2KFB - JenaLib

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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 8)

NMR Structure (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_010733	R	15	C	CRGD_HUMAN	Disease (CTRCT4)	121909595	A	R	15	C
2	UniProt	VAR_034955	P	24	S	CRGD_HUMAN	Disease (CTRCT4)	28931605	A	T	24	S
3	UniProt	VAR_021145	P	24	T	CRGD_HUMAN	Disease (CTRCT4)	28931605	A	T	24	T
4	UniProt	VAR_010734	R	37	S	CRGD_HUMAN	Disease (CTRCT4)	121909597	A	R	37	S
5	UniProt	VAR_064829	W	43	R	CRGD_HUMAN	Disease (CTRCT4)	---	A	W	43	R
6	UniProt	VAR_010735	R	59	H	CRGD_HUMAN	Disease (CTRCT4)	121909596	A	R	59	H
7	UniProt	VAR_021146	M	102	V	CRGD_HUMAN	Polymorphism	---	A	M	102	V
8	UniProt	VAR_034956	E	107	A	CRGD_HUMAN	Disease (CTRCT4)	---	A	E	107	A

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

NMR Structure * (8, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_010733	R	15	C	CRGD_HUMAN	Disease (CTRCT4)	121909595	A	R	15	C
2	UniProt	VAR_034955	P	24	S	CRGD_HUMAN	Disease (CTRCT4)	28931605	A	T	24	S
3	UniProt	VAR_021145	P	24	T	CRGD_HUMAN	Disease (CTRCT4)	28931605	A	T	24	T
4	UniProt	VAR_010734	R	37	S	CRGD_HUMAN	Disease (CTRCT4)	121909597	A	R	37	S
5	UniProt	VAR_064829	W	43	R	CRGD_HUMAN	Disease (CTRCT4)	---	A	W	43	R
6	UniProt	VAR_010735	R	59	H	CRGD_HUMAN	Disease (CTRCT4)	121909596	A	R	59	H
7	UniProt	VAR_021146	M	102	V	CRGD_HUMAN	Polymorphism	---	A	M	102	V
8	UniProt	VAR_034956	E	107	A	CRGD_HUMAN	Disease (CTRCT4)	---	A	E	107	A

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

PROSITE Motifs (1, 4)

Exons (3, 3)

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)

CATH Domains (1, 2)

Pfam Domains (1, 2)

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.

Visualization

Interactive Views

NMR Structure
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2kfb)

	Sites
(no "Sites" information available for 2kfb)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2kfb)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2kfb
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CRGD_HUMAN \| P07320
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	115700
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CRGD_HUMAN \| P07320
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description