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(-) Description

Title :  MOLECULAR ARCHITECTURE OF THE ERBB2 EXTRACELLULAR DOMAIN HOMODIMER
 
Authors :  S. Hu, Z. Y. Lou, Y. J. Guo
Date :  15 Nov 13  (Deposition) - 27 May 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.09
Chains :  Asym. Unit :  A,B,C,D,H,L
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,H,L  (1x)
Keywords :  Hydrolase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hu, Y. Sun, Y. Meng, X. Wang, W. Yang, W. Fu, H. Guo, W. Qian, S. Hou, B. Li, Z. Rao, Z. Lou, Y. Guo
Molecular Architecture Of The Erbb2 Extracellular Domain Homodimer
Oncotarget V. 6 1695 2015
PubMed-ID: 25633808

(-) Compounds

Molecule 1 - RECEPTOR TYROSINE-PROTEIN KINASE ERBB-2
    Chains: A, B
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Gene: ERBB2, HER2, MLN19, NEU, NGL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: METASTATIC LYMPH NODE GENE 19 PROTEIN, MLN 19, PROTO- ONCOGENE NEU, PROTO-ONCOGENE C-ERBB-2, TYROSINE KINASE-TYPE CELL SURFACE RECEPTOR HER2, P185ERBB2
 
Molecule 2 - ANTIBODY H CHAIN
    Chains: H, C
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ANTIBODY L CHAIN
    Chains: L, D
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDHL
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:230 , ASN A:237 , SER A:239BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 237 RESIDUES 1001 TO 1002
2AC2SOFTWAREASN B:237 , SER B:239 , SER B:272BINDING SITE FOR MONO-SACCHARIDE NAG B1001 BOUND TO ASN B 237

(-) SS Bonds  (49, 49)

Asymmetric Unit
No.Residues
1A:4 -A:31
2A:140 -A:170
3A:173 -A:182
4A:177 -A:190
5A:198 -A:205
6A:202 -A:213
7A:214 -A:222
8A:218 -A:230
9A:233 -A:242
10A:246 -A:273
11A:277 -A:289
12A:293 -A:309
13A:312 -A:316
14A:320 -A:345
15A:453 -A:482
16A:489 -A:498
17A:493 -A:506
18A:509 -A:518
19A:522 -A:538
20A:541 -A:554
21A:545 -A:562
22B:4 -B:31
23B:140 -B:170
24B:173 -B:182
25B:177 -B:190
26B:198 -B:205
27B:202 -B:213
28B:214 -B:222
29B:218 -B:230
30B:233 -B:242
31B:246 -B:273
32B:277 -B:289
33B:293 -B:309
34B:312 -B:316
35B:320 -B:345
36B:453 -B:482
37B:489 -B:498
38B:493 -B:506
39B:509 -B:518
40B:522 -B:538
41B:541 -B:554
42C:22 -C:96
43C:144 -C:200
44D:22 -D:90
45D:137 -D:197
46H:22 -H:96
47H:144 -H:200
48L:22 -L:90
49L:137 -L:197

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Phe H:150 -Pro H:151
2Gln L:1 -Ser L:2
3Met L:49 -Ile L:50
4Gly L:70 -Asn L:71
5Thr L:72 -Ala L:73
6Tyr L:143 -Pro L:144
7Phe C:150 -Pro C:151
8Glu C:152 -Pro C:153
9Gln D:1 -Ser D:2
10Gln D:16 -Ser D:17
11Met D:49 -Ile D:50
12Gly D:70 -Asn D:71
13Thr D:72 -Ala D:73
14Tyr D:143 -Pro D:144

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WLW)

(-) 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:555
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.............hhhhhhhhhhh...eee..eeee.......hhhhhhh.ee...eeee.............ee....hhhh.eeeeee....................ee...eeeee......hhhhhhhhhhh........eee.......................hhhhh..................hhhhh......................eee..eee......eee......eee.....eee..eee......................eee.........eee.......................hhhhhhhhh...ee...eeehhhhhh.hhhhh......hhhhhhhhh.eeee.eee.................eeeeeehhhh.eeeeee.............ee...eeeee...........hhhhhh......eeee....hhhhhhh.......hhhhh..............ee....ee...........eee....eee........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wlw A   1 TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLSPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVA 564
                                    10        20        30        40        50        60        70        80        90       100||     119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559     
                                                                                                                              101|                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                                               111                                                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:555
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.............hhhhhhhhhhh...eee..eeee.......hhhhhhh.ee...eeee.............ee....hhhh.eeeeee....................ee...eeeee...........hhhhhh........eee.......................hhhhh..................hhhhh......................eee..eee.......................ee....ee.......ee.....ee......eeee.......eeee.......................hhhhhhhhh....ee..eeehhhhhh.hhhhh......hhhhhhhhh.eee..eee.........hhhhh...ee....hhhh.eeeeee.............ee...eeeeeee.........hhhhhh......eeeeee..hhhhhh........hhhhh..................................ee....ee......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wlw B   1 TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLSPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVA 564
                                    10        20        30        40        50        60        70        80        90       100||     119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559     
                                                                                                                              101|                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                                               111                                                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...ee..........eeee..hhhh.eeeeeee.....eeeeeeee.....eee...........eehhh.ee...............eeeee....eeee.....ee...........ee...hhhhh........eeeeee......eee........eee...ee.....eeeeeee...........eeeee.........eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wlw C   1 EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQAPGQGLEWMGWISAYNGNTNYAQKLQGRVTMTTDTSTSTAYMELRSLRSDDTAVYYCAREGDGAFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................ee...............eeeeee......ee...........................ee.........eeeeee.......ee...ee.............ee.....hhhhh....ee..............ee........................................eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wlw D   1 QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTLVFGGGTKLTVLGTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....ee..eeee..hhhh.eeeeeee.....eeeeeeee.....eee.......eeeeee....eeeeee.............eee....eeee.....eee........ee..................eeeeee.....eeee.........ee...ee.....eeeeee...hhhhh.....eeeee........eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wlw H   1 EVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQAPGQGLEWMGWISAYNGNTNYAQKLQGRVTMTTDTSTSTAYMELRSLRSDDTAVYYCAREGDGAFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eee..............eeeeee......ee..........................eee.........eeeeee.......ee...ee...........eeee..hhhhhh......eeeeeee.....eeeeee..eee.....eee.........eeeee.............eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wlw L   1 QSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTSSSTLVFGGGTKLTVLGTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3WLW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (73, 73)

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  3wlw
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  ERBB2_HUMAN | P04626
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  2.7.10.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        ERBB2_HUMAN | P04626: 1mfg 1mfl 1mw4 1n8z 1ovc 1qr1 1s78 2a91 2jwa 2ks1 2l4k 2n2a 3be1 3h3b 3mzw 3n85 3pp0 3rcd 3wsq 4gfu 4hrl 4hrm 4hrn 4nnd 5k33 5kwg

(-) Related Entries Specified in the PDB File

3wn3