3SG5 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DIMERIC GCAMP3-D380Y, QP(LINKER 1), LP(LINKER 2)

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

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
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 12)

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
3	GOL	2	Ligand/Ion	GLYCEROL
4	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

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:472	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:495	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:479	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:494	BINDING SITE FOR RESIDUE CA A 454
5	AC5	SOFTWARE	PRO A:213 , TRP A:214 , HIS A:296 , TYR A:300 , HOH A:466 , HOH A:522	BINDING SITE FOR RESIDUE SO4 A 455
6	AC6	SOFTWARE	LYS A:118 , THR A:307 , GLU A:308	BINDING SITE FOR RESIDUE SO4 A 456
7	AC7	SOFTWARE	LYS A:74 , ARG A:408 , HIS A:409 , SO4 A:458	BINDING SITE FOR RESIDUE SO4 A 457
8	AC8	SOFTWARE	LYS A:65 , LYS A:74 , ASN A:76 , TYR A:94 , ARG A:408 , SO4 A:457 , GOL A:459	BINDING SITE FOR RESIDUE SO4 A 458
9	AC9	SOFTWARE	TYR A:94 , THR A:254 , PHE A:256 , ARG A:408 , ASP A:424 , SO4 A:458	BINDING SITE FOR RESIDUE GOL A 459

(no "SS Bond" information available for 3SG5)

Asymmetric Unit

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

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	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	T	412	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	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	T	412	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:309-344 A:345-375 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

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:309-344 A:345-375 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	8	A:322-334 A:358-370 A:395-407 A:431-443

(no "Exon" information available for 3SG5)

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:388
 aligned with CALM1_RAT | P0DP29 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:394
                                                                                                                                                                                                                                                                                   1                                                                                                                                                  
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143    
            CALM1_RAT     - -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT 147
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh....eeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee......hhhhhh..eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....................hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhh------hhhhhhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhh 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:345-375           -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
                 3sg5 A  38 SSRRKWNKTGHAVRAIGRLSSQPNVYIKADKQKNGIKANFKIRHNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSVQSKLSKDPNEKRDHMVLLEFVTAAGITLSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLgVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNLPDQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGDGTIDFPEFLTMMA------DSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT 448
                                    47        57        67        77        87        97       107       117       127       137     ||162       172       182       192       202       212       223|      234       244       254       264       274       284       294       304       314       324       334       344       354       364       374|      384       394       404       414       424       434       444    
                                                                                                                                   143|                                                           221||                                                                                                                                                   375    382                                                                  
                                                                                                                                    159                                                            223-CRO                                                                                                                                                                                                                            
                                                                                                                                                                                                    225

Chain A from PDB  Type:PROTEIN  Length:388
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:391
                                                                                                                                      1                                                                                                                                                 149        150                   172   173                           203       204     212    213     221        222       232  233  238   
                                     -         -         -         -         -         -         -         -         -         -      |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144    |    -     | 154       164       | -   |   179       189       199   |     -   |   210 |     214      |  -       224       | -  |    | - 
            GFP_AEQVI     - ----------------------------------------------------------------------------------------------------------MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHN----------VYIMADKQKNGIKVNFKIRHNIE-----DGSVQLADHYQQNTPIGDGPVLLPDNHYLST---------QSALSKDPN------EKRDHMVLL----------EFVTAAGITHG----MDELYK---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh....eeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee....-..hhhhhh..eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeee.......hhhhhh...--.hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....................hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh...hhhhhhhhhhhhh......eehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------------------------------------I------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sg5 A  38 SSRRKWNKTGHAVRAIGRLSSQPNVYIKADKQKNGIKANFKIRHNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSVQSKLSKDPNEKRDHMVLLEFVTAAGITL-SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTL--gVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNLPDQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGDGTIDFPEFLTMMADSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT 448
                                    47        57        67        77        87        97       107       117       127       137     | 161       171       181       191       201       211       221  ||   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371   ||  387       397       407       417       427       437       447 
                                                                                                                                   143 |                                                           221  ||                                                                                                                                                   375|                                                                  
                                                                                                                                     159                                                              223-CRO                                                                                                                                                 382                                                                  
                                                                                                                                                                                                       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 3SG5)

(no "CATH Domain" information available for 3SG5)

(no "Pfam Domain" information available for 3SG5)

Asymmetric Unit(hide GO term definitions)

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.

Chain A (CALM1_RAT | P0DP29)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		AC9	[ RasMol ]	+environment [ RasMol ]

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

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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3sg2	CRYSTAL STRUCTURE OF GCAMP2-T116V,D381Y
3sg3	CRYSTAL STRUCTURE OF GCAMP3-D380Y
3sg4	CRYSTAL STRUCTURE OF GCAMP3-D380Y, LP(LINKER 2)
3sg6	CRYSTAL STRUCTURE OF DIMERIC GCAMP2-LIA(LINKER 1)
3sg7	CRYSTAL STRUCTURE OF GCAMP3-KF(LINKER 1)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (9, 9)

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)

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Related Entries

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Related Entries Specified in the PDB File