3EK7 - JenaLib

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Title :   CALCIUM-SATURATED GCAMP2 DIMER

Authors :   J. Akerboom, J. D. Velez Rivera, L. L. Looger, E. R. Schreiter

Date :   18 Sep 08 (Deposition) - 16 Dec 08 (Release) - 21 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Geci, Gcamp2, Cpegfp, Calmodulin, M13 Peptide, Methylation, Phosphoprotein, Signaling Protein, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Akerboom, J. D. Rivera, M. M. Guilbe, E. C. Malave, H. H. Hernandez, L. Tian, S. A. Hires, J. S. Marvin, L. L. Looger, E. R. Schreiter
Crystal Structures Of The Gcamp Calcium Sensor Reveal The Mechanism Of Fluorescence Signal Change And Aid Rational Design
J. Biol. Chem. V. 284 6455 2009
PubMed-ID: 19098007 | Reference-DOI: 10.1074/JBC.M807657200
(for further references see the PDB file header)

Molecule 1 - MYOSIN LIGHT CHAIN KINASE, GREEN FLUORESCENT PROTEIN, CALMODULIN CHIMERA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSETA
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	GFP, CALM1, CALM, CAM, CAM1, CAMI
	Organism Common	:	JELLYFISH, RAT
	Organism Scientific	:	ARTIFICIAL GENE, AEQUOREA VICTORIA, RATTUS NORVEGICUS
	Organism Taxid	:	32630, 6100, 10116

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	CRO	1	Mod. Amino Acid	{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CRO	2	Mod. Amino Acid	{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:323 , ASP A:325 , ASP A:327 , THR A:329 , GLU A:334 , HOH A:507	BINDING SITE FOR RESIDUE CA A 452
2	AC2	SOFTWARE	ASP A:359 , ASP A:361 , ASN A:363 , THR A:365 , GLU A:370 , HOH A:518	BINDING SITE FOR RESIDUE CA A 453
3	AC3	SOFTWARE	ASP A:396 , ASP A:398 , ASN A:400 , TYR A:402 , GLU A:407 , HOH A:550	BINDING SITE FOR RESIDUE CA A 454
4	AC4	SOFTWARE	ASP A:432 , ASP A:434 , ASP A:436 , GLN A:438 , GLU A:443 , HOH A:525	BINDING SITE FOR RESIDUE CA A 455

(no "SS Bond" information available for 3EK7)

Asymmetric Unit

No.	Residues
1	Met A:246	-	Pro A:247

Asymmetric Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GFP_AEQVI_001 *	F	100	Y	GFP_AEQVI	---	---	A	F	258	Y
2	UniProt	VAR_GFP_AEQVI_002 *	T	108	S	GFP_AEQVI	---	---	A	T	266	S
3	UniProt	VAR_GFP_AEQVI_003 *	L	141	M	GFP_AEQVI	---	---	A	L	299	M
4	UniProt	VAR_GFP_AEQVI_004 *	V	219	I	GFP_AEQVI	---	---	A	R	393	I
	* ID not provided by source

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

Biological Unit 1 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GFP_AEQVI_001 *	F	100	Y	GFP_AEQVI	---	---	A	F	258	Y
2	UniProt	VAR_GFP_AEQVI_002 *	T	108	S	GFP_AEQVI	---	---	A	T	266	S
3	UniProt	VAR_GFP_AEQVI_003 *	L	141	M	GFP_AEQVI	---	---	A	L	299	M
4	UniProt	VAR_GFP_AEQVI_004 *	V	219	I	GFP_AEQVI	---	---	A	R	393	I
	* ID not provided by source

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

Asymmetric 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.	CALM1_RAT	8-43 44-79 81-116 117-149	4	A:310-345 A:346-381 A:383-418 A:419-449
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM1_RAT	21-33 57-69 94-106 130-142	4	A:323-335 A:359-371 A:396-408 A:432-444

Biological Unit 1 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM1_RAT	8-43 44-79 81-116 117-149	8	A:310-345 A:346-381 A:383-418 A:419-449
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM1_RAT	21-33 57-69 94-106 130-142	8	A:323-335 A:359-371 A:396-408 A:432-444

(no "Exon" information available for 3EK7)

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:390
 aligned with CALM1_RAT | P0DP29 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:390
                                                                                                                                                                                                                                                                               1                                                                                                                                                  
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -   |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147
            CALM1_RAT     - ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT 147
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh...eeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee....hhhhhh....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.................hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------------------I-------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EF_HAND_2  PDB: A:310-345           EF_HAND_2  PDB: A:346-381           -EF_HAND_2  PDB: A:383-418           EF_HAND_2  PDB: A:419-449       PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ----- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ek7 A  39 SSRRKWNKTGHAVRAIGRLSSLENVYIMADKQKNGIKANFKIRHNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLsVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT 449
                                    48        58        68        78        88        98       108       118       128       138     ||163       173       183       193       203       213       224|      235       245       255       265       275       285       295      |309       319       329       339       349       359       369       379       389       399       409       419       429       439       449
                                                                                                                                   144|                                                           222||                                                                         302|                                                                                                                                              
                                                                                                                                    160                                                            224-CRO                                                                       307                                                                                                                                              
                                                                                                                                                                                                    226

Chain A from PDB  Type:PROTEIN  Length:390
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:393
                                                                                                                                                                                                                                                                                                                                                                     214                                                             
                                                                                                                                      1                                                                                                                                            144    145                        172   173                                     213 |     222   223            238                                
                                     -         -         -         -         -         -         -         -         -         -      |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144      |148       158       168   |   173       183       193       203       213 |     222     | 227       237|        -         -         -   
            GFP_AEQVI     - ----------------------------------------------------------------------------------------------------------MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYN------YNSHNVYIMADKQKNGIKVNFKIRHNIE-----DGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNE-KRDHMVLLE-----FVTAAGITHGMDELYK--------------------------------   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh...eeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee....-hhhhhh....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...-.-hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.................hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------------------I-------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ek7 A  39 SSRRKWNKTGHAVRAIGRLSSLENVYIMADKQKNGIKANFKIRHNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITL-SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTL-s-VQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT 449
                                    48        58        68        78        88        98       108       118       128       138     | 162       172       182       192       202       212       222 | |   232       242       252       262       272       282       292       302|      316       326       336       346       356       366       376       386       396       406       416       426       436       446   
                                                                                                                                   144 |                                                           222 | |                                                                         302|                                                                                                                                              
                                                                                                                                     160                                                             224-CRO                                                                        307                                                                                                                                              
                                                                                                                                                                                                       226

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 '\|'

(no "SCOP Domain" information available for 3EK7)

(no "CATH Domain" information available for 3EK7)

(no "Pfam Domain" information available for 3EK7)

Asymmetric Unit(hide GO term definitions)

Chain A (CALM1_RAT | P0DP29)

Chain A (GFP_AEQVI | P42212)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
	GO:0008218	bioluminescence	The production of light by certain enzyme-catalyzed reactions in cells.
	GO:0006091	generation of precursor metabolites and energy	The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Asymmetric Unit
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	Cis Peptide Bonds
		Met A:246 - Pro A:247	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3ek7
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	GFP_AEQVI \| P42212
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3ek4	CALCIUM-SATURATED GCAMP2 MONOMER
3ek8	CALCIUM-SATURATED GCAMP2 T116V/G174R MONOMER
3ekh	CALCIUM-SATURATED GCAMP2 T116V/K387W MONOMER
3ekj

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (63, 63)

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