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(-) Description

Title :  CALCIUM-SATURATED GCAMP2 MONOMER
 
Authors :  J. Akerboom, J. D. Velez Rivera, L. L. Looger, E. R. Schreiter
Date :  18 Sep 08  (Deposition) - 16 Dec 08  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Geci, Gcamp2, Cpgfp, Calmodulin, M13 Peptide, Chromophore, Luminescence, Photoprotein, 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)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CRO1Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:323 , ASP A:325 , ASP A:327 , THR A:329 , GLU A:334BINDING SITE FOR RESIDUE CA A 452
2AC2SOFTWAREASP A:359 , ASP A:361 , ASN A:363 , THR A:365 , ASP A:367 , GLU A:370BINDING SITE FOR RESIDUE CA A 453
3AC3SOFTWAREASP A:396 , ASP A:398 , ASN A:400 , TYR A:402 , GLU A:407BINDING SITE FOR RESIDUE CA A 454

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EK4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:246 -Pro A:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GFP_AEQVI_001 *F100YGFP_AEQVI  ---  ---AF258Y
2UniProtVAR_GFP_AEQVI_002 *T108SGFP_AEQVI  ---  ---AT266S
3UniProtVAR_GFP_AEQVI_003 *L141MGFP_AEQVI  ---  ---AL299M
4UniProtVAR_GFP_AEQVI_004 *V219IGFP_AEQVI  ---  ---AR393I
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALM1_RAT8-43
44-79
81-116
117-149		  3A:310-345
A:346-381
A:383-414
-
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALM1_RAT21-33
57-69
94-106
130-142		  3A:323-335
A:359-371
A:396-408
-

(-) Exons   (0, 0)

(no "Exon" information available for 3EK4)

(-) Sequences/Alignments

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:349
 aligned with CALM1_RAT | P0DP29 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:349
                                                                                                                                                                                                                                                                         1                                                                                                               
                                     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93       103         
            CALM1_RAT     - ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTN 112
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeeee......eeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee......hhhhhhh..eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.................hhhhhhhhhhhhhhhh.....eehhhhhhhhhhh.....hhhhhhhhhhh........eehhhhhhhhhhhhhh..hhhhhhhhhh..........hhhhhhhhhhh 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:383-414        PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    ------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ek4 A  46 KTGHAVRAIGRLSSLENVYIMADKQKNGIKANFKIRHNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLsVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTN 414
                                    55        65        75        85        95       105       115       125       135       159       169       179       189       199       209       219  |||  231       241       251       261       271       281       291       301||     315       325       335       345       355       365       375       385       395       405         
                                                                                                                            144|                                                            222||                                                                         302|                                                                                                           
                                                                                                                             159                                                             224-CRO                                                                       307                                                                                                           
                                                                                                                                                                                              226                                                                                                                                                                                        


Chain A from PDB  Type:PROTEIN  Length:349
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:351
                                                                                                                                                                                                                                                                                                                                                              214                          
                                                                                                                               1                                                                                                                                            144    145                        172   173                                     213 |     222   223            
                                     -         -         -         -         -         -         -         -         -         1        11        21        31        41        51        61        71        81        91       101       111       121       131       141  |    145       155       165      |  -  |    180       190       200       210  | |  219  |    224       234 
            GFP_AEQVI     - ---------------------------------------------------------------------------------------------------MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYN------YNSHNVYIMADKQKNGIKVNFKIRHNIE-----DGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNE-KRDHMVLLE-----FVTAAGITHGMDE 235
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeeee......eeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee......hhhhhhh..eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeee.......hhhhhh...-.-hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.................hhhhhhhhhhhhhhhh.....eehhhhhhhhhhh.....hhhhhhhhhhh........eehhhhhhhhhhhhhh..hhhhhhhhhh..........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------------------I--------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ek4 A  46 KTGHAVRAIGRLSSLENVYIMADKQKNGIKANFKIRHNIEDGGVQLAYHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTL-s-VQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTN 414
                                    55        65        75        85        95       105       115       125       135       159       169       179       189       199       209       219  | | |229       239       249       259       269       279       289       299  ||   313       323       333       343       353       363       373       383       393       403       413 
                                                                                                                            144|                                                            222 | |                                                                         302|                                                                                                           
                                                                                                                             159                                                              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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3EK4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EK4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EK4)

(-) Gene Ontology  (63, 63)

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.

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  3ek4
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  GFP_AEQVI | P42212
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CALM1_RAT | P0DP29: 1aji 1cm1 1cm4 1deg 1g4y 1k90 1k93 1lvc 1niw 1nkf 1qiv 1qiw 1qx5 1qx7 1sk6 1up5 2hqw 2mgu 2pq3 2ygg 3b32 3bxk 3bxl 3cln 3ek7 3ek8 3ekh 3ekj 3evr 3evu 3evv 3ifk 3sg2 3sg3 3sg4 3sg5 3sg6 3sg7 3sjq 3wlc 3wld 4ehq 4g27 4g28 4i2y 4il1 4j9y 4j9z 4oy4 4qnh 4rjd
        GFP_AEQVI | P42212: 1b9c 1bfp 1c4f 1cv7 1ema 1emb 1emc 1eme 1emf 1emg 1emk 1eml 1emm 1f09 1f0b 1gfl 1h6r 1hcj 1huy 1jby 1jbz 1jc0 1jc1 1kp5 1kyp 1kyr 1kys 1myw 1q4a 1q4b 1q4c 1q4d 1q4e 1q73 1qxt 1qy3 1qyf 1qyo 1qyq 1rm9 1rmm 1rmo 1rmp 1rrx 1s6z 1w7s 1w7t 1w7u 1yfp 1yhg 1yhh 1yhi 1yj2 1yjf 1z1p 1z1q 2ah8 2aha 2awj 2awk 2awl 2awm 2b3p 2b3q 2due 2duf 2dug 2duh 2dui 2emd 2emn 2emo 2fwq 2fzu 2g16 2g2s 2g3d 2g5z 2g6e 2h6v 2h9w 2hcg 2hfc 2hgd 2hgy 2hjo 2hqz 2hrs 2jad 2o24 2o29 2o2b 2okw 2oky 2q57 2q6p 2qrf 2qt2 2qu1 2qz0 2wsn 2wso 2wur 2y0g 2ydz 2ye0 2ye1 2yfp 3cb9 3cbe 3cd1 3cd9 3dpw 3dpx 3dpz 3dq1 3dq2 3dq3 3dq4 3dq5 3dq6 3dq7 3dq8 3dq9 3dqa 3dqc 3dqd 3dqe 3dqf 3dqh 3dqi 3dqj 3dqk 3dql 3dqm 3dqn 3dqo 3dqu 3ed8 3ek7 3ek8 3ekh 3ekj 3evp 3evr 3evu 3evv 3g9a 3gex 3gj1 3gj2 3i19 3k1k 3la1 3o77 3o78 3ogo 3osq 3osr 3p28 3sg2 3sg3 3sg4 3sg5 3sg6 3sg7 3sry 3ss0 3ssh 3ssk 3ssl 3ssp 3sst 3ssv 3ssy 3st0 3sv5 3svb 3svc 3svd 3sve 3u8p 3ufz 3ug0 3v3d 3vht 3w1c 3w1d 3wlc 3wld 3ztf 4anj 4ar7 4as8 4b5y 4bdu 4en1 4eul 4ges 4gf6 4h47 4h48 4ik1 4ik3 4ik4 4ik5 4ik8 4ik9 4j88 4j89 4j8a 4jfg 4jrb 4ka9 4kag 4kex 4kf5 4kw4 4kw8 4kw9 4l12 4l13 4l1i 4lqt 4lqu 4lw5 4n3d 4ndj 4ndk 4ogs 4orn 4p1q 4p7h 4pa0 4pfe 4u2v 4xbi 4xgy 4xl5 4xov 4xow 4xvp 4z4k 4z4m 4zf3 4zf4 4zf5 5aqb 5dpg 5dph 5dpi 5dpj 5dqb 5dqm 5drf 5drg 5dtx 5dty 5dtz 5du0 5ehu 5f9g 5fgu 5fji 5hbd 5hge 5hw9 5hzo 5j2o 5j3n 5ktg 5t3i

(-) Related Entries Specified in the PDB File

3ek7 CALCIUM-SATURATED GCAMP2 DIMER
3ek8 CALCIUM-SATURATED GCAMP2 T116V/G174R MONOMER
3ekh CALCIUM-SATURATED GCAMP2 T116V/K387W MONOMER
3ekj