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(-) Description

Title :  STRUCTURE OF ALPHA-1 GLYCINE RECEPTOR BY SINGLE PARTICLE ELECTRON CRYO-MICROSCOPY, STRYCHNINE-BOUND STATE
 
Authors :  J. Du, W. Lu, S. P. Wu, Y. F. Cheng, E. Gouaux
Date :  08 Jun 15  (Deposition) - 09 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  3.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Cys Loop Receptor, Alpha-1 Glycine Receptor, Strychnine, Signaling Protein-Antagonist Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Du, W. Lu, S. Wu, Y. Cheng, E. Gouaux
Glycine Receptor Mechanism Elucidated By Electron Cryo-Microscopy.
Nature V. 526 224 2015
PubMed-ID: 26344198  |  Reference-DOI: 10.1038/NATURE14853

(-) Compounds

Molecule 1 - GLYCINE RECEPTOR SUBUNIT ALPHAZ1
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: GLRA1
    Organism Common: ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: ALPHA1 GLYCINE RECEPTOR

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SY95Ligand/IonSTRYCHNINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:79 , ARG A:81 , LEU A:133 , ARG A:135 , LEU A:143 , PHE E:175 , GLY E:176 , TYR E:218 , THR E:220 , PHE E:223BINDING SITE FOR RESIDUE SY9 A 503
02AC2SOFTWAREPHE A:175 , GLY A:176 , TYR A:218 , THR A:220 , PHE A:223 , PHE B:79 , ARG B:81 , LEU B:133 , ARG B:135 , LEU B:143BINDING SITE FOR RESIDUE SY9 B 401
03AC3SOFTWAREPHE B:175 , GLY B:176 , TYR B:218 , THR B:220 , PHE B:223 , PHE C:79 , ARG C:81 , LEU C:133 , ARG C:135 , LEU C:143BINDING SITE FOR RESIDUE SY9 C 401
04AC4SOFTWAREPHE C:175 , GLY C:176 , TYR C:218 , THR C:220 , PHE C:223 , PHE D:79 , ARG D:81 , LEU D:133 , ARG D:135 , LEU D:143BINDING SITE FOR RESIDUE SY9 D 401
05AC5SOFTWAREPHE D:175 , GLY D:176 , TYR D:218 , THR D:220 , PHE D:223 , PHE E:79 , ARG E:81 , LEU E:133 , ARG E:135 , LEU E:143BINDING SITE FOR RESIDUE SY9 E 401
06AC6SOFTWAREPRO A:51 , PRO A:52 , ASN A:54BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 501 TO 502
07AC7SOFTWAREPRO B:51 , PRO B:52 , ASN B:54BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 402 TO 403
08AC8SOFTWAREPRO C:51 , PRO C:52 , ASN C:54BINDING SITE FOR CHAIN C OF POLYSACCHARIDE RESIDUES 402 TO 403
09AC9SOFTWAREPRO D:51 , PRO D:52 , ASN D:54BINDING SITE FOR CHAIN D OF POLYSACCHARIDE RESIDUES 402 TO 403
10BC1SOFTWAREPRO E:51 , PRO E:52 , ASN E:54BINDING SITE FOR DI-SACCHARIDE NAG E 402 AND NAG E 403

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:214 -A:225
2B:214 -B:225
3C:214 -C:225
4D:214 -D:225
5E:214 -E:225

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3JAD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3JAD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JAD)

(-) Exons   (0, 0)

(no "Exon" information available for 3JAD)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.................eeeeeeeeeeeeeeee....eeeeeeeeeeeee..................hhhhh.....eee..eeeeee........eeee....eeeeeeeeeeee............eeeeeeeeee.......eeee......eee........eeeeeeeeeeeeeeee..eeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jad A  25 APSEFLDKLMGKVSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARKLFISRAKRIDTVSRVAFPLVFLIFNIFYWITYKLV 364
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324||     337       347       357       
                                                                                                                                                                                                                                                                                                                                      325|                                   
                                                                                                                                                                                                                                                                                                                                       329                                   


Chain B from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.................eeeeeeeeeeeeeeee....eeeeeeeeeeeee..................hhhhh.....eee..eeeeee........eeee....eeeeeeeeeeee............eeeeeeeeee.......eeee......eee........eeeeeeeeeeeeeeee..eeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jad B  25 APSEFLDKLMGKVSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARKLFISRAKRIDTVSRVAFPLVFLIFNIFYWITYKLV 364
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324||     337       347       357       
                                                                                                                                                                                                                                                                                                                                      325|                                   
                                                                                                                                                                                                                                                                                                                                       329                                   


Chain C from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.................eeeeeeeeeeeeeeee....eeeeeeeeeeeee..................hhhhh.....eee..eeeeee........eeee....eeeeeeeeeeee............eeeeeeeeee.......eeee......eee........eeeeeeeeeeeeeeee..eeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jad C  25 APSEFLDKLMGKVSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARKLFISRAKRIDTVSRVAFPLVFLIFNIFYWITYKLV 364
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324||     337       347       357       
                                                                                                                                                                                                                                                                                                                                      325|                                   
                                                                                                                                                                                                                                                                                                                                       329                                   


Chain D from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.................eeeeeeeeeeeeeeee....eeeeeeeeeeeee..................hhhhh.....eee..eeeeee........eeee....eeeeeeeeeeee............eeeeeeeeee.......eeee......eee........eeeeeeeeeeeeeeee..eeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jad D  25 APSEFLDKLMGKVSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARKLFISRAKRIDTVSRVAFPLVFLIFNIFYWITYKLV 364
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324||     337       347       357       
                                                                                                                                                                                                                                                                                                                                      325|                                   
                                                                                                                                                                                                                                                                                                                                       329                                   


Chain E from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.................eeeeeeeeeeeeeeee....eeeeeeeeeeeee..................hhhhh.....eee..eeeeee........eeee....eeeeeeeeeeee............eeeeeeeeee.......eeee......eee........eeeeeeeeeeeeeeee..eeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jad E  25 APSEFLDKLMGKVSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARKLFISRAKRIDTVSRVAFPLVFLIFNIFYWITYKLV 364
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324||     337       347       357       
                                                                                                                                                                                                                                                                                                                                      325|                                   
                                                                                                                                                                                                                                                                                                                                       329
   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 3JAD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        GLRA1_DANRE | O93430: 3jae 3jaf

(-) Related Entries Specified in the PDB File

3jae 3jaf