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(-) Description

Title :  AN ENGINEERED AXL 'DECOY RECEPTOR' EFFECTIVELY SILENCES THE GAS6-AXL SIGNALING AXIS
 
Authors :  M. S. Kariolis, S. Kapur, I. I. Mathews, J. R. Cochran
Date :  09 Sep 14  (Deposition) - 24 Sep 14  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.07
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Axl, Gas6, Cancer, Metastasis, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Kariolis, Y. R. Miao, D. S. Jones, S. Kapur, I. I. Mathews, A. J. Giaccia, J. R. Cochran
An Engineered Axl 'Decoy Receptor' Effectively Silences The Gas6-Axl Signaling Axis.
Nat. Chem. Biol. V. 10 977 2014
PubMed-ID: 25242553  |  Reference-DOI: 10.1038/NCHEMBIO.1636

(-) Compounds

Molecule 1 - GROWTH ARREST-SPECIFIC PROTEIN 6
    Chains: A, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 322-721
    Gene: GAS6, AXLLG
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GAS-6, AXL RECEPTOR TYROSINE KINASE LIGAND
 
Molecule 2 - TYROSINE-PROTEIN KINASE RECEPTOR UFO
    Chains: C, D
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK-IBA12
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 33-227
    Gene: AXL, UFO
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AXL ONCOGENE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NI2Ligand/IonNICKEL (II) ION
5SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:329 , GLU A:331 , ARG A:440 , ASP A:656BINDING SITE FOR RESIDUE CA A 703
2AC2SOFTWAREARG A:446BINDING SITE FOR RESIDUE CL A 704
3AC3SOFTWAREASP B:329 , GLU B:331 , ARG B:440 , ASP B:656BINDING SITE FOR RESIDUE CA B 703
4AC4SOFTWAREHIS C:179BINDING SITE FOR RESIDUE NI C 301
5AC5SOFTWAREARG C:141 , PHE C:149 , ASN C:150BINDING SITE FOR RESIDUE SO4 C 302
6AC6SOFTWAREHIS D:179BINDING SITE FOR RESIDUE NI D 301
7AC7SOFTWAREGLN A:596 , ARG D:141 , PHE D:149 , ASN D:150BINDING SITE FOR RESIDUE SO4 D 302
8AC8SOFTWAREGLY A:339 , HIS A:340 , ASN A:420 , GLU C:56BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 420 RESIDUES 701 TO 702
9AC9SOFTWAREARG B:308 , ARG B:310 , GLY B:338 , GLY B:339 , ASN B:420 , PRO D:57BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 420 RESIDUES 701 TO 702

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:283 -A:570
2A:444 -A:470
3A:643 -A:670
4B:283 -B:570
5B:444 -B:470
6B:643 -B:670
7C:49 -C:110
8C:153 -C:198
9D:49 -D:110
10D:153 -D:198

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Lys A:549 -Lys A:550
2Gly C:157 -Pro C:158
3Pro C:158 -Pro C:159
4Glu C:160 -Pro C:161
5Ala D:145 -Asn D:146
6Gly D:157 -Pro D:158
7Pro D:158 -Pro D:159
8Glu D:160 -Pro D:161
9His D:179 -Gly D:180

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RA0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RA0)

(-) Exons   (0, 0)

(no "Exon" information available for 4RA0)

(-) 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee..........eeeeeee......eeeeeeee....eeeeeee.....eeeeeeee..eeeeeeee...eeeeeeeee......eeeeee....eeeeee..eeeeeee......eee..eeeeeeee.....hhhhh.........eeeeeeee......hhhhhhhhhhhhh.........ee.....eee........eeeeeeeee....eeeeeee........eeeeee..........eeeeeee..eeeeeeee.......eeeeeeee..eeeeee..........hhhhhhhhhhhhhhhhh..eeee..................eeeeeee..ee.hhhhh.ee............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ra0 A 281 LPCVPFSVAKSVKSLYLGRMFSGTPVIRLRFKRLQPTRLVAEFDFRTFDPEGILLFAGGHQDSTWIVLALRAGRLELQLRYNGVGRVTSSGPVINHGMWQTISVEELARNLVIKVNRDAVMKIAVAGDLFQPERGLYHLNLTVGGIPFHEKDLVQPINPRLDGCMRSWNWLNGEDTTIQETVKVNTRMQCFSVTERGSFYPGSGFAFYSLDYMTWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDYHSTKKLKKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEPA 676
                                   290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490  ||   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670      
                                                                                                                                                                                                                                              493|                                                                                                                                                                            
                                                                                                                                                                                                                                               504                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:377
                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee..........eeeeeee......eeeeeeee....eeeeeee.....eeeeeeee..eeeeeeee..eeeeeeeeee......eeeeeeee..eeeeee..eeeeeee......eee..eeeeeeee.....hhhhh.........eeeeeeee......hhhhhhhhhhhhh........eeee....eeee.........eeeeeee....eeeeeee.........eeeee...eeeeee..eeeeeee.hhhhh..eeeeeeee..eeeeee..ee.........hhhhhhhhhhhhhh..eeee.................eeeeeeee..ee.hhhhh.ee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ra0 B 281 LPCVPFSVAKSVKSLYLGRMFSGTPVIRLRFKRLQPTRLVAEFDFRTFDPEGILLFAGGHQDSTWIVLALRAGRLELQLRYNGVGRVTSSGPVINHGMWQTISVEELARNLVIKVNRDAVMKIAVAGDLFQPERGLYHLNLTVGGIPFHEKDLVQPINPRLDGCMRSWNWLNGEDTTIQETVKVNTRMQCFSVTERGSFYPGSGFAFYSLDYMTWEVEVVAHIRPAADTGVLFALWAPDLRAVPLSVALVDKQLVVLAVEHTALALMEIKVCDGQEHVVTVSLRDGEATLEVDGTRGQSEVSAAQLQERLAVLERHLRSPVLTFAGGLPDVPVTSAPVTAFYRGCMTLEVNRRLLDLDEAAYKHSDITAHSCPPVEP 675
                                   290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490  ||   510       520       530       540||     558       568       578       588       598       608       618       628       638       648       658       668       
                                                                                                                                                                                                                                              493|                                  541|                                                                                                                             
                                                                                                                                                                                                                                               504                                   550                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eee.....eeeeeeeeee.....eeeee..ee....eeeeeeee.......eeeeeeeeee...hhhhheeeeeeeee..eeee...eeeee....eeee....eee.....eeee.eee......eeeeee..ee...........eeee......eeeeeeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ra0 C  27 ESPFVSNPGNITGARGLTGTLRCQLQVQGEPPEVHWLRDGQILELADSTQTQVPLGEDEQGDWIVASQLRITSLQLSDTGQYQCLVFLGHQTFVSQPGYVRLEGLPYFLEEPEDRTVAANTPFNLSCQAQGPPEPVDLLWLQDAVPLATAPGHGPQRSLHVPGLNKTSSFSCEAHNAKGVTTSRTATITVL 217
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216 


Chain D from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....eee.....eeeeeeeeee.....eeeee..ee....eeeeeeee.......eeeeeeeeee...hhhhheeeeeeee....eee...eeeee....eeee....eee.....eeee.eee......eeeeee...............eeee......eeeeeeee....eee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ra0 D  27 ESPFVSNPGNITGARGLTGTLRCQLQVQGEPPEVHWLRDGQILELADSTQTQVPLGEDEQGDWIVASQLRITSLQLSDTGQYQCLVFLGHQTFVSQPGYVRLEGLPYFLEEPEDRTVAANTPFNLSCQAQGPPEPVDLLWLQDAVPLATAPGHGPQRSLHVPGLNKTSSFSCEAHNAKGVTTSRTATITVL 217
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
   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 4RA0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RA0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RA0)

(-) Gene Ontology  (129, 153)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala D:145 - Asn D:146   [ RasMol ]  
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    Gly C:157 - Pro C:158   [ RasMol ]  
    Gly D:157 - Pro D:158   [ RasMol ]  
    His D:179 - Gly D:180   [ RasMol ]  
    Lys A:549 - Lys A:550   [ RasMol ]  
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  4ra0
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  GAS6_HUMAN | Q14393
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 Related Entries

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

UniProtKB/Swiss-Prot
        GAS6_HUMAN | Q14393: 1h30 2c5d 5vxz
        UFO_HUMAN | P30530: 2c5d 5vxz

(-) Related Entries Specified in the PDB File

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