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(-) Description

Title :  CRYSTAL STRUCTURE OF GANTENERUMAB FAB FRAGMENT IN COMPLEX WITH ABETA 1-11
 
Authors :  J. Benz, D. Burger, H. R. Loetscher, B. Bohrmann
Date :  23 Jul 15  (Deposition) - 12 Aug 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,D,E,H,L
Biol. Unit 1:  D,H,L  (1x)
Biol. Unit 2:  A,B,E  (1x)
Keywords :  Antibody, Alzheimer, Abeta, Gantenerumab, Gant_abeta_1_11 09-A, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bohrmann, K. Baumann, J. Benz, F. Gerber, W. Huber, F. Knoflach, J. Messer, K. Oroszlan, R. Rauchenberger, W. F. Richter, C. Rothe, M. Urban, M. Bardroff, M. Winter, C. Nordstedt, H. Loetscher
Gantenerumab: A Novel Human Anti-Abeta Antibody Demonstrate Sustained Cerebral Amyloid-Beta Binding And Elicits Cell-Mediated Removal Of Human Amyloid-Beta.
J. Alzheimers Dis. V. 28 49 2012
PubMed-ID: 21955818  |  Reference-DOI: 10.3233/JAD-2011-110977

(-) Compounds

Molecule 1 - GANTENERUMAB FAB FRAGMENT HEAVY CHAIN
    Chains: H, A
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - GANTENERUMAB FAB FRAGMENT LIGHT CHAIN
    Chains: L, B
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - AMYLOID BETA A4 PROTEIN
    Chains: D, E
    Engineered: YES
    Fragment: UNP RESIDUES 672-682
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ABPP,APPI,APP,ALZHEIMER DISEASE AMYLOID PROTEIN,CEREBRAL VASCULAR AMYLOID PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABDEHL
Biological Unit 1 (1x):   D HL
Biological Unit 2 (1x): AB E  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS D:6 , SER D:8 , GLY D:9 , ARG H:57 , NAG H:300binding site for residue SO4 D 101
2AC2SOFTWAREARG A:57 , NAG A:300 , HIS E:6 , SER E:8 , GLY E:9binding site for residue SO4 E 101
3AC3SOFTWAREASN A:52 , ALA A:53 , SER A:54 , THR A:56 , ARG A:57 , GLU E:3 , SO4 E:101binding site for Mono-Saccharide NAG A 300 bound to ASN A 52
4AC4SOFTWAREALA D:2 , GLU D:3 , SO4 D:101 , ASN H:52 , SER H:54 , THR H:56 , ARG H:57binding site for Mono-Saccharide NAG H 300 bound to ASN H 52

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:96
2A:153 -A:209
3B:23 -B:89
4B:135 -B:195
5H:22 -H:96
6H:153 -H:209
7L:23 -L:89
8L:135 -L:195

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Phe H:159 -Pro H:160
2Glu H:161 -Pro H:162
3Ser L:7 -Pro L:8
4Met L:95 -Pro L:96
5Tyr L:141 -Pro L:142
6Phe A:159 -Pro A:160
7Glu A:161 -Pro A:162
8Ser B:7 -Pro B:8
9Met B:95 -Pro B:96
10Tyr B:141 -Pro B:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CSZ)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee....eeeee...eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5csz A   2 VELVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAINASGTRTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGKGYVRYFDVWGQGTLVTVSSASTKGPSVFPLAPSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 227
                                    11        21        31        41        51        61        71        81        91       101|      118       128       138 ||    155       165       175       185       195       205       215       225  
                                                                                                                             101|                            140|                                                                               
                                                                                                                              109                             148                                                                               


Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....hhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5csz B   1 DIVLTQSPATLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGVPARFSGSGSGTDFTLTISSLEPEDFATYYCLQIYNMPITFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 214
                                    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:11
                                           
               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
                 5csz D   1 DAEFRHDSGYE  11
                                    10 


Chain E from PDB  Type:PROTEIN  Length:10
                                          
               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
                 5csz E   1 DAEFRHDSGY  10
                                    10


Chain H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeee....eeeee...eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5csz H   2 VELVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAINASGTRTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGKGYVRYFDVWGQGTLVTVSSASTKGPSVFPLAPSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 228
                                    11        21        31        41        51        61        71        81        91       101|      118       128       138 ||    155       165       175       185       195       205       215       225   
                                                                                                                             101|                            140|                                                                                
                                                                                                                              109                             148                                                                                


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....hhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5csz L   1 DIVLTQSPATLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGVPARFSGSGSGTDFTLTISSLEPEDFATYYCLQIYNMPITFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 213
                                    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)
    → 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 5CSZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (111, 111)

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 Related Entries

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

UniProtKB/Swiss-Prot
        A4_HUMAN | P05067: 1aap 1amb 1amc 1aml 1ba4 1ba6 1bjb 1bjc 1brc 1ca0 1hz3 1iyt 1mwp 1owt 1qcm 1qwp 1qxc 1qyt 1taw 1tkn 1uo7 1uo8 1uoa 1uoi 1x11 1z0q 1ze7 1ze9 1zjd 2beg 2bom 2bp4 2fjz 2fk1 2fk2 2fk3 2fkl 2fma 2g47 2ipu 2lfm 2llm 2lmn 2lmo 2lmp 2lmq 2lnq 2loh 2lp1 2lz3 2lz4 2m4j 2m9r 2m9s 2mgt 2mj1 2mpz 2mvx 2mxu 2nao 2otk 2r0w 2wk3 2y29 2y2a 2y3j 2y3k 2y3l 3ayu 3bae 3bkj 3dxc 3dxd 3dxe 3gci 3ifl 3ifn 3ifo 3ifp 3jq5 3jql 3jti 3ktm 3l33 3l81 3moq 3mxc 3mxy 3nyj 3nyl 3ovj 3ow9 3sv1 3u0t 3umh 3umi 3umk 4hix 4jfn 4m1c 4mdr 4mvi 4mvk 4mvl 4nge 4ojf 4onf 4ong 4pqd 4pwq 4xxd 5aef 5am8 5amb 5buo 5c67 5how 5hox 5hoy 5kk3 5kna 5myo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5CSZ)