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(-) Description

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

(-) Compounds

Molecule 1 - MYOSIN LIGHT CHAIN KINASE, GREEN FLUORESCENT PROTEIN, CALMODULIN-1 CHIMERA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentSEE REMARK 999
    GeneGFP, CALM1, CALM, CAM, CAM1, CAMI
    MutationYES
    Organism CommonCHICKEN, JELLYFISH, RAT
    Organism ScientificGALLUS GALLUS, AEQUOREA VICTORIA, RATTUS NORVEGICUS
    Organism Taxid9031, 6100, 10116

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1CA4Ligand/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
3GOL1Ligand/IonGLYCEROL
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CRO2Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3GOL2Ligand/IonGLYCEROL
4SO48Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:431 , ASP A:433 , ASP A:435 , GLN A:437 , GLU A:442 , HOH A:472BINDING SITE FOR RESIDUE CA A 451
2AC2SOFTWAREASP A:322 , ASP A:324 , ASP A:326 , THR A:328 , GLU A:333 , HOH A:495BINDING SITE FOR RESIDUE CA A 452
3AC3SOFTWAREASP A:395 , ASP A:397 , ASN A:399 , TYR A:401 , GLU A:406 , HOH A:479BINDING SITE FOR RESIDUE CA A 453
4AC4SOFTWAREASP A:358 , ASP A:360 , ASP A:362 , THR A:364 , GLU A:369 , HOH A:494BINDING SITE FOR RESIDUE CA A 454
5AC5SOFTWAREPRO A:213 , TRP A:214 , HIS A:296 , TYR A:300 , HOH A:466 , HOH A:522BINDING SITE FOR RESIDUE SO4 A 455
6AC6SOFTWARELYS A:118 , THR A:307 , GLU A:308BINDING SITE FOR RESIDUE SO4 A 456
7AC7SOFTWARELYS A:74 , ARG A:408 , HIS A:409 , SO4 A:458BINDING SITE FOR RESIDUE SO4 A 457
8AC8SOFTWARELYS A:65 , LYS A:74 , ASN A:76 , TYR A:94 , ARG A:408 , SO4 A:457 , GOL A:459BINDING SITE FOR RESIDUE SO4 A 458
9AC9SOFTWARETYR A:94 , THR A:254 , PHE A:256 , ARG A:408 , ASP A:424 , SO4 A:458BINDING SITE FOR RESIDUE GOL A 459

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GFP_AEQVI_001 *F100YGFP_AEQVI  ---  ---AF257Y
2UniProtVAR_GFP_AEQVI_002 *T108SGFP_AEQVI  ---  ---AT265S
3UniProtVAR_GFP_AEQVI_003 *L141MGFP_AEQVI  ---  ---AL298M
4UniProtVAR_GFP_AEQVI_004 *V219IGFP_AEQVI  ---  ---AT412I
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GFP_AEQVI_001 *F100YGFP_AEQVI  ---  ---AF257Y
2UniProtVAR_GFP_AEQVI_002 *T108SGFP_AEQVI  ---  ---AT265S
3UniProtVAR_GFP_AEQVI_003 *L141MGFP_AEQVI  ---  ---AL298M
4UniProtVAR_GFP_AEQVI_004 *V219IGFP_AEQVI  ---  ---AT412I
   * ID not provided by source

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

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALM1_RAT8-43
44-79
81-116
117-149
  4A:309-344
A:345-375
A:382-417
A:418-448
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALM1_RAT21-33
57-69
94-106
130-142
  4A:322-334
A:358-370
A:395-407
A:431-443
Biological Unit 1 (2, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CALM1_RAT8-43
44-79
81-116
117-149
  8A:309-344
A:345-375
A:382-417
A:418-448
2EF_HAND_1PS00018 EF-hand calcium-binding domain.CALM1_RAT21-33
57-69
94-106
130-142
  8A:322-334
A:358-370
A:395-407
A:431-443

(-) Exons   (0, 0)

(no "Exon" information available for 3SG5)

(-) 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: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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (79, 81)

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)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CALM1_RAT | P0DP291aji 1cm1 1cm4 1deg 1g4y 1k90 1k93 1lvc 1niw 1nkf 1qiv 1qiw 1qx5 1qx7 1sk6 1up5 2hqw 2mgu 2pq3 2ygg 3b32 3bxk 3bxl 3cln 3ek4 3ek7 3ek8 3ekh 3ekj 3evr 3evu 3evv 3ifk 3sg2 3sg3 3sg4 3sg6 3sg7 3sjq 3wlc 3wld 4ehq 4g27 4g28 4i2y 4il1 4j9y 4j9z 4oy4 4qnh 4rjd
        GFP_AEQVI | P422121b9c 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 3ek4 3ek7 3ek8 3ekh 3ekj 3evp 3evr 3evu 3evv 3g9a 3gex 3gj1 3gj2 3i19 3k1k 3la1 3o77 3o78 3ogo 3osq 3osr 3p28 3sg2 3sg3 3sg4 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
        Q6LDG3_CHICK | Q6LDG34oy4
UniProtKB/TrEMBL
        Q6LDG3_CHICK | Q6LDG33sg2 3sg3 3sg4 3sg6 3sg7 3wlc 3wld 4i2y

(-) Related Entries Specified in the PDB File

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)