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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 5-HT2B RECEPTOR SOLVED USING SERIAL FEMTOSECOND CRYSTALLOGRAPHY IN LIPIDIC CUBIC PHASE.
 
Authors :  W. Liu, D. Wacker, C. Gati, G. W. Han, D. James, D. Wang, G. Nelson, U. Weie V. Katritch, A. Barty, N. A. Zatsepin, D. Li, M. Messerschmidt, S. Bout G. J. Williams, J. E. Koglin, M. M. Seibert, C. Wang, S. T. A. Shah, S. Bas R. Fromme, C. Kupitz, K. N. Rendek, I. Grotjohann, P. Fromme, R. A. Kiri K. R. Beyerlein, T. A. White, H. N. Chapman, M. Caffrey, J. C. H. Spence, R. C. Stevens, V. Cherezov, Gpcr Network (Gpcr)
Date :  23 Oct 13  (Deposition) - 18 Dec 13  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Serial Femtosecond Crystallography, Human 5Ht2B Receptor, Ergotamine, Novel Protein Engineering, Gpcr Network, Membrane Protein, Lipidic Cubic Phase, Psi-Biology, Free Electron Laser, Structural Genomics, Gpcr, Membrane, Signaling Protein, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Liu, D. Wacker, C. Gati, G. W. Han, D. James, D. Wang, G. Nelson, U. Weierstall, V. Katritch, A. Barty, N. A. Zatsepin, D. Li, M. Messerschmidt, S. Boutet, G. J. Williams, J. E. Koglin, M. M. Seibert, C. Wang, S. T. Shah, S. Basu, R. Fromme, C. Kupitz, K. N. Rendek, I. Grotjohann, P. Fromme, R. A. Kirian, K. R. Beyerlein, T. A. White, H. N. Chapman, M. Caffrey, J. C. Spence, R. C. Stevens, V. Cherezov
Serial Femtosecond Crystallography Of G Protein-Coupled Receptors.
Science V. 342 1521 2013
PubMed-ID: 24357322  |  Reference-DOI: 10.1126/SCIENCE.1244142

(-) Compounds

Molecule 1 - CHIMERA PROTEIN OF HUMAN 5-HYDROXYTRYPTAMINE RECEPTOR 2B AND E. COLI SOLUBLE CYTOCHROME B562
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PFASTBAC
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: PLASMID
    Fragment: BRIL
    Gene: HTR2B, CYBC
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS, ESCHERICHIA COLI
    Organism Taxid: 9606, 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 14)

Asymmetric/Biological Unit (8, 14)
No.NameCountTypeFull Name
1CLR1Ligand/IonCHOLESTEROL
2DGA2Ligand/IonDIACYL GLYCEROL
3ERM1Ligand/IonERGOTAMINE
4OLA3Ligand/IonOLEIC ACID
5OLC4Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
7PLM1Ligand/IonPALMITIC ACID
8TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:62 , CYS A:353 , ILE A:395 , THR A:396 , CYS A:397BINDING SITE FOR RESIDUE PLM A 1201
02AC2SOFTWAREASP A:135 , SER A:139 , THR A:140 , VAL A:208 , LEU A:209 , PHE A:217 , MET A:218 , ALA A:225 , PHE A:340 , ASN A:344 , GLN A:359 , HOH A:1302BINDING SITE FOR RESIDUE ERM A 1202
03AC3SOFTWAREILE A:61 , ILE A:69 , GLY A:70 , TYR A:394 , TYR A:399BINDING SITE FOR RESIDUE CLR A 1203
04AC4SOFTWARESER A:150 , MET A:233 , THR A:240 , LEU A:326BINDING SITE FOR RESIDUE OLC A 1204
05AC5SOFTWARETYR A:399BINDING SITE FOR RESIDUE OLC A 1205
06AC6SOFTWARETYR A:87 , TYR A:380 , ASN A:384BINDING SITE FOR RESIDUE PEG A 1206
07AC7SOFTWARELEU A:77 , HOH A:1305BINDING SITE FOR RESIDUE OLC A 1207
08AC8SOFTWARELYS A:193 , ASP A:216 , PHE A:217 , OLA A:1212BINDING SITE FOR RESIDUE OLC A 1208
09AC9SOFTWAREASP A:216BINDING SITE FOR RESIDUE TRS A 1209
10BC1SOFTWAREMET A:63BINDING SITE FOR RESIDUE OLA A 1211
11BC2SOFTWAREILE A:174 , OLC A:1208BINDING SITE FOR RESIDUE OLA A 1212
12BC3SOFTWARELEU A:239 , HIS A:242 , DGA A:1214BINDING SITE FOR RESIDUE DGA A 1213
13BC4SOFTWAREHIS A:55 , HIS A:242 , DGA A:1213 , HOH A:1306BINDING SITE FOR RESIDUE DGA A 1214

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:128 -A:207
2A:350 -A:353

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NC3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NC3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NC3)

(-) Exons   (0, 0)

(no "Exon" information available for 4NC3)

(-) 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:370
                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nc3 A   48 EEQGNKLHWAALLILMVIIPTIGGNTLVILAVSLEKKLQYATNYFLMSLAVADLLVGLFVMPIALLTIMFEAMWPLPLVLCPAWLFLDVLFSTASIWHLCAISVDRYIAIKKPIQANQYNSRATAFIKITVVWLISIGIAIPVPIKGIETVDNPNNITCVLTKERFGDFMLFGSLAAFFTPLAIMIVTYFLTIHALQKKAADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLQTISNEQRASKVLGIVFFLFLLMWCPFFITNITLVLCDSCNQTTLQMLLEIFVWIGYVSSGVNPLVYTLFNKTFRDAFGRYITCNYR  400
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197|      208       218       228       238       248|     1010      1020      1030    ||1063      1073      1083      1093      1103  ||   320       330       340       350       360       370       380       390       400
                                                                                                                                                                               197|                                              248|                              1035|                                           1106|                                                                                      
                                                                                                                                                                                199                                              1001                               1059                                             314
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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 4NC3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NC3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NC3)

(-) Gene Ontology  (70, 70)

Asymmetric/Biological Unit(hide GO term definitions)

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  4nc3
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  C562_ECOLX | P0ABE7
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 Related Entries

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

UniProtKB/Swiss-Prot
        5HT2B_HUMAN | P41595: 4ib4 5tvn
        C562_ECOLX | P0ABE7: 1apc 1lm3 1m6t 1qpu 1qq3 256b 2bc5 2qla 3c62 3c63 3de8 3de9 3foo 3fop 3hni 3hnj 3hnk 3hnl 3iq5 3iq6 3l1m 3m15 3m4b 3m4c 3m79 3nmi 3nmj 3nmk 3tol 3tom 3u8p 4ea3 4eiy 4iaq 4iar 4ib4 4je9 4jea 4jeb 4jkv 4l6r 4n6h 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwa 4rwd 4u9d 4u9e 4yay 4z34 4z35 4z36 4zud 5awi 5bu7 5dhg 5dhh 5iu4 5iu7 5iu8 5iua 5iub 5jtb 5k2a 5k2b 5k2c 5k2d 5l31 5l32 5l7d 5l7i 5ndd 5ndz 5nj6 5tvn 5uen 5uig 5unf 5ung 5unh 5uvi

(-) Related Entries Specified in the PDB File

4ib4 CRYSTAL STRUCTURE OF THE CHIMERIC PROTEIN OF 5-HT2B-BRIL IN COMPLEX WITH ERGOTAMINE RELATED ID: GPCR-4 RELATED DB: TARGETTRACK