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(-) Description

Title :  CRYSTAL STRUCTURE OF AN EGFR/HER3 KINASE DOMAIN HETERODIMER CONTAINING THE CANCER-ASSOCIATED HER3-E909G MUTATION
 
Authors :  P. Littlefield, L. Liu, N. Jura
Date :  07 Oct 14  (Deposition) - 10 Dec 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.98
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Receptor Tyrosine Kinase, Pseudokinase, Kinase, Atp Binding, Membrane, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Littlefield, L. Liu, V. Mysore, Y. Shan, D. E. Shaw, N. Jura
Structural Analysis Of The Egfr/Her3 Heterodimer Reveals Th Molecular Basis For Activating Her3 Mutations.
Sci. Signal. V. 7 Ra114 2014
PubMed-ID: 25468994  |  Reference-DOI: 10.1126/SCISIGNAL.2005786

(-) Compounds

Molecule 1 - RECEPTOR TYROSINE-PROTEIN KINASE ERBB-3
    Chains: A, C
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: KINASE DOMAIN, UNP RESIDUES 698-1020
    Gene: ERBB3, HER3
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTO-ONCOGENE-LIKE PROTEIN C-ERBB-3, TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER3
 
Molecule 2 - EPIDERMAL GROWTH FACTOR RECEPTOR
    Chains: B, D
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: KINASE DOMAIN, UNP RESIDUES 682-1022
    Gene: EGFR
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTO-ONCOGENE C-ERBB-1, RECEPTOR TYROSINE-PROTEIN KINASE ERBB-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:697 , SER A:698 , GLY A:699 , VAL A:700 , VAL A:704 , CYS A:721 , LYS A:723 , GLN A:769 , LEU A:771 , ASN A:815 , ARG A:819 , ASN A:820 , LEU A:822 , ASP A:833 , MG A:1102BINDING SITE FOR RESIDUE ANP A 1101
2AC2SOFTWAREASN A:820 , ASP A:833 , ANP A:1101BINDING SITE FOR RESIDUE MG A 1102
3AC3SOFTWAREPHE B:699 , VAL B:702 , ALA B:719 , LYS B:721 , THR B:766 , GLN B:767 , LEU B:768 , MET B:769 , CYS B:773 , ASN B:818 , LEU B:820 , ASP B:831 , MG B:1002BINDING SITE FOR RESIDUE ADP B 1001
4AC4SOFTWAREASN B:818 , ADP B:1001BINDING SITE FOR RESIDUE MG B 1002
5AC5SOFTWAREGLY C:697 , SER C:698 , GLY C:699 , VAL C:700 , VAL C:704 , LYS C:723 , GLN C:769 , LEU C:771 , ASN C:815 , ARG C:819 , ASN C:820 , LEU C:822 , ASP C:833 , MG C:1102BINDING SITE FOR RESIDUE ANP C 1101
6AC6SOFTWAREASN C:820 , ASP C:833 , ANP C:1101BINDING SITE FOR RESIDUE MG C 1102
7AC7SOFTWARELEU D:694 , PHE D:699 , VAL D:702 , ALA D:719 , LYS D:721 , THR D:766 , GLN D:767 , LEU D:768 , MET D:769 , ARG D:817 , ASN D:818 , LEU D:820 , ASP D:831 , MG D:1002BINDING SITE FOR RESIDUE ADP D 1001
8AC8SOFTWAREASN D:818 , ADP D:1001BINDING SITE FOR RESIDUE MG D 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RIY)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RIY)

(-) Sequences/Alignments

Asymmetric 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:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee....eeeeeee........eeeeeeeee...........hhhhhhhhhh.......eeeee...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee..eeee...hhhhhh.......hhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4riy A 680 VLARIFKETELRKLKVLGSGVFGTVHKGVWIPEGESIKIPVCIKVIEDKSGRQSFQAVTDHMLAIGSLDHAHIVRLLGLCPGSSLQLVTQYLPLGSLLDHVRQHRGALGPQLLLNWGVQIAKGMYYLEEHGMVHRNLAARNVLLKSPSQVQVADFGVADLLPPPIKWMALESIHFGKYTHQSDVWSYGVTVWELMTFGAEPYAGLRLAEVPDLLEKGGRLAQPQICTIDVYMVMVKCWMIDENIRPTFKELANEFTRMARDPPRYLVIK 960
                                   689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839  ||   861       871       881       891       901       911       921       931       941       951         
                                                                                                                                                                                            842|                                                                                                         
                                                                                                                                                                                             855                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhh.eeeeeeeee...eeeeeeee........eeeeeeee........hhhhhhhhhhhhhh.......eeeee.....eeeee....eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee.......ee..hhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhh............hhhhhhhhh.........hhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4riy B 664 LVEPLTPSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGD 960
                                   673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843   ||  857       867       877       887       897       907       917       927       937       947       957   
                                                                                                                                                                                                                 847|                                                                                                            
                                                                                                                                                                                                                  852                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee....eeeeeee........eeeeeeee......hhhhhhhhh..........eee....eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee..eeee...hhhhhh....hhhhhh...hhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4riy C 680 VLARIFKETELRKLKVLGSGVFGTVHKGVWIPEGESIKIPVCIKVIESFQAVTDHMLAIGSLDHAHIVRLLGLCPGSSLQLVTQYLPLGSLLDHVRQHRGALGPQLLLNWGVQIAKGMYYLEEHGMVHRNLAARNVLLKSPSQVQVADFGVADLLPPDDKQLLYSEAKTPIKWMALESIHFGKYTHQSDVWSYGVTVWELMTFGAEPYAGLRLAEVPDLLEKGGRLAQPQICTIDVYMVMVKCWMIDENIRPTFKELANEFTRMARDPPRYLVIK 960
                                   689       699       709       719      |735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955     
                                                                        726|                                                                                                                                                                                                                                   
                                                                         733                                                                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhh.eeeeeeeee....eeeeeee........eeeeeee......hhhhhhhhhhhhhhhhh.......eeeeee...eeeeee....eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.......ee......hhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhh............hhhhhhhhh.........hhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4riy D 664 LVEPLTPSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGD 960
                                   673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953
   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 4RIY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (134, 167)

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 Related Entries

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

UniProtKB/Swiss-Prot
        EGFR_HUMAN | P00533: 1dnq 1dnr 1ivo 1m14 1m17 1mox 1nql 1xkk 1yy9 1z9i 2eb2 2eb3 2exp 2exq 2gs2 2gs6 2gs7 2itn 2ito 2itp 2itq 2itt 2itu 2itv 2itw 2itx 2ity 2itz 2j5e 2j5f 2j6m 2jit 2jiu 2jiv 2ks1 2m0b 2m20 2n5s 2rf9 2rfd 2rfe 2rgp 3b2u 3b2v 3bel 3buo 3c09 3g5v 3g5y 3gop 3gt8 3ika 3lzb 3njp 3ob2 3op0 3p0y 3pfv 3poz 3qwq 3ug1 3ug2 3vjn 3vjo 3vrp 3vrr 3w2o 3w2p 3w2q 3w2r 3w2s 3w32 3w33 4g5j 4g5p 4hjo 4i1z 4i20 4i21 4i22 4i23 4i24 4jq7 4jq8 4jr3 4jrv 4krl 4krm 4kro 4krp 4li5 4ll0 4lqm 4lrm 4r3p 4r3r 4r5s 4riw 4rix 4rj4 4rj5 4rj6 4rj7 4rj8 4tks 4uip 4uv7 4wd5 4wkq 4wrg 4zau 4zjv 4zse 5c8k 5c8m 5c8n 5cal 5can 5cao 5cap 5caq 5cas 5cau 5cav 5cnn 5cno 5czh 5czi 5d41 5edp 5edq 5edr 5em5 5em6 5em7 5em8 5fed 5fee 5feq 5gmp 5gnk 5hcx 5hcy 5hcz 5hg5 5hg7 5hg8 5hg9 5hib 5hic 5j9y 5j9z 5jeb 5lv6 5sx4 5sx5 5u8l 5ug8 5ug9 5uga 5ugb 5ugc
        ERBB3_HUMAN | P21860: 1m6b 2l9u 3kex 3lmg 3p11 4leo 4otw 4p59 4riw 4rix 5cus

(-) Related Entries Specified in the PDB File

4riw 4rix