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(-) Description

Title :  RET RECOGNITION OF GDNF-GFRALPHA1 LIGAND BY A COMPOSITE BINDING SITE PROMOTES MEMBRANE-PROXIMAL SELF-ASSOCIATION
 
Authors :  K. Goodman, S. Kjaer, F. Beuron, P. Knowles, A. Nawrotek, E. Burns, A. Pu R. George, M. Santoro, E. P. Morris, N. Q. Mcdonald
Date :  19 Aug 14  (Deposition) - 01 Oct 14  (Release) - 08 Oct 14  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  24.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Signaling Protein, Vertebrate Development, Human Diseases, Part Of The Ret-Gfl- Gfra Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Goodman, S. Kjaer, F. Beuron, P. P. Knowles, A. Nawrotek, E. M. Burns, A. G. Purkiss, R. George, M. Santoro, E. P. Morris, N. Q. Mcdonald
Ret Recognition Of Gdnf-Gfralpha1 Ligand By A Composite Binding Site Promotes Membrane-Proximal Self-Association.
Cell Rep. V. 8 1894 2014
PubMed-ID: 25242331  |  Reference-DOI: 10.1016/J.CELREP.2014.08.040

(-) Compounds

Molecule 1 - PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
    Chains: A, B
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO LEC8
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Fragment: RET EXTRACELLULAR DOMAIN, RESIDUES 29-635
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CADHERIN FAMILY MEMBER 12, PROTO-ONCOGENE C-RET, RET RECEPTOR TYROSINE KINASE
 
Molecule 2 - GDNF FAMILY RECEPTOR ALPHA-1
    Chains: C, E
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO LEC8
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GFR ALPHA 1
 
Molecule 3 - GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR
    Chains: D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: MATURE, UNP RESIDUES 78-211
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HGDNF, ASTROCYTE-DERIVED TROPHIC FACTOR, ATF, GDNF

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:178 , ASP A:264 , GLU A:265 , ASP A:267 , ASP A:302BINDING SITE FOR RESIDUE CA A1603
02AC2SOFTWAREGLU A:178 , ASP A:230 , GLU A:232 , ASP A:267BINDING SITE FOR RESIDUE CA A1604
03AC3SOFTWAREASP A:266 , SER A:268 , ASP A:300 , ASP A:302 , GLY A:308 , ARG A:360BINDING SITE FOR RESIDUE CA A1605
04AC4SOFTWAREGLU B:178 , ASP B:264 , GLU B:265 , ASP B:267 , ASP B:302BINDING SITE FOR RESIDUE CA B1603
05AC5SOFTWAREGLU B:178 , ASP B:230 , GLU B:232 , ASP B:267BINDING SITE FOR RESIDUE CA B1604
06AC6SOFTWAREASP B:266 , SER B:268 , ASP B:300 , ASP B:302 , GLY B:308 , ARG B:360BINDING SITE FOR RESIDUE CA B1605
07AC7SOFTWAREHIS D:47 , LEU D:48 , ASN D:49 , ASP D:52 , NAG D:1136BINDING SITE FOR RESIDUE NAG D1135
08AC8SOFTWARENAG D:1135BINDING SITE FOR RESIDUE NAG D1136
09AC9SOFTWAREHIS F:47 , LEU F:48 , ASN F:49 , ASP F:52 , NAG F:1136BINDING SITE FOR RESIDUE NAG F1135
10BC1SOFTWARENAG F:1135BINDING SITE FOR RESIDUE NAG F1136

(-) SS Bonds  (33, 33)

Asymmetric/Biological Unit
No.Residues
1A:137 -A:142
2A:157 -A:197
3A:166 -A:243
4B:137 -B:142
5B:157 -B:197
6B:166 -B:243
7C:17 -C:23
8C:154 -C:214
9C:161 -C:167
10C:178 -C:192
11C:187 -C:233
12C:216 -C:221
13C:243 -C:313
14C:250 -C:256
15C:267 -C:285
16C:277 -C:337
17C:315 -C:325
18D:68 -D:131
19D:72 -D:133
20D:101 -F:101
21E:17 -E:23
22E:154 -E:214
23E:161 -E:167
24E:178 -E:192
25E:187 -E:233
26E:216 -E:221
27E:243 -E:313
28E:250 -E:256
29E:267 -E:285
30E:277 -E:337
31E:315 -E:325
32F:68 -F:131
33F:72 -F:133

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Trp A:139 -Pro A:140
2Pro A:320 -Gly A:321
3Thr A:323 -Trp A:324
4Trp B:139 -Pro B:140
5Pro B:320 -Gly B:321
6Thr B:323 -Trp B:324

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UX8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UX8)

(-) Exons   (0, 0)

(no "Exon" information available for 4UX8)

(-) 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:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeeeee.......eeee..ee..........ee..eee.hhh.eeee...eee.....eeee....hhhhhhhhhhh.......eeeeeee........eeeeeeeee.....hhhhhhhhhhhh......eeee......eeee..hhhhhhhh....eeeeee......ee......eeee..........eeeeeeeeee...eeeeeeeeeeee......ee....ee...eee.......eeeee...ee.....hhhhhh...eeee..........eee.......eeee...........eeee...........eeee..eee........ee..........eeeeehhhhhhhhhh....eeeee...........ee.......eeee............eeeeeeeee.........eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ux8 A  29 LYFSRDAYWEKLYVDQAAGTPLLYVHALRDAPEEVPSFRLGQHLYGTYRTRLHENNWIRIQEDTGLLYLQRSLDHSSWEKLSVRNRGFPLLTVYLKVFLSPCQWPGCARVYFSFFNTSFPACSSLKPRELCFPETRPSFRIRENRPPGTFHQFRLLPVQFLCPQISVAYRLLEGEGLPFRSAPDSLEVSTRWALDREQREKYELVAVCTVHREEVVMVPFPVTVYDEDDSAPTFPAGVDTASAVVEFKRKEDTVVATLRVFDADVVPASGELVRRYTSTLLPGDTWAQQTFRVEHWPNETSVQANGSFVRATVHDYRLVLNRNLSISENRTMQLAVLVNDSLHLPSTYSLSVSRRARRFAQIGKVCVENCQAFSGINVQYKLHSSGANCSTLGVVTSAEDTSGILFVNDTKALRRPKCAELHYMVVATDQQTSRQAQAQLLVTVEGSY 508
                                    38        48        58        68        78        88        98       108       118       128||     145       155       165       175       185       195       205       215       225       235       245||     258       268       278       288       298       308       318       328       338       348       358       368       378||     410       420       430       440       450       460       470       480       490       500        
                                                                                                                              129|                                                                                                          246|                                                                                                                              379|                                                                                                          
                                                                                                                               137                                                                                                           250                                                                                                                               402                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeeeee.......eeee..ee..........ee..eee.hhh.eeee...eee.....eeee....hhhhhhhhhhh.......eeeeeee........eeeeeeeee.....hhhhhhhhhhhh......eeee......eeee..hhhhhhhh....eeeeee......ee......eeee..........eeeeeeeeee...eeeeeeeeeeee......ee....ee...ee........eeeee...ee.....hhhhhh...eeee..........eee.......eeee...........eeee...........eeee..ee.........ee..........eeeeehhhhhhhhhh....eeeee...........ee.......eeee............eeeeeeeee.........eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ux8 B  29 LYFSRDAYWEKLYVDQAAGTPLLYVHALRDAPEEVPSFRLGQHLYGTYRTRLHENNWIRIQEDTGLLYLQRSLDHSSWEKLSVRNRGFPLLTVYLKVFLSPCQWPGCARVYFSFFNTSFPACSSLKPRELCFPETRPSFRIRENRPPGTFHQFRLLPVQFLCPQISVAYRLLEGEGLPFRSAPDSLEVSTRWALDREQREKYELVAVCTVHREEVVMVPFPVTVYDEDDSAPTFPAGVDTASAVVEFKRKEDTVVATLRVFDADVVPASGELVRRYTSTLLPGDTWAQQTFRVEHWPNETSVQANGSFVRATVHDYRLVLNRNLSISENRTMQLAVLVNDSLHLPSTYSLSVSRRARRFAQIGKVCVENCQAFSGINVQYKLHSSGANCSTLGVVTSAEDTSGILFVNDTKALRRPKCAELHYMVVATDQQTSRQAQAQLLVTVEGSY 508
                                    38        48        58        68        78        88        98       108       118       128||     145       155       165       175       185       195       205       215       225       235       245||     258       268       278       288       298       308       318       328       338       348       358       368       378||     410       420       430       440       450       460       470       480       490       500        
                                                                                                                              129|                                                                                                          246|                                                                                                                              379|                                                                                                          
                                                                                                                               137                                                                                                           250                                                                                                                               402                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh...............hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........ee.......ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ux8 C   6 DRLDCVKASDQCLKEQSCSTKYRTLRQCVAGKETNFSLTSGLEAKDECRSAMEALKQKSLYNCRCKRGMKKEKNCLRIYWSMYQSKGNNCLDAAKACNLDDTCKKYRSAYITPCTTSMSNEVCNRRKCHKALRQFFDKVPAKHSYGMLFCSCRDIACTERRRQTIVPVCSYEERERPNCLSLQDSCKTNYICRSRLADFFTNCQPESRSVSNCLKENYADCLLAYSGLIGTVMTPNYVDSSSLSVAPWCDCSNSGNDLEDCLKFLNFFKDNTCLKNAIQAFGNG 348
                                    15        25        35        45        55        65        75        85    || 154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344    
                                                                                                               90|                                                                                                                                                                                                      
                                                                                                               150                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhh.......eeeeeee........hhhhhhhhhhhhh...........eeeeeee...eeee.....eeee....eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4ux8 D  42 VLTAIHLNVTDLGLGYETKEELIFRYCSGSCDAAETTYDKILKNLSRNRRLVSDKVGQACCRPIAFDDDLSFLDDNLVYHILRKHSAKRCGCI 134
                                    51        61        71        81        91       101       111       121       131   


Chain E from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh...............hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh........ee.......ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ux8 E   6 DRLDCVKASDQCLKEQSCSTKYRTLRQCVAGKETNFSLTSGLEAKDECRSAMEALKQKSLYNCRCKRGMKKEKNCLRIYWSMYQSKGNNCLDAAKACNLDDTCKKYRSAYITPCTTSMSNEVCNRRKCHKALRQFFDKVPAKHSYGMLFCSCRDIACTERRRQTIVPVCSYEERERPNCLSLQDSCKTNYICRSRLADFFTNCQPESRSVSNCLKENYADCLLAYSGLIGTVMTPNYVDSSSLSVAPWCDCSNSGNDLEDCLKFLNFFKDNTCLKNAIQAFGNG 348
                                    15        25        35        45        55        65        75        85    || 154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344    
                                                                                                               90|                                                                                                                                                                                                      
                                                                                                               150                                                                                                                                                                                                      


Chain F from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhh.......eeeeeee........hhhhhhhhhhhhh...........eeeeeee...eeee.....eeee....eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4ux8 F  42 VLTAIHLNVTDLGLGYETKEELIFRYCSGSCDAAETTYDKILKNLSRNRRLVSDKVGQACCRPIAFDDDLSFLDDNLVYHILRKHSAKRCGCI 134
                                    51        61        71        81        91       101       111       121       131
   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 4UX8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UX8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UX8)

(-) Gene Ontology  (105, 124)

Asymmetric/Biological Unit(hide GO term definitions)

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  4ux8
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  RET_HUMAN | P07949
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 Related Entries

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

UniProtKB/Swiss-Prot
        GDNF_HUMAN | P39905: 2v5e 3fub
        GFRA1_RAT | Q62997: 1q8d 2v5e 3fub
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(-) Related Entries Specified in the PDB File

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