1H4A - JenaLib

Title :   HUMAN GAMMA-D CRYSTALLIN R58H MUTANT STRUCTURE AT 1.15 A RESOLUTION

Authors :   A. K. Basak, C. Slingsby

Date :   25 Feb 03 (Deposition) - 08 May 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.15

Chains :   Asym./Biol. Unit : X

Keywords :   Eye Lens Protein, Crystallin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Basak, O. Bateman, C. Slingsby, A. Pande, N. Asherie, O. Ogun, G. Benedek, J. Pande
High-Resolution X-Ray Crystal Structures Of Human Gammad Crystallin (1. 25A) And The R58H Mutant (1. 15A) Associated With Aculeiform Cataract
J. Mol. Biol. V. 328 1137 2003
PubMed-ID: 12729747 | Reference-DOI: 10.1016/S0022-2836(03)00375-9
(for further references see the PDB file header)

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)

Asymmetric/Biological Unit (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	X	R	14	C
2	UniProt	VAR_034955	P	24	S	CRGD_HUMAN	Disease (CTRCT4)	28931605	X	P	23	S
3	UniProt	VAR_021145	P	24	T	CRGD_HUMAN	Disease (CTRCT4)	28931605	X	P	23	T
4	UniProt	VAR_010734	R	37	S	CRGD_HUMAN	Disease (CTRCT4)	121909597	X	R	36	S
5	UniProt	VAR_064829	W	43	R	CRGD_HUMAN	Disease (CTRCT4)	---	X	W	42	R
6	UniProt	VAR_010735	R	59	H	CRGD_HUMAN	Disease (CTRCT4)	121909596	X	H	58	H
7	UniProt	VAR_021146	M	102	V	CRGD_HUMAN	Polymorphism	---	X	M	102	V
8	UniProt	VAR_034956	E	107	A	CRGD_HUMAN	Disease (CTRCT4)	---	X	E	107	A

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

PROSITE Motifs (1, 4)

Exons (3, 3)

Sequences/Alignments

Asymmetric/Biological 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 X from PDB  Type:PROTEIN  Length:173
 aligned with CRGD_HUMAN | P07320 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:173
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171   
           CRGD_HUMAN     2 GKITLYEDRGFQGRHYECSSDHPNLQPYLSRCNSARVDSGCWMLYEQPNYSGLQYFLRRGDYADHQQWMGLSDSVRSCRLIPHSGSHRIRLYEREDYRGQMIEFTEDCSCLQDRFRFNEIHSLNVLEGSWVLYELSNYRGRQYLLMPGDYRRYQDWGATNARVGSLRRVIDFS 174
               SCOP domains d1h4ax1 X:1-85 gamma-Crystallin                                                      d1h4ax2 X:87-174 gamma-Crystallin                                                        SCOP domains
               CATH domains 1h4aX01 X:1-83 Crystallins                                                         1h4aX02 X:84-174 Crystallins                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhheeeeeee...............eeeeee.eeeeeee...eeeeeee..eee.hhhhhh.......eeeee......eeeeeeehhheeeeeee.....hhhhh.......eeeeee..eeeeee...eeeeeee..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: X:1-39     CRYSTALLIN_BETA_GAMMA  PDB: X:40-82        ----CRYSTALLIN_BETA_GAMMA  PDB: X:88-128     CRYSTALLIN_BETA_GAMMA  PDB: X:129-171      --- PROSITE
               Transcript 1 1.Exon 1.2  PDB: X:3-83 UniProt: 4-84                                              Exon 1.3  PDB: X:84-174 (gaps) UniProt: 85-174                                             Transcript 1
                 1h4a X   1 GKITLYEDRGFQGRHYECSSDHPNLQPYLSRCNSARVDSGCWMLYEQPNYSGLQYFLHRGDYADHQQWMGLSDSVRSCRLIPHSGSHRIRLYEREDYRGQMIEFTEDCSCLQDRFRFNEIHSLNVLEGSWVLYELSNYRGRQYLLMPGDYRRYQDWGATNARVGSLRRVIDFS 174
                                    10        20        30        40        50        60        70        80    ||  91       101       111       121       131       141       151       161       171   
                                                                                                               85|                                                                                       
                                                                                                                87

Legend:		→ Mismatch	(orange background)
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	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 (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain X (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)

Related Entries Specified in the PDB File

1a45	GAMMAF CRYSTALLIN FROM BOVINE LENS
1a5d	GAMMAE CRYSTALLIN FROM RAT LENS
1a7h	GAMMA S CRYSTALLIN C-TERMINAL DOMAIN
1amm	1.2 ANGSTROM STRUCTURE OF GAMMA-B CRYSTALLIN AT 150K
1auw	H91N DELTA 2 CRYSTALLIN FROM DUCK
1bd7	CIRCULARLY PERMUTED BB2 - CRYSTALLIN
1blb	BETA B2 CRYSTALLIN TETRAMER
1dcn	INACTIVE MUTANT H162N OF DELTA 2 CRYSTALLIN WITH BOUND ARGININOSUCCINATE
1dsl	GAMMA B CRYSTALLIN C-TERMINAL DOMAIN
1duf	THE NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUS DILUTE LIQUID CRYSTALLINE PHASE
1e7n	THE N-TERMINAL DOMAIN OF BETA-B2- CRYSTALLIN RESEMBLES THE PUTATIVE ANCESTRAL DIMERIC
1elp	GAMMA-D CRYSTALLIN STRUCTURE AT 1.95 A RESOLUTION
1gam	GAMMA B CRYSTALLIN TRUNCATED C-TERMINAL DOMAIN
1gcs	GAMMA-B CRYSTALLIN (PREVIOUSLY CALLED GAMMA- II CRYSTALLIN) LOW TEMPERATURE (150 K) STRUCTURE
1gip	THE NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUSDILUTE LIQUID CRYSTALLINE PHASE
1ha4	GAMMAS CRYSTALLIN C TERMINAL DOMAIN FROM HOMO SAPIENS
1hdf	EVOLUTION OF THE EYE LENS BETA-GAMMA- CRYSTALLIN DOMAIN FOLD
1hk0	HUMAN GAMMA-D CRYSTALLIN STRUCTURE AT 1.25 A RESOLUTION
1hy0	CRYSTAL STRUCTURE OF WILD TYPE DUCK DELTA 1 CRYSTALLIN (EYELENS PROTEIN)
1hy1	CRYSTAL STRUCTURE OF WILD TYPE DUCK DELTA 2 CRYSTALLIN (EYELENS PROTEIN)
1i0a	CRYSTAL STRUCTURE OF WILD TYPE TURKEY DELTA 1 CRYSTALLIN(EYE LENS PROTEIN)
1i5i	THE C18S MUTANT OF BOVINE (GAMMA-B)- CRYSTALLIN
1ld0	THEORETICAL MODEL OF HUMAN GAMMA D CRYSTALLIN
1ler	THEORETICAL MODEL OF HUMAN GAMMA A CRYSTALLIN
1leu	THEORETICAL MODEL OF HUMAN GAMMA B CRYSTALLIN
1lfe	THEORETICAL MODEL OF HUMAN GAMMA C CRYSTALLIN
1llg	HOMOLOGY MODELLING OF RHO-CRYSTALLIN FROM BULL FROG (RANACATESBEIANA) LENS
1o9j	THE X-RAY CRYSTAL STRUCTURE OF ETA- CRYSTALLIN
4gcr	GAMMA-B CRYSTALLIN (PREVIOUSLY GAMMA-II CRYSTALLIN)

Description