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(-) Description

Title :  CRYSTAL STRUCTURE OF ACTIVE CONFORMATION OF GPCR OPSIN STABILIZED BY OCTYLGLUCOSIDE
 
Authors :  J. H. Park, T. Morizumi, Y. Li, J. E. Hong, E. F. Pai, K. P. Hofmann, H. W. Ch O. P. Ernst
Date :  07 Feb 13  (Deposition) - 30 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  G-Protein Coupled Receptor, Photoreceptor Protein, Receptor Retinal Protein, Transducer, Transmembrane, Glycoprotein, Lipoprotein, Sensory Transduction, Signaling Protein, Galpha Subunit, Gtp- Binding, Myristate, Nucleotide-Binding, Retinal Binding, Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Park, T. Morizumi, Y. Li, J. E. Hong, E. F. Pai, K. P. Hofmann, H. W. Choe, O. P. Ernst
Opsin, A Structural Model For Olfactory Receptors?
Angew. Chem. Int. Ed. Engl. V. 52 11021 2013
PubMed-ID: 24038729  |  Reference-DOI: 10.1002/ANIE.201302374

(-) Compounds

Molecule 1 - RHODOPSIN
    Chains: A
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Strain: BOVINE
 
Molecule 2 - GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-1
    Chains: B
    Engineered: YES
    Fragment: C-TERMINAL DERIVED PEPTIDE, UNP RESIDUES 340-350
    Mutation: YES
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Other Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED WITH K341L AND C347V MUTATION
    Synonym: TRANSDUCIN ALPHA-1 CHAIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 13)

Asymmetric/Biological Unit (8, 13)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BMA1Ligand/IonBETA-D-MANNOSE
3BOG4Ligand/IonB-OCTYLGLUCOSIDE
4MAN1Ligand/IonALPHA-D-MANNOSE
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
6PLM1Ligand/IonPALMITIC ACID
7SO42Ligand/IonSULFATE ION
8TRE1Ligand/IonTREHALOSE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:118 , CYS A:187 , GLY A:188 , ILE A:189 , MET A:207 , TYR A:268 , ALA A:295BINDING SITE FOR RESIDUE BOG A 405
02AC2SOFTWARELYS A:231 , GLU A:247 , THR A:251BINDING SITE FOR RESIDUE BOG A 406
03AC3SOFTWAREPRO A:27 , TYR A:29 , TRP A:35 , TYR A:96 , HIS A:100BINDING SITE FOR RESIDUE BOG A 407
04AC4SOFTWARETYR A:136 , PRO A:142 , PHE A:221 , GLN A:225BINDING SITE FOR RESIDUE BOG A 408
05AC5SOFTWAREARG A:252 , THR A:297 , VAL A:300 , TYR A:301 , LEU A:321 , CYS A:322 , CYS A:323BINDING SITE FOR RESIDUE PLM A 409
06AC6SOFTWAREGLY A:284 , PRO A:285 , ILE A:286 , PHE A:287BINDING SITE FOR RESIDUE SO4 A 410
07AC7SOFTWAREPHE A:273BINDING SITE FOR RESIDUE ACT A 411
08AC8SOFTWARELYS A:66 , ARG A:69 , GLU A:150BINDING SITE FOR RESIDUE TRE A 412
09AC9SOFTWAREILE B:340 , LEU B:341 , GLU B:342 , HOH B:502BINDING SITE FOR RESIDUE SO4 B 401
10BC1SOFTWAREASN A:15 , GLY A:18 , VAL A:20 , ARG A:21 , HOH A:511 , HOH A:518 , HOH A:519 , HOH A:520BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 15 RESIDUES 401 TO 404

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:110 -A:187

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J4Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J4Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J4Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4J4Q)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh....eeee....eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j4q A   1 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKN 326
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      


Chain B from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4j4q B 340 ILENLKDVGLF 350
                                   349
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4J4Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J4Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J4Q)

(-) Gene Ontology  (55, 71)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        GNAT1_BOVIN | P04695: 1aqg 1fqj 1fqk 1got 1lvz 1tad 1tag 1tnd 2x72 3dqb 3pqr 3v00 4bey
        OPSD_BOVIN | P02699: 1boj 1bok 1eds 1edv 1edw 1edx 1f88 1fdf 1gzm 1hzx 1jfp 1l9h 1ln6 1n3m 1nzs 1ov0 1ov1 1u19 1vqx 1y6y 2g87 2hpy 2i35 2i36 2i37 2iqk 2j4y 2ped 2x72 3c9l 3c9m 3cap 3dqb 3oax 3pqr 3pxo 4a4m 4bey 4bez 4pxf 4x1h 5dys 5en0 5te3 5te5

(-) Related Entries Specified in the PDB File

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