2G98 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   HUMAN GAMMA-D-CRYSTALLIN

Authors :   S. Kmoch, J. Brynda, B. Awsav, K. Bezouska, P. Novak, P. Rezacova

Date :   06 Mar 06 (Deposition) - 02 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Crystalline, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kmoch, J. Brynda, B. Awsav, K. Bezouska, P. Novak, P. Rezacova, L. Ondrova, M. Filipec, J. Sedlacek, M. Elleder
Link Between A Novel Human Gamma-D-Crystallin Allele And A Unique Cataract Phenotype Explained By Protein Crystallography.
Hum. Mol. Genet. V. 12 1779 2000
PubMed-ID: 10915766 | Reference-DOI: 10.1093/HMG/9.12.1779

Molecule 1 - GAMMA CRYSTALLIN D
	Chains	:	A, B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GAMMA CRYSTALLIN 4

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2G98)

(no "Site" information available for 2G98)

(no "SS Bond" information available for 2G98)

(no "Cis Peptide Bond" information available for 2G98)

Asymmetric Unit (8, 16)

								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/B	R	14	C
2	UniProt	VAR_034955	P	24	S	CRGD_HUMAN	Disease (CTRCT4)	28931605	A/B	P	23	S
3	UniProt	VAR_021145	P	24	T	CRGD_HUMAN	Disease (CTRCT4)	28931605	A/B	P	23	T
4	UniProt	VAR_010734	R	37	S	CRGD_HUMAN	Disease (CTRCT4)	121909597	A/B	S	36	S
5	UniProt	VAR_064829	W	43	R	CRGD_HUMAN	Disease (CTRCT4)	---	A/B	W	42	R
6	UniProt	VAR_010735	R	59	H	CRGD_HUMAN	Disease (CTRCT4)	121909596	A/B	R	58	H
7	UniProt	VAR_021146	M	102	V	CRGD_HUMAN	Polymorphism	---	A/B	M	101	V
8	UniProt	VAR_034956	E	107	A	CRGD_HUMAN	Disease (CTRCT4)	---	A/B	E	106	A

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

Biological Unit 1 (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	14	C
2	UniProt	VAR_034955	P	24	S	CRGD_HUMAN	Disease (CTRCT4)	28931605	A	P	23	S
3	UniProt	VAR_021145	P	24	T	CRGD_HUMAN	Disease (CTRCT4)	28931605	A	P	23	T
4	UniProt	VAR_010734	R	37	S	CRGD_HUMAN	Disease (CTRCT4)	121909597	A	S	36	S
5	UniProt	VAR_064829	W	43	R	CRGD_HUMAN	Disease (CTRCT4)	---	A	W	42	R
6	UniProt	VAR_010735	R	59	H	CRGD_HUMAN	Disease (CTRCT4)	121909596	A	R	58	H
7	UniProt	VAR_021146	M	102	V	CRGD_HUMAN	Polymorphism	---	A	M	101	V
8	UniProt	VAR_034956	E	107	A	CRGD_HUMAN	Disease (CTRCT4)	---	A	E	106	A

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

Biological Unit 2 (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	B	R	14	C
2	UniProt	VAR_034955	P	24	S	CRGD_HUMAN	Disease (CTRCT4)	28931605	B	P	23	S
3	UniProt	VAR_021145	P	24	T	CRGD_HUMAN	Disease (CTRCT4)	28931605	B	P	23	T
4	UniProt	VAR_010734	R	37	S	CRGD_HUMAN	Disease (CTRCT4)	121909597	B	S	36	S
5	UniProt	VAR_064829	W	43	R	CRGD_HUMAN	Disease (CTRCT4)	---	B	W	42	R
6	UniProt	VAR_010735	R	59	H	CRGD_HUMAN	Disease (CTRCT4)	121909596	B	R	58	H
7	UniProt	VAR_021146	M	102	V	CRGD_HUMAN	Polymorphism	---	B	M	101	V
8	UniProt	VAR_034956	E	107	A	CRGD_HUMAN	Disease (CTRCT4)	---	B	E	106	A

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

Asymmetric Unit (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRYSTALLIN_BETA_GAMMA	PS50915	Crystallins beta and gamma 'Greek key' motif profile.	CRGD_HUMAN	2-40 41-83 88-128 129-171	8	A:1-39 B:1-39 A:40-82 B:40-82 A:87-127 B:87-127 A:128-170 B:128-170

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRYSTALLIN_BETA_GAMMA	PS50915	Crystallins beta and gamma 'Greek key' motif profile.	CRGD_HUMAN	2-40 41-83 88-128 129-171	4	A:1-39 - A:40-82 - A:87-127 - A:128-170 -

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CRYSTALLIN_BETA_GAMMA	PS50915	Crystallins beta and gamma 'Greek key' motif profile.	CRGD_HUMAN	2-40 41-83 88-128 129-171	4	- B:1-39 - B:40-82 - B:87-127 - B:128-170

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000264376	1	ENSE00001072759	chr2:208989225-208989189	37	CRGD_HUMAN	1-3	3	2	A:1-2 B:1-2	2 2
1.2	ENST00000264376	2	ENSE00001635690	chr2:208989078-208988836	243	CRGD_HUMAN	4-84	81	2	A:3-83 B:3-83	81 81
1.3	ENST00000264376	3	ENSE00000796728	chr2:208986669-208986331	339	CRGD_HUMAN	85-174	90	2	A:84-171 B:84-170	88 87

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
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Chain A from PDB  Type:PROTEIN  Length:171
 aligned with CRGD_HUMAN | P07320 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 
           CRGD_HUMAN     2 GKITLYEDRGFQGRHYECSSDHPNLQPYLSRCNSARVDSGCWMLYEQPNYSGLQYFLRRGDYADHQQWMGLSDSVRSCRLIPHSGSHRIRLYEREDYRGQMIEFTEDCSCLQDRFRFNEIHSLNVLEGSWVLYELSNYRGRQYLLMPGDYRRYQDWGATNARVGSLRRVID 172
               SCOP domains d2g98a1 A:1-85 automated matches                                                     d2g98a2 A:86-171 automated matches                                                     SCOP domains
               CATH domains 2g98A01 A:1-83 Crystallins                                                         2g98A02 A:84-171 Crystallins                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhh..eeee...............eeeeeeeeeeee.........eeeeeeee.hhhhhh.......eeee.............................hhhhh...............eeeeee...eeeeeee......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:1-39     CRYSTALLIN_BETA_GAMMA  PDB: A:40-82        ----CRYSTALLIN_BETA_GAMMA  PDB: A:87-127     CRYSTALLIN_BETA_GAMMA  PDB: A:128-170      - PROSITE
               Transcript 1 1.Exon 1.2  PDB: A:3-83 UniProt: 4-84                                              Exon 1.3  PDB: A:84-171 UniProt: 85-174 [INCOMPLETE]                                     Transcript 1
                 2g98 A   1 GKITLYEDRGFQGRHYECSSDHPNLQPYLSRCNSASVDSGCWMLYEQPNYSGLQYFLRRGDYADHQQWMGLSDSVRSCRLIPHSGSHRIRLYEREDYRGQMIEFTEDCSCLQDRFRFNEIHSLNVLEGSWVLYELSNYRGRQYLLMPGDYRRYQDWGATNARVGSLRRVID 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain B from PDB  Type:PROTEIN  Length:170
 aligned with CRGD_HUMAN | P07320 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
           CRGD_HUMAN     2 GKITLYEDRGFQGRHYECSSDHPNLQPYLSRCNSARVDSGCWMLYEQPNYSGLQYFLRRGDYADHQQWMGLSDSVRSCRLIPHSGSHRIRLYEREDYRGQMIEFTEDCSCLQDRFRFNEIHSLNVLEGSWVLYELSNYRGRQYLLMPGDYRRYQDWGATNARVGSLRRVI 171
               SCOP domains d2g98b1 B:1-85 automated matches                                                     d2g98b2 B:86-170 automated matches                                                    SCOP domains
               CATH domains 2g98B01 B:1-83 Crystallins                                                         2g98B02 B:84-170 Crystallins                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhheeeeeee...............eeeeee..eeee.hhhhh...eee...ee.hhhhhh.......eeee.........ee..........ee..........................eeeeee...eeeeeee......hhhhhh............. 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: B:1-39     CRYSTALLIN_BETA_GAMMA  PDB: B:40-82        ----CRYSTALLIN_BETA_GAMMA  PDB: B:87-127     CRYSTALLIN_BETA_GAMMA  PDB: B:128-170       PROSITE
               Transcript 1 1.Exon 1.2  PDB: B:3-83 UniProt: 4-84                                              Exon 1.3  PDB: B:84-170 UniProt: 85-174 [INCOMPLETE]                                    Transcript 1
                 2g98 B   1 GKITLYEDRGFQGRHYECSSDHPNLQPYLSRCNSASVDSGCWMLYEQPNYSGLQYFLRRGDYADHQQWMGLSDSVRSCRLIPHSGSHRIRLYEREDYRGQMIEFTEDCSCLQDRFRFNEIHSLNVLEGSWVLYELSNYRGRQYLLMPGDYRRYQDWGATNARVGSLRRVI 170
                                    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)
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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: gamma-Crystallin-like (65)

Superfamily: gamma-Crystallin-like (65)

Family: Crystallins/Ca-binding development proteins (34)

Protein domain: automated matches (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2g98a1	A:1-85
1b	d2g98a2	A:86-171
1c	d2g98b1	B:1-85
1d	d2g98b2	B:86-170

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Gamma-B Crystallin; domain 1 (45)

Homologous Superfamily: Crystallins (39)

Human (Homo sapiens) (7)

1a	2g98A02	A:84-171
1b	2g98B02	B:84-170
1c	2g98A01	A:1-83
1d	2g98B01	B:1-83

(no "Pfam Domain" information available for 2G98)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	2g98
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	CRGD_HUMAN \| P07320	:	1h4a 1hk0 1ld0 2kfb 2klj 4gr7 4jgf

(no "Related Entries Specified in the PDB File" available for 2G98)

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

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Sequence-Structure Mapping

SAPs(SNPs)/Variants (8, 16)

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Exons (3, 6)

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SCOP Domains (1, 4)

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