3SG7 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF GCAMP3-KF(LINKER 1)

Authors :   E. R. Schreiter, J. Akerboom, L. L. Looger

Date :   14 Jun 11 (Deposition) - 20 Jun 12 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Calcium Sensor, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Akerboom, T. W. Chen, T. J. Wardill, L. Tian, J. S. Marvin, S. Mutlu, N. C. Calderon, F. Esposti, B. G. Borghuis, X. R. Sun, A. Gordus, M. B. Orger, R. Portugues, F. Engert, J. J. Macklin, A. Filosa, A. Aggarwal, R. A. Kerr, R. Takagi, S. Kracun, E. Shigetomi, B. S. Khakh H. Baier, L. Lagnado, S. S. Wang, C. I. Bargmann, B. E. Kimmel, V. Jayaraman, K. Svoboda, D. S. Kim, E. R. Schreiter, L. L. Looger
Optimization Of A Gcamp Calcium Indicator For Neural Activity Imaging.
J. Neurosci. V. 32 13819 2012
PubMed-ID: 23035093 | Reference-DOI: 10.1523/JNEUROSCI.2601-12.2012

Molecule 1 - MYOSIN LIGHT CHAIN KINASE, GREEN FLUORESCENT PROTEIN, CALMODULIN-1 CHIMERA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	SEE REMARK 999
	Gene	:	GFP, CALM1, CALM, CAM, CAM1, CAMI
	Mutation	:	YES
	Organism Common	:	CHICKEN, JELLYFISH, RAT
	Organism Scientific	:	GALLUS GALLUS, AEQUOREA VICTORIA, RATTUS NORVEGICUS
	Organism Taxid	:	9031, 6100, 10116

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological 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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:431 , ASP A:433 , ASP A:435 , GLN A:437 , GLU A:442 , HOH A:497	BINDING SITE FOR RESIDUE CA A 451
2	AC2	SOFTWARE	ASP A:322 , ASP A:324 , ASP A:326 , THR A:328 , GLU A:333 , HOH A:522	BINDING SITE FOR RESIDUE CA A 452
3	AC3	SOFTWARE	ASP A:395 , ASP A:397 , ASN A:399 , TYR A:401 , GLU A:406 , HOH A:510	BINDING SITE FOR RESIDUE CA A 453
4	AC4	SOFTWARE	ASP A:358 , ASP A:360 , ASP A:362 , THR A:364 , GLU A:369 , HOH A:493	BINDING SITE FOR RESIDUE CA A 454

(no "SS Bond" information available for 3SG7)

Asymmetric/Biological Unit

No.	Residues
1	Met A:245	-	Pro A:246

Asymmetric/Biological 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	257	Y
2	UniProt	VAR_GFP_AEQVI_002 *	T	108	S	GFP_AEQVI	---	---	A	T	265	S
3	UniProt	VAR_GFP_AEQVI_003 *	L	141	M	GFP_AEQVI	---	---	A	L	298	M
4	UniProt	VAR_GFP_AEQVI_004 *	V	219	I	GFP_AEQVI	---	---	A	R	392	I
	* ID not provided by source

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.	CALM1_RAT	8-43 44-79 81-116 117-149	4	A:309-344 A:345-380 A:382-417 A:418-448
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM1_RAT	21-33 57-69 94-106 130-142	4	A:322-334 A:358-370 A:395-407 A:431-443

(no "Exon" information available for 3SG7)

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:399
 aligned with CALM1_RAT | P0DP29 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:399
                                                                                                                                                                                                                                                                                        1                                                                                                                                                  
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88        98       108       118       128       138         
            CALM1_RAT     - ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT 147
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....eeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.........hhhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....................hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-------S--------------------------------M---------------------------------------------------------------------------------------------I-------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EF_HAND_2  PDB: A:309-344           EF_HAND_2  PDB: A:345-380           -EF_HAND_2  PDB: A:382-417           EF_HAND_2  PDB: A:418-448       PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ----- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sg7 A  37 DSSRRKWNKTGHAVRAIGRLSSKFNVYIKADKQKNGIKANFKIRHNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSVQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDESKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLgVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNTRDQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGDGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT 448
                                    46        56        66        76        86        96       106       116       126       136       146||     167       177       187       197       207       217   ||| 229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439         
                                                                                                                                        147|                                                           221||                                                                                                                                                                                                                               
                                                                                                                                         159                                                            223-CRO                                                                                                                                                                                                                            
                                                                                                                                                                                                         225

Chain A from PDB  Type:PROTEIN  Length:399
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:402
                                                                                                                                                                                                                                                                                                                                                                              214                                                             
                                                                                                                                           1                                                                                                                                                 149        150                   172   173                                     213 |     222   223            238                                
                                     -         -         -         -         -         -         -         -         -         -         - |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149         -|      159       169  |    174       184       194       204        |-|       |-    |  228       238         -         -         -  
            GFP_AEQVI     - ---------------------------------------------------------------------------------------------------------------MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHN----------VYIMADKQKNGIKVNFKIRHNIE-----DGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNE-KRDHMVLLE-----FVTAAGITHGMDELYK--------------------------------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....eeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee........-.hhhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...--.hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....................hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhh......hhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-------S--------------------------------M---------------------------------------------------------------------------------------------I-------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3sg7 A  37 DSSRRKWNKTGHAVRAIGRLSSKFNVYIKADKQKNGIKANFKIRHNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSVQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDE-SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTL--gVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNTRDQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGDGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT 448
                                    46        56        66        76        86        96       106       116       126       136       146| |    166       176       186       196       206       216    |  226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446  
                                                                                                                                        147 |                                                           221  ||                                                                                                                                                                                                                               
                                                                                                                                          159                                                              223-CRO                                                                                                                                                                                                                            
                                                                                                                                                                                                            225

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 3SG7)

(no "CATH Domain" information available for 3SG7)

(no "Pfam Domain" information available for 3SG7)

Asymmetric/Biological 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/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CRO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Met A:245 - Pro A:246	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3sg7
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CALM1_RAT \| P0DP29
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	GFP_AEQVI \| P42212
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q6LDG3_CHICK \| Q6LDG3
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CALM1_RAT \| P0DP29
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	GFP_AEQVI \| P42212
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q6LDG3_CHICK \| Q6LDG3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

3sg2	CRYSTAL STRUCTURE OF GCAMP2-T116V,D381Y
3sg3	CRYSTAL STRUCTURE OF GCAMP3-D380Y
3sg4	CRYSTAL STRUCTURE OF GCAMP3-D380Y, LP(LINKER 2)
3sg5	CRYSTAL STRUCTURE OF DIMERIC GCAMP3-D380Y, QP(LINKER 1), LP(LINKER 2)
3sg6	CRYSTAL STRUCTURE OF DIMERIC GCAMP2-LIA(LINKER 1)

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

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (79, 81)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File