST0000039356781ENSE00001723532chr16:70871791-70871593199HYDIN_HUMAN4347-4413670--
1.82ENST0000039356782ENSE00001647566chr16:70869737-70869579159HYDIN_HUMAN4414-4466530--
1.83ENST0000039356783ENSE00001708586chr16:70868067-70867790278HYDIN_HUMAN4467-4559930--
1.84ENST0000039356784ENSE00001593919chr16:70866970-70866751220HYDIN_HUMAN4559-4632740--
1.85ENST0000039356785ENSE00001664237chr16:70863733-70863521213HYDIN_HUMAN4633-4703710--
1.86ENST0000039356786ENSE00001637123chr16:70862332-70862169164HYDIN_HUMAN4704-4758550--
1.87ENST0000039356787ENSE00001695705chr16:70861314-70861164151HYDIN_HUMAN4758-4808510--
1.88ENST0000039356788ENSE00001768927chr16:70852475-70852245231HYDIN_HUMAN4809-4885770--
1.90ENST0000039356790ENSE00001032206chr16:70843910-70843686225HYDIN_HUMAN4886-4960750--
1.91ENST0000039356791ENSE00001313157chr16:70841965-70841292674HYDIN_HUMAN4961-51201600--

(-) Sequences/Alignments

NMR Structure
   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:122
 aligned with HYDIN_HUMAN | Q4G0P3 from UniProtKB/Swiss-Prot  Length:5121

    Alignment length:146
                                   160       170       180       190       200       210       220       230       240       250       260       270       280       290      
          HYDIN_HUMAN   151 GHKVAPGVPSIFRILFTPEENKDYAHTLTCVTEREKFIVPIKARGARAILDFPDKLNFSTCPVKYSTQKILLVRNIGNKNAVFHIKTCRPFSIEPAIGTLNVGESMQLEVEFEPQSVGDHSGRLIVCYDTGEKVFVSLYGAAIDMN 296
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......------------------------.......................eee...ee....eeeeeeee......eeeeee....eeee..eeee....eeeeeeee........eeeeeeee....eeeeeee..ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:1-7  Exon 1.6  PDB: A:8-65 UniProt: 173-239 [INCOMPLETE]                -----------------------------------------Exon 1.8         Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.7  PDB: A:65-107 UniProt: 239-281   --------------- Transcript 1 (2)
                 2ys4 A   1 GSSGSSG------------------------TEREKFIVPIKARGARAILDFPDKLNFSTCPVKYSTQKILLVRNIGNKNAVFHIKTCRPFSIEPAIGTLNVGESMQLEVEFEPQSVGDHSGRLIVCYDTGEKVFVSLYGAAIDMN 122
                                  |  -         -         - |      16        26        36        46        56        66        76        86        96       106       116      
                                  7                        8
   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 2YS4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YS4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YS4)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (HYDIN_HUMAN | Q4G0P3)
biological process
    GO:1904158    axonemal central apparatus assembly    The aggregation, arrangement and bonding together of a set of components to form an axonemal central apparatus.
    GO:0003341    cilium movement    The directed, self-propelled movement of a cilium.
    GO:0002064    epithelial cell development    The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface.
    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:0060438    trachea development    The process whose specific outcome is the progression of a trachea over time, from its formation to the mature structure. The trachea is the portion of the airway that attaches to the bronchi as it branches.
    GO:0021591    ventricular system development    The process whose specific outcome is the progression of the brain ventricular system over time, from its formation to the mature structure. The brain ventricular system consists of four communicating cavities within the brain that are continuous with the central canal of the spinal cord. These cavities include two lateral ventricles, the third ventricle and the fourth ventricle. Cerebrospinal fluid fills the ventricles and is produced by the choroid plexus.
cellular component
    GO:1990718    axonemal central pair projection    Part of the 9+2 axoneme, that occurs in most motile cilia, consisting of the projections off of the central pair of single microtubules.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005929    cilium    A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.

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    Arg A:65 - Pro A:66   [ RasMol ]  
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  2ys4
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 Related Entries

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

UniProtKB/Swiss-Prot
        HYDIN_HUMAN | Q4G0P3: 2e6j

(-) Related Entries Specified in the PDB File

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