1QX2 - JenaLib

Title :   X-RAY STRUCTURE OF CALCIUM-LOADED CALBINDOMODULIN (A CALBINDIN D9K RE-ENGINEERED TO UNDERGO A CONFORMATIONAL OPENING) AT 1.44 A RESOLUTION

Authors :   C. G. Bunick, M. R. Nelson, S. Mangahas, L. S. Mizoue, G. J. Bunick, W. J. C

Date :   04 Sep 03 (Deposition) - 25 May 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.44

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)
Biol. Unit 4: A (1x),B (1x)
Biol. Unit 5: A,B  (1x)

Keywords :   Ef-Hand (Helix-Loop-Helix) Calcium Binding Protein, Four-Helix Domain, Protein Engineering, Calcium-Induced Conformational Response, Calmodulin, Calbindin D9K, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. G. Bunick, M. R. Nelson, S. Mangahas, M. J. Hunter, J. H. Sheehan, L. S. Mizoue, G. J. Bunick, W. J. Chazin
Designing Sequence To Control Protein Function In An Ef-Han Protein
J. Am. Chem. Soc. V. 126 5990 2004
PubMed-ID: 15137763 | Reference-DOI: 10.1021/JA0397456

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	FME	2	Mod. Amino Acid	N-FORMYLMETHIONINE
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	FME	1	Mod. Amino Acid	N-FORMYLMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	FME	1	Mod. Amino Acid	N-FORMYLMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	FME	1	Mod. Amino Acid	N-FORMYLMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	FME	1	Mod. Amino Acid	N-FORMYLMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 5 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	FME	2	Mod. Amino Acid	N-FORMYLMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:54 , ASN A:56 , ASP A:58 , GLU A:60 , GLU A:65 , HOH A:1017	BINDING SITE FOR RESIDUE CA A 1001
2	AC2	SOFTWARE	ASP B:54 , ASN B:56 , ASP B:58 , GLU B:60 , GLU B:65 , HOH B:1016	BINDING SITE FOR RESIDUE CA B 1002
3	AC3	SOFTWARE	GLU A:11 , ASP A:47 , HOH A:1114 , GLU B:5	BINDING SITE FOR RESIDUE ZN B 1003
4	AC4	SOFTWARE	GLU A:5 , GLU B:11 , GLU B:48 , GLU B:51	BINDING SITE FOR RESIDUE ZN B 1004
5	AC5	SOFTWARE	ALA A:14 , GLU A:17 , ASP A:19 , GLN A:22 , GLU A:27 , HOH A:1010	BINDING SITE FOR RESIDUE CA A 1005
6	AC6	SOFTWARE	ALA B:14 , GLY B:18 , ASP B:19 , GLN B:22 , GLU B:27 , HOH B:1010	BINDING SITE FOR RESIDUE CA B 1006

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S100G_BOVIN	45-79	2	A:41-75 B:41-74
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S100G_BOVIN	53-74	2	A:51-68 B:51-68
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S100G_BOVIN	58-70	2	A:54-66 B:54-66

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S100G_BOVIN	45-79	1	A:41-75 -
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S100G_BOVIN	53-74	1	A:51-68 -
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S100G_BOVIN	58-70	1	A:54-66 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S100G_BOVIN	45-79	1	- B:41-74
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S100G_BOVIN	53-74	1	- B:51-68
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S100G_BOVIN	58-70	1	- B:54-66

Biological Unit 3 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S100G_BOVIN	45-79	2	A:41-75 B:41-74
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S100G_BOVIN	53-74	2	A:51-68 B:51-68
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S100G_BOVIN	58-70	2	A:54-66 B:54-66

Biological Unit 4 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S100G_BOVIN	45-79	2	A:41-75 B:41-74
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S100G_BOVIN	53-74	2	A:51-68 B:51-68
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S100G_BOVIN	58-70	2	A:54-66 B:54-66

Biological Unit 5 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	S100G_BOVIN	45-79	2	A:41-75 B:41-74
2	S100_CABP	PS00303	S-100/ICaBP type calcium binding protein signature.	S100G_BOVIN	53-74	2	A:51-68 B:51-68
3	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	S100G_BOVIN	58-70	2	A:54-66 B:54-66

Exons (2, 4)

Sequences/Alignments

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
	(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:76
 aligned with S100G_BOVIN | P02633 from UniProtKB/Swiss-Prot  Length:79

    Alignment length:76
                                    13        23        33        43        53        63        73      
           S100G_BOVIN    4 KKSPEELKGIFEKYAAKEGDPNQLSKEELKLLLQTEFPSLLKGPSTLDELFEELDKNGDGEVSFEEFQVLVKKISQ 79
               SCOP domains d1qx2a_ A: Calbindin D9K                                                     SCOP domains
               CATH domains -1qx2A00 A:1-75 EF-hand                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh.....hhhhhhhhhh.....eehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------EF_HAND_2  PDB: A:41-75             PROSITE (1)
                PROSITE (2) -------------------------------------------------S100_CABP  PDB: A:51-6----- PROSITE (2)
                PROSITE (3) ------------------------------------------------------EF_HAND_1    --------- PROSITE (3)
               Transcript 1 Exon 1.2  PDB: A:0-41 UniProt: 1-45       Exon 1.3  PDB: A:42-75             Transcript 1
                  1qx2 A  0 mKSPEEIKGAFEVFAAKEGDPNQISKEELKLVMQTLGPSLLKGMSTLDEMIEEVDKNGDGEVSFEEFLVMMKKISQ 75
                            |        9        19        29        39        49        59        69      
                            |                                                                           
                            0-FME

Chain B from PDB  Type:PROTEIN  Length:75
 aligned with S100G_BOVIN | P02633 from UniProtKB/Swiss-Prot  Length:79

    Alignment length:75
                                    13        23        33        43        53        63        73     
           S100G_BOVIN    4 KKSPEELKGIFEKYAAKEGDPNQLSKEELKLLLQTEFPSLLKGPSTLDELFEELDKNGDGEVSFEEFQVLVKKIS 78
               SCOP domains d1qx2b_ B: Calbindin D9K                                                    SCOP domains
               CATH domains -1qx2B00 B:1-74 EF-hand                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh........hhhhhhhhhh......eehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------EF_HAND_2  PDB: B:41-74            PROSITE (1)
                PROSITE (2) -------------------------------------------------S100_CABP  PDB: B:51-6---- PROSITE (2)
                PROSITE (3) ------------------------------------------------------EF_HAND_1    -------- PROSITE (3)
               Transcript 1 Exon 1.2  PDB: B:0-41 UniProt: 1-45       Exon 1.3  PDB: B:42-74            Transcript 1
                  1qx2 B  0 mKSPEEIKGAFEVFAAKEGDPNQISKEELKLVMQTLGPSLLKGMSTLDEMIEEVDKNGDGEVSFEEFLVMMKKIS 74
                            |        9        19        29        39        49        59        69     
                            0-FME

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 (0, 0)

Gene Ontology (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain A,B (S100G_BOVIN | P02633)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005499	vitamin D binding	Interacting selectively and non-covalently with vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
cellular component
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0016323	basolateral plasma membrane	The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.

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