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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTIBODY 93F3 UNSTABLE VARIANT
 
Authors :  F. Wang
Date :  02 Feb 13  (Deposition) - 13 Mar 13  (Release) - 22 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.58
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Antibody Maturation, Antibody Stability, Clonal Selection, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Wang, S. Sen, Y. Zhang, I. Ahmad, X. Zhu, I. A. Wilson, V. V. Smider, T. J. Magliery, P. G. Schultz
Somatic Hypermutation Maintains Antibody Thermodynamic Stability During Affinity Maturation.
Proc. Natl. Acad. Sci. Usa V. 110 4261 2013
PubMed-ID: 23440204  |  Reference-DOI: 10.1073/PNAS.1301810110

(-) Compounds

Molecule 1 - ANTIBODY 93F3 LIGHT CHAIN
    Chains: A, C, E
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - ANTIBODY 93F3 HEAVY CHAIN
    Chains: B, D, F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4J1U)

(-) Sites  (0, 0)

(no "Site" information available for 4J1U)

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:23 -A:94
2A:139 -A:199
3B:22 -B:95
4B:144 -B:200
5C:23 -C:94
6C:139 -C:199
7D:22 -D:95
8D:144 -D:200
9E:23 -E:94
10E:139 -E:199
11F:22 -F:95
12F:144 -F:200

(-) Cis Peptide Bonds  (29, 29)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Gly A:47 -Gln A:48
3Tyr A:145 -Pro A:146
4Arg A:147 -Glu A:148
5Gly B:55 -Ser B:56
6Gly B:104 -Asp B:105
7Phe B:150 -Pro B:151
8Glu B:152 -Pro B:153
9Val B:154 -Thr B:155
10Ser C:7 -Pro C:8
11Gly C:47 -Gln C:48
12Gln C:48 -Ser C:49
13Tyr C:145 -Pro C:146
14Gly D:104 -Asp D:105
15Val D:113 -Thr D:114
16Phe D:150 -Pro D:151
17Glu D:152 -Pro D:153
18Val D:154 -Thr D:155
19Ile D:199 -Cys D:200
20Asn D:201 -Val D:202
21Ser E:7 -Pro E:8
22Gly E:47 -Gln E:48
23Tyr E:145 -Pro E:146
24Arg E:147 -Glu E:148
25Ser E:161 -Gly E:162
26Ala F:140 -Ala F:141
27Phe F:150 -Pro F:151
28Glu F:152 -Pro F:153
29Pro F:217 -Lys F:218

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J1U)

(-) Exons   (0, 0)

(no "Exon" information available for 4J1U)

(-) 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:210
                                                                                                                                                                                                                                                  
               SCOP domains d4j1ua1 A:1-112 automated matches                                                                           d4j1ua2 A:113-214 automated matches                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh...eeeeee.......eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j1u A   1 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNKNYLAWYQQKPGQSPTKLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYDLPTFGAGTKLELKRSVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSF 214
                                    10        20        30||      44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214
                                                         31|                                                                                                                                                                                  
                                                          36                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeee.........eeeee........eeeee......eeeeeeeeeee......eee.hhh....eee...ee.....eeeeeeeeee.hhhh...eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1u B   1 QVQLKESGPGLVAPSQSLSITCTVSGFSLTDYGVSWIRQPPGKGLEWLGVIWGGGSTYYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTAMYYCAKPGDSWGQGTSVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 217
                                    10        20        30        40        50        60        70        80        90      |105       115       125      |139       149       159       169       179       189       199       209        
                                                                                                                           97|                          132|                                                                                
                                                                                                                           103                           137                                                                                


Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4j1uc1 C:1-112 automated matches                                                                               d4j1uc2 C:113-216 automated matches                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee....eeeeee.....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee........eeeeeee.....ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeee.......eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1u C   1 DIVMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPTKLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYDLPTFGAGTKLELKRSVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHACEVTHQGLSSPVTKSFNR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190   ||  203       213   
                                                                                                                                                                                                                           194|                  
                                                                                                                                                                                                                            198                  


Chain D from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..........eeeeeeee.......eeeeeee......eeeeee.....eee...hhh.eeeeee....eeeeee...hhhhh.eeeeeee.........................eeeee....eeeeeeeeeee......eee.........ee...ee.....eeeeeeeeee.hhhh.....eeeeehhhhee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j1u D   2 VQLKESGPGLVAPSQSLSITCTVSGFSLTDYGVSWIRQPPGKGLEWLGVIWGGGSTYYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTAMYYCAKHTYGGPGDSWGQGTSVTVSSASTKGPSVFPLAPGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       137       147       157       167       177       187       197       207       217
                                                                                                                                                          130|                                                                                
                                                                                                                                                           137                                                                                


Chain E from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d4j1ue1 E:3-112 automated matches                                                                             d4j1ue2 E:113-216 automated matches                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.....ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1u E   3 VMSQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPTKLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSYDLPTFGAGTKLELKRSVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212    


Chain F from PDB  Type:PROTEIN  Length:207
                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeee........eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhhh.eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1u F   2 VQLKESGPGLVAPSQSLSITCTVSGFSLTDYGVSWIRQPPGKGLEWLGVIWGGGSTYYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTAMYYCAKHTDSWGQGTSVTVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 218
                                    11        21        31        41        51        61        71        81        91       106       116       126   ||  141       151       161       171       181       191       201       211       
                                                                                                                            99|                      130|                                                                                  
                                                                                                                            105                       136
   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  (2, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J1U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J1U)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4J1U)

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(no "Sites" information available for 4j1u)
 
  Cis Peptide Bonds
    Ala F:140 - Ala F:141   [ RasMol ]  
    Arg A:147 - Glu A:148   [ RasMol ]  
    Arg E:147 - Glu E:148   [ RasMol ]  
    Asn D:201 - Val D:202   [ RasMol ]  
    Gln C:48 - Ser C:49   [ RasMol ]  
    Glu B:152 - Pro B:153   [ RasMol ]  
    Glu D:152 - Pro D:153   [ RasMol ]  
    Glu F:152 - Pro F:153   [ RasMol ]  
    Gly A:47 - Gln A:48   [ RasMol ]  
    Gly B:104 - Asp B:105   [ RasMol ]  
    Gly B:55 - Ser B:56   [ RasMol ]  
    Gly C:47 - Gln C:48   [ RasMol ]  
    Gly D:104 - Asp D:105   [ RasMol ]  
    Gly E:47 - Gln E:48   [ RasMol ]  
    Ile D:199 - Cys D:200   [ RasMol ]  
    Phe B:150 - Pro B:151   [ RasMol ]  
    Phe D:150 - Pro D:151   [ RasMol ]  
    Phe F:150 - Pro F:151   [ RasMol ]  
    Pro F:217 - Lys F:218   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Ser C:7 - Pro C:8   [ RasMol ]  
    Ser E:161 - Gly E:162   [ RasMol ]  
    Ser E:7 - Pro E:8   [ RasMol ]  
    Tyr A:145 - Pro A:146   [ RasMol ]  
    Tyr C:145 - Pro C:146   [ RasMol ]  
    Tyr E:145 - Pro E:146   [ RasMol ]  
    Val B:154 - Thr B:155   [ RasMol ]  
    Val D:113 - Thr D:114   [ RasMol ]  
    Val D:154 - Thr D:155   [ RasMol ]  
 
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  4j1u
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