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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GRANCALCIN WITH BOUND CALCIUM

Authors :   J. Jia, Q. Han, N. Borregaard, K. Lollike, M. Cygler

Date :   08 Jun 00 (Deposition) - 27 Sep 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Penta-Ef-Hand Protein, Calcium Binding Protein, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Jia, Q. Han, N. Borregaard, K. Lollike, M. Cygler
Crystal Structure Of Human Grancalcin, A Member Of The Penta-Ef-Hand Protein Family.
J. Mol. Biol. V. 300 1271 2000
PubMed-ID: 10903868 | Reference-DOI: 10.1006/JMBI.2000.3925
(for further references see the PDB file header)

Molecule 1 - GRANCALCIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX2T
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:132 , ASP B:134 , SER B:136 , THR B:138 , GLU B:143	BINDING SITE FOR RESIDUE CA B 999

(no "SS Bond" information available for 1F4O)

(no "Cis Peptide Bond" information available for 1F4O)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_048657	S	80	A	GRAN_HUMAN	Polymorphism	17783344	A/B	S	80	A

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

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	GRAN_HUMAN	64-83 119-154 89-117	6	A:64-83 B:64-83 A:119-154 B:119-154 A:89-117 B:89-117
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	GRAN_HUMAN	132-144	2	A:132-144 B:132-144

(no "Exon" information available for 1F4O)

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 A from PDB  Type:PROTEIN  Length:165
 aligned with GRAN_HUMAN | P28676 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:165
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
           GRAN_HUMAN    53 SVYTYFSAVAGQDGEVDAEELQRCLTQSGINGTYSPFSLETCRIMIAMLDRDHTGKMGFNAFKELWAALNAWKENFMTVDQDGSGTVEHHELRQAIGLMGYRLSPQTLTTIVKRYSKNGRIFFDDYVACCVKLRALTDFFRKRDHLQQGSANFIYDDFLQGTMAI 217
               SCOP domains d1f4oa_ A: Grancalcin                                                                                                                                                 SCOP domains
               CATH domains 1f4oA00 A:53-217 EF-hand                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.....eehhhhhhhhhhhh........hhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------A----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------EF_HAND_2           -----EF_HAND_2  PDB: A:89-117     -EF_HAND_2  PDB: A:119-154           --------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------EF_HAND_1    ------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f4o A  53 SVYTYFSAVAGQDGEVDAEELQRCLTQSGINGTYSPFSLETCRIMIAMLDRDHTGKMGFNAFKELWAALNAWKENFMTVDQDGSGTVEHHELRQAIGLMGYRLSPQTLTTIVKRYSKNGRIFFDDYVACCVKLRALTDFFKKRDHLQQGSADFIYDDFLQGTMAI 217
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

Chain B from PDB  Type:PROTEIN  Length:165
 aligned with GRAN_HUMAN | P28676 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:165
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
           GRAN_HUMAN    53 SVYTYFSAVAGQDGEVDAEELQRCLTQSGINGTYSPFSLETCRIMIAMLDRDHTGKMGFNAFKELWAALNAWKENFMTVDQDGSGTVEHHELRQAIGLMGYRLSPQTLTTIVKRYSKNGRIFFDDYVACCVKLRALTDFFRKRDHLQQGSANFIYDDFLQGTMAI 217
               SCOP domains d1f4ob_ B: Grancalcin                                                                                                                                                 SCOP domains
               CATH domains 1f4oB00 B:53-217 EF-hand                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.....eehhhhhhhhhhhh........hhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------A----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------EF_HAND_2           -----EF_HAND_2  PDB: B:89-117     -EF_HAND_2  PDB: B:119-154           --------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------EF_HAND_1    ------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f4o B  53 SVYTYFSAVAGQDGEVDAEELQRCLTQSGINGTYSPFSLETCRIMIAMLDRDHTGKMGFNAFKELWAALNAWKENFMTVDQDGSGTVEHHELRQAIGLMGYRLSPQTLTTIVKRYSKNGRIFFDDYVACCVKLRALTDFFKKRDHLQQGSADFIYDDFLQGTMAI 217
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Penta-EF-hand proteins (30)

Protein domain: Grancalcin (4)

Human (Homo sapiens) [TaxId: 9606] (4)

1a	d1f4oa_	A:
1b	d1f4ob_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Human (Homo sapiens) (106)

1a	1f4oA00	A:53-217
1b	1f4oB00	B:53-217

(no "Pfam Domain" information available for 1F4O)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GRAN_HUMAN | P28676)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004198	calcium-dependent cysteine-type endopeptidase activity	Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain by a mechanism using a cysteine residue at the enzyme active center, and requiring the presence of calcium.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0061025	membrane fusion	The membrane organization process that joins two lipid bilayers to form a single membrane.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	GRAN_HUMAN \| P28676	:	1f4q 1k94 1k95

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (2, 8)

Exons (0, 0)

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