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(-) Description

Title :  CRYO-EM STRUCTURE OF THE ACTIVATED GLUCAGON-LIKE PEPTIDE-1 RECEPTOR IN COMPLEX WITH G PROTEIN
 
Authors :  Y. Zhang, B. Sun, D. Feng, H. Hu, M. Chu, Q. Qu, J. T. Tarrasch, S. Li, T. S. K B. K. Kobilka, G. Skiniotis
Date :  27 Mar 17  (Deposition) - 24 May 17  (Release) - 21 Jun 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.10
Chains :  Asym./Biol. Unit :  A,B,G,N,P,R
Keywords :  Class B Gpcr, Glp-1, Glp-1R, Complex, Signaling Protein-Hormone Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, B. Sun, D. Feng, H. Hu, M. Chu, Q. Qu, J. T. Tarrasch, S. Li, T. Sun Kobilka, B. K. Kobilka, G. Skiniotis
Cryo-Em Structure Of The Activated Glp-1 Receptor In Comple With A G Protein.
Nature V. 546 248 2017
PubMed-ID: 28538729  |  Reference-DOI: 10.1038/NATURE22394

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: R
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: GLP1R
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 2 - GLUCAGON-LIKE PEPTIDE 1
    Chains: P
    Engineered: YES
    Fragment: UNP RESIDUES 98-128
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - GUANINE NUCLEOTIDE-BINDING PROTEIN G(S) SUBUNIT ALPHA ISOFORMS SHORT
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: UNP RESIDUEWS 1-380
    Gene: GNAS, GNAS1, GSP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ADENYLATE CYCLASE-STIMULATING G ALPHA PROTEIN
 
Molecule 4 - GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(T) SUBUNIT BETA-1
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: GNB1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: TRANSDUCIN BETA CHAIN 1
 
Molecule 5 - GUANINE NUCLEOTIDE-BINDING PROTEIN G(I)/G(S)/G(O) SUBUNIT GAMMA-2
    Chains: G
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 1-68
    Gene: GNG2
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: G GAMMA-I
 
Molecule 6 - NANOBODY 35
    Chains: N
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABGNPR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5VAI)

(-) Sites  (0, 0)

(no "Site" information available for 5VAI)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1N:22 -N:96
2N:99 -N:107
3R:46 -R:71
4R:62 -R:104
5R:85 -R:126
6R:226 -R:296

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5VAI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5VAI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5VAI)

(-) Exons   (0, 0)

(no "Exon" information available for 5VAI)

(-) 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:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee.......hhhhhh.....eeeee..eeeeeee.........hhhhhh....eeeeeee.......hhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhh..hhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.....ee..........hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5vai A   9 TEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKSTIVKQSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVASSSYNMTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENIRRVFNDCRDIIQRMHLRQYELL 394
                                    18        28        38        48        58||     213       223       233       243       253 ||    270       280       290       300       310       320       330       340       350       360       370       380       390    
                                                                             59|                                               255|                                                                                                                                   
                                                                             205                                                263                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh............eeeeee.....eeeeee.....eeeeee...eeeeee.....eeeeee.......eeee.....eeeee.....eeeee.........eeeee......eeeeee....eeeeee....eeeee....eeeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeee........eeeeee.....eeeeee....eeeee.....eeeee......eeeeee......eeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vai B   1 QSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN 340
                                    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       330       340


Chain G from PDB  Type:PROTEIN  Length:58
                                                                                          
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 5vai G   5 NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR  62
                                    14        24        34        44        54        


Chain N from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee........eeeeeee.......................eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vai N   1 QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQGTQVTVSS 128
                                    10        20        30        40        50        60        70        80        90       100       110       120        


Chain P from PDB  Type:PROTEIN  Length:31
                                                               
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 5vai P   7 HAEGTFTSDVSSYLEGQAAKEFIAWLVKGRG  37
                                    16        26        36 


Chain R from PDB  Type:PROTEIN  Length:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh...........ee....ee......eeeeee..............eeeeee..................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vai R  29 TVSLSETVQKWREYRRQCQHFLTEAPPLATGLFCNRTFDDYACWPDGAPGSFVNVSCPWYLPWASNVLQGHVYRFCTAEGHWLPKDNSSLPWRDLSECEESSPEERLLSLYIIYTVGYALSFSALVIASAILLGFRHLHCTRNYIHLNLFASFILRALSVFIKDAALKWMYSTAAQQHQWDGLLSYQDSLGCRLVFLLMQYCVAANYYWLLVEGAYLYTLLAFAVFSEQRIFKLYLSIGWGVPLLFVIPWGIVKYLYEDEGCWTRNSNMNYWLIIRLPILFAIGVNFLIFIRVICIVVSKLKANLMCKTDIKCRLAKSTLTLIPLLGTHEVIFAFVMDEHARGTLRFVKLFTELSFTSFQGLMVAILYCFVNNEVQMEFRKSWERWR 421
                                    38        48        58        68        78        88        98       108       118       128|      144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       
                                                                                                                             128|                                                                                                                                                                                                                                                                                              
                                                                                                                              135
   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 5VAI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5VAI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5VAI)

(-) Gene Ontology  (97, 132)

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
        GBB1_RAT | P54311: 3sn6 5tdh
        GBG2_BOVIN | P63212: 1gg2 1gp2 1omw 1xhm 2bcj 3ah8 3cik 3krw 3krx 3psc 3pvu 3pvw 3sn6 3uzs 3v5w 4mk0 4pnk 5tdh
        GLUC_HUMAN | P01275: 1bh0 1d0r 1nau 2g49 2l63 2l64 2m5p 2m5q 3iol 4apd 4zgm
        GNAS2_HUMAN | P63092: 5g53 5uz7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5VAI)