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(-) Description

Title :  X-RAY STRUCTURE OF THE FAB FRAGMENT OF THE ANTI TAU ANTIBODY RB86 IN COMPLEX WITH THE PHOSPHORYLATED TAU PEPTIDE (416-430)
 
Authors :  J. Benz, S. Lorenz, G. Georges, A. Jochner, U. Goepfert, F. Grueninger, A. Bujotzek
Date :  08 Sep 15  (Deposition) - 16 Dec 15  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  C,D,E,F,H,L,P,X,Z
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  C,D,Z  (1x)
Biol. Unit 3:  E,F,X  (1x)
Keywords :  Antibody, Fab Fragment, Tau Protein, Tau-Pser422, Tau-Pser422 Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bujotzek, F. Lipsmeier, S. F. Harris, J. Benz, A. Kuglstatter, G. Georges
Vh-Vl Orientation Prediction For Antibody Humanization Candidate Selection: A Case Study.
Mabs V. 8 288 2016
PubMed-ID: 26637054  |  Reference-DOI: 10.1080/19420862.2015.1117720

(-) Compounds

Molecule 1 - RB86 ANTIBODY FAB FRAGMENT HEAVY CHAIN
    Chains: H, C, E
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 2 - RB86 ANTIBODY FAB FRAGMENT LIGHT CHAIN
    Chains: L, D, F
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 3 - MICROTUBULE-ASSOCIATED PROTEIN
    Chains: Z, P, X
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : CDEFHLPXZ
Biological Unit 1 (1x):     HLP  
Biological Unit 2 (1x): CD      Z
Biological Unit 3 (1x):   EF   X 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SEP3Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (0, 0)

(no "Site" information available for 5DMG)

(-) SS Bonds  (15, 15)

Asymmetric Unit
No.Residues
1C:122 -C:330
2C:1026 -C:1082
3D:523 -D:734
4D:756 -D:797
5D:2026 -D:2086
6E:122 -E:330
7E:1026 -E:1082
8F:523 -F:734
9F:756 -F:797
10F:2026 -F:2086
11H:122 -H:330
12H:1026 -H:1082
13L:523 -L:734
14L:756 -L:797
15L:2026 -L:2086

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Phe H:1032 -Pro H:1033
2Glu H:1034 -Pro H:1035
3Leu H:1075 -Gly H:1076
4Ser L:509 -Pro L:510
5Tyr L:2032 -Pro L:2033
6Phe C:1032 -Pro C:1033
7Glu C:1034 -Pro C:1035
8Ser D:509 -Pro D:510
9Tyr D:2032 -Pro D:2033
10Phe E:1032 -Pro E:1033
11Glu E:1034 -Pro E:1035
12Ser E:1074 -Leu E:1075
13Ser F:509 -Pro F:510
14Ser F:757 -Ile F:794
15Ser F:2019 -Gly F:2020
16Tyr F:2032 -Pro F:2033

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DMG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DMG)

(-) Exons   (0, 0)

(no "Exon" information available for 5DMG)

(-) 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 C from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.......eeeee...eeeeee...hhhhheeeeeee..ee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeee..hhhhhh..eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dmg C  102 QSVEESGGRLVTPGTPLTLTCTVSGFSLSSNAINWVRQAPGKGLEWIGYIAVSGNTYYASWAKGRFTISKASTTVDLKMTSPTAEDTGTYFCGKSNIWGPGTLVTVSLASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 1101
                                   111       121   ||  156|  ||  206       252 ||    295   ||  306 ||    318       328   ||||403      1001      1011||    1029      1039      1049      1059      1069      1079      1089      1099  
                                                 125|  156|  ||          214|  ||        299|    308|                  332||||       411|        1012|                                                                                
                                                  151   196  ||           251  ||         301     311                   351|||       1000         1021                                                                                
                                                           199|              254|                                        398||                                                                                                        
                                                            201               288                                         399|                                                                                                        
                                                                                                                           401                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee.....eeeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee........eee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dmg D  502 QVLTQTTSPVSAAVGSTVTISCQSSQSVRTNKLAWFQQKPGQPPKRLIYSASTLDFGVPSRFSASGSGTQFTLTISDVQCDDAATYYCLGYFDCSIADCVAFGGGTEVVVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 2105
                                   511       521 || |||581|  ||  606       651|    ||704       716       726       752    || 798||     809||    2008      2018      2028      2038      2048      2058      2068      2078      2088      2098       
                                               523| ||||||| 601           615||  699|        712|                734|   757|  799|      810|                                                                                                         
                                                551 |||||||  |             651|   701         715                 751    794   801      2000                                                                                                         
                                                  553||||||  |              694                                                                                                                                                                      
                                                   556|||||  |                                                                                                                                                                                       
                                                    561||||  |                                                                                                                                                                                       
                                                     562|||  |                                                                                                                                                                                       
                                                      571||  |                                                                                                                                                                                       
                                                       581|  |                                                                                                                                                                                       
                                                        596  |                                                                                                                                                                                       


Chain E from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee........eeeeee.....eeeeeee.....eee.......eeeee...eeeeee...hhhhheeeeeee..ee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee.......eeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5dmg E  102 QSVEESGGRLVTPGTPLTLTCTVSGFSLSSNAINWVRQAPGKGLEWIGYIAVSGNTYYASWAKGRFTISKASTTVDLKMTSPTAEDTGTYFCGKSNIWGPGTLVTVSLASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLQTYICNVNHKPSNTKVDKKVEP 1099
                                   111       121   ||  156|  ||  206       252 ||    295   ||  306 ||    318       328   ||||403      1001      1011||    1029      1039      1049      1059      1069     |1081      1091        
                                                 125|  156|  ||          214|  ||        299|    308|                  332||||       411|        1012|                                                  1075|                     
                                                  151   196  ||           251  ||         301     311                   351|||       1000         1021                                                   1078                     
                                                           199|              254|                                        398||                                                                                                    
                                                            201               288                                         399|                                                                                                    
                                                                                                                           401                                                                                                    


Chain F from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee.....eeeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeeee........eee...eeeee.......ee.....hhhhhh..eeeeeeeeeee......eeeee........ee............eeeeeeeeeehhhhh...eeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dmg F  502 QVLTQTTSPVSAAVGSTVTISCQSSQSVRTNKLAWFQQKPGQPPKRLIYSASTLDFGVPSRFSASGSGTQFTLTISDVQCDDAATYYCLGYFDCSIADCVAFGGGTEVVVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGSPVTKSFNRGE 2105
                                   511       521 || |||581|  ||  606       651|    ||704       716       726       752    || 798||     809||    2008      2018      2028      2038      2048      2058      2068      2078      2088   || 2100     
                                               523| ||||||| 601           615||  699|        712|                734|   757|  799|      810|                                                                                        2092|          
                                                551 |||||||  |             651|   701         715                 751    794   801      2000                                                                                         2095          
                                                  553||||||  |              694                                                                                                                                                                    
                                                   556|||||  |                                                                                                                                                                                     
                                                    561||||  |                                                                                                                                                                                     
                                                     562|||  |                                                                                                                                                                                     
                                                      571||  |                                                                                                                                                                                     
                                                       581|  |                                                                                                                                                                                     
                                                        596  |                                                                                                                                                                                     


Chain H from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee......eeeeeee........eeeeee.....eeeeeee.....eee.hhhh..eeeee...eeeeee...hhhhheeeeeee..ee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee..........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5dmg H  102 QSVEESGGRLVTPGTPLTLTCTVSGFSLSSNAINWVRQAPGKGLEWIGYIAVSGNTYYASWAKGRFTISKASTTVDLKMTSPTAEDTGTYFCGKSNIWGPGTLVTVSLASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 1101
                                   111       121   ||  156|  ||  206       252 ||    295   ||  306 ||    318       328   ||||403      1001      1011||    1029      1039      1049      1059      1069      1079      1089      1099  
                                                 125|  156|  ||          214|  ||        299|    308|                  332||||       411|        1012|                                                                                
                                                  151   196  ||           251  ||         301     311                   351|||       1000         1021                                                                                
                                                           199|              254|                                        398||                                                                                                        
                                                            201               288                                         399|                                                                                                        
                                                                                                                           401                                                                                                        


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee....eeee....eeeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee........eee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5dmg L  503 VLTQTTSPVSAAVGSTVTISCQSSQSVRTNKLAWFQQKPGQPPKRLIYSASTLDFGVPSRFSASGSGTQFTLTISDVQCDDAATYYCLGYFDCSIADCVAFGGGTEVVVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 2105
                                   512       522|| ||||596  ||   607       694    || 705      |717       727      |753   ||  799|      810|     2009      2019      2029      2039      2049      2059      2069      2079      2089      2099      
                                              523| ||||||| 601           615||  699|        712|                734|   757|  799|      810|                                                                                                         
                                               551 |||||||  |             651|   701         715                 751    794   801      2000                                                                                                         
                                                 553||||||  |              694                                                                                                                                                                      
                                                  556|||||  |                                                                                                                                                                                       
                                                   561||||  |                                                                                                                                                                                       
                                                    562|||  |                                                                                                                                                                                       
                                                     571||  |                                                                                                                                                                                       
                                                      581|  |                                                                                                                                                                                       
                                                       596  |                                                                                                                                                                                       


Chain P from PDB  Type:PROTEIN  Length:12
                                             
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                5dmg P  419 MVDsPQLATLAD  430
                               |   428  
                             422-SEP    


Chain X from PDB  Type:PROTEIN  Length:7
                                        
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                5dmg X  419 MVDsPQL  425
                               |   
                             422-SEP


Chain Z from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                5dmg Z  420 VDsPQLATL  428
                              |      
                              |      
                            422-SEP
   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 5DMG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DMG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DMG)

(-) Gene Ontology  (53, 58)

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  Cis Peptide Bonds
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 Related Entries

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        TAU_HUMAN | P10636: 1i8h 2mz7 2on9 3ovl 4e0m 4e0n 4e0o 4fl5 4glr 4np8 4tqe 4y32 4y3b 4y5i 5e2v 5e2w 5hf3 5k7n

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