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(-) Description

Title :  THE STRUCTURE OF THE CATARACT CAUSING P23T MUTANT OF HUMAN GAMMA-D CRYSTALLIN
 
Authors :  J. Jung, I. L. Byeon, Y. Wang, J. King, A. M. Gronenborn
Date :  12 Feb 09  (Deposition) - 28 Jul 09  (Release) - 19 Jun 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Crystallin, Cataract, Protein, Lens, Disease Mutation, Eye Lens Protein, Oxidation, Sensory Transduction, Vision, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Jung, I. J. Byeon, Y. Wang, J. King, A. M. Gronenborn
The Structure Of The Cataract-Causing P23T Mutant Of Human Gammad-Crystallin Exhibits Distinctive Local Conformational And Dynamic Changes.
Biochemistry V. 48 2597 2009
PubMed-ID: 19216553  |  Reference-DOI: 10.1021/BI802292Q

(-) Compounds

Molecule 1 - GAMMA-CRYSTALLIN D
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Variant(DE3)
    Expression System VectorPET16B
    GeneCRYGD, CRYG4
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsROSETTA 2
    SynonymGAMMA-D-CRYSTALLIN, GAMMA-CRYSTALLIN 4

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2KFB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

NMR Structure (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_010733R15CCRGD_HUMANDisease (CTRCT4)121909595AR15C
2UniProtVAR_034955P24SCRGD_HUMANDisease (CTRCT4)28931605AT24S
3UniProtVAR_021145P24TCRGD_HUMANDisease (CTRCT4)28931605AT24T
4UniProtVAR_010734R37SCRGD_HUMANDisease (CTRCT4)121909597AR37S
5UniProtVAR_064829W43RCRGD_HUMANDisease (CTRCT4)  ---AW43R
6UniProtVAR_010735R59HCRGD_HUMANDisease (CTRCT4)121909596AR59H
7UniProtVAR_021146M102VCRGD_HUMANPolymorphism  ---AM102V
8UniProtVAR_034956E107ACRGD_HUMANDisease (CTRCT4)  ---AE107A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_010733R15CCRGD_HUMANDisease (CTRCT4)121909595AR15C
2UniProtVAR_034955P24SCRGD_HUMANDisease (CTRCT4)28931605AT24S
3UniProtVAR_021145P24TCRGD_HUMANDisease (CTRCT4)28931605AT24T
4UniProtVAR_010734R37SCRGD_HUMANDisease (CTRCT4)121909597AR37S
5UniProtVAR_064829W43RCRGD_HUMANDisease (CTRCT4)  ---AW43R
6UniProtVAR_010735R59HCRGD_HUMANDisease (CTRCT4)121909596AR59H
7UniProtVAR_021146M102VCRGD_HUMANPolymorphism  ---AM102V
8UniProtVAR_034956E107ACRGD_HUMANDisease (CTRCT4)  ---AE107A

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

(-) PROSITE Motifs  (1, 4)

NMR Structure (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRYSTALLIN_BETA_GAMMAPS50915 Crystallins beta and gamma 'Greek key' motif profile.CRGD_HUMAN2-40
41-83
88-128
129-171
  4A:2-40
A:41-83
A:88-128
A:129-171
NMR Structure * (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRYSTALLIN_BETA_GAMMAPS50915 Crystallins beta and gamma 'Greek key' motif profile.CRGD_HUMAN2-40
41-83
88-128
129-171
  4A:2-40
A:41-83
A:88-128
A:129-171

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002643761ENSE00001072759chr2:208989225-20898918937CRGD_HUMAN1-331A:1-33
1.2ENST000002643762ENSE00001635690chr2:208989078-208988836243CRGD_HUMAN4-84811A:4-8481
1.3ENST000002643763ENSE00000796728chr2:208986669-208986331339CRGD_HUMAN85-174901A:85-17490

(-) 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:174
 aligned with CRGD_HUMAN | P07320 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
           CRGD_HUMAN     1 MGKITLYEDRGFQGRHYECSSDHPNLQPYLSRCNSARVDSGCWMLYEQPNYSGLQYFLRRGDYADHQQWMGLSDSVRSCRLIPHSGSHRIRLYEREDYRGQMIEFTEDCSCLQDRFRFNEIHSLNVLEGSWVLYELSNYRGRQYLLMPGDYRRYQDWGATNARVGSLRRVIDFS 174
               SCOP domains d2kfba1 A:1-86 automated matches                                                      d2kfba2 A:87-174 automated matches                                                       SCOP domains
               CATH domains 2kfbA01 A:1-84 Crystallins                                                          2kfbA02 A:85-174 Crystallins                                                               CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------Crystall-2kfbA01 A:89-170                                                         ---- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------Crystall-2kfbA02 A:89-170                                                         ---- Pfam domains (2)
         Sec.struct. author ..eeeeeee...eeeeeee...............eeeeee.eeeee........eeee..eee.hhhhhh.......eeeee......eeeeeee...eeeeeee.....hhhhh.......eeeeee..eeee........eeee..eee.hhhhhh.......eeee..... Sec.struct. author
             SAPs(SNPs) (1) --------------C--------S------------S-----R---------------H------------------------------------------V----A------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------T------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE -CRYSTALLIN_BETA_GAMMA  PDB: A:2-40     CRYSTALLIN_BETA_GAMMA  PDB: A:41-83        ----CRYSTALLIN_BETA_GAMMA  PDB: A:88-128     CRYSTALLIN_BETA_GAMMA  PDB: A:129-171      --- PROSITE
               Transcript 1 1.1Exon 1.2  PDB: A:4-84 UniProt: 4-84                                              Exon 1.3  PDB: A:85-174 UniProt: 85-174                                                    Transcript 1
                 2kfb A   1 QGKITLYEDRGFQGRHYECSSDHTNLQPYLSRCNSARVDSGCWMLYEQPNYSGLQYFLRRGDYADHQQWMGLSDSVRSCRLIPHSGSHRIRLYEREDYRGQMIEFTEDCSCLQDRFRFNEIHSLNVLEGSWVLYELSNYRGRQYLLMPGDYRRYQDWGATNARVGSLRRVIDFS 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    

   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)

NMR Structure

(-) CATH Domains  (1, 2)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

NMR Structure

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (CRGD_HUMAN | P07320)
molecular function
    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:0005212    structural constituent of eye lens    The action of a molecule that contributes to the structural integrity of the lens of an eye.
biological process
    GO:0034614    cellular response to reactive oxygen species    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
    GO:0002088    lens development in camera-type eye    The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.
    GO:0070306    lens fiber cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a lens fiber cell, any of the elongated, tightly packed cells that make up the bulk of the mature lens in the camera-type eye. The cytoplasm of a lens fiber cell is devoid of most intracellular organelles including the cell nucleus, and contains primarily crystallins, a group of water-soluble proteins expressed in vary large quantities.
    GO:0050896    response to stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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 Related Entries

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

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        CRGD_HUMAN | P073201h4a 1hk0 1ld0 2g98 2klj 4gr7 4jgf

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