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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-MOUSE CD3EPSILON ANTIBODY 2C11 FAB FRAGMENT
 
Authors :  D. A. Shore, X. Zhu, I. A. Wilson
Date :  07 Mar 11  (Deposition) - 25 Jan 12  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,H,L
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  H,L  (1x)
Keywords :  Antibody, Anti-Cd3Epsilon, T-Cell Receptor, Signalling, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Fernandes, D. A. Shore, M. T. Vuong, C. Yu, X. Zhu, S. Pereira-Lopes, H. Brouwer, J. A. Fennelly, C. M. Jessup, E. J. Evans I. A. Wilson, S. J. Davis
T Cell Receptors Are Structures Capable Of Initiating Signaling In The Absence Of Large Conformational Rearrangements.
J. Biol. Chem. V. 287 13324 2012
PubMed-ID: 22262845  |  Reference-DOI: 10.1074/JBC.M111.332783

(-) Compounds

Molecule 1 - ANTI-MOUSE CD3EPSILON ANTIBODY 2C11 FAB LIGHT CHAIN
    Cell: HYBRIDOMA
    Chains: A, C, E, L
    Engineered: YES
    Organism Scientific: CRICETULUS MIGRATORIUS
    Organism Taxid: 10032
 
Molecule 2 - ANTI-MOUSE CD3EPSILON ANTIBODY 2C11 FAB HEAVY CHAIN
    Cell: HYBRIDOMA
    Chains: B, D, F, H
    Engineered: YES
    Organism Scientific: CRICETULUS MIGRATORIUS
    Organism Taxid: 10032

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFHL
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       HL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3R06)

(-) Sites  (0, 0)

(no "Site" information available for 3R06)

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:142 -B:208
5C:23 -C:88
6C:134 -C:194
7D:22 -D:92
8D:142 -D:208
9E:23 -E:88
10E:134 -E:194
11F:22 -F:92
12F:142 -F:208
13H:22 -H:92
14H:142 -H:208
15L:23 -L:88
16L:134 -L:194

(-) Cis Peptide Bonds  (24, 24)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Tyr A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:148 -Pro B:149
5Glu B:150 -Pro B:151
6Trp B:200 -Pro B:202
7Ser C:7 -Pro C:8
8Tyr C:94 -Pro C:95
9Tyr C:140 -Pro C:141
10Phe D:148 -Pro D:149
11Glu D:150 -Pro D:151
12Trp D:200 -Pro D:202
13Ser E:7 -Pro E:8
14Tyr E:94 -Pro E:95
15Tyr E:140 -Pro E:141
16Phe F:148 -Pro F:149
17Glu F:150 -Pro F:151
18Trp F:200 -Pro F:202
19Phe H:148 -Pro H:149
20Glu H:150 -Pro H:151
21Trp H:200 -Pro H:202
22Ser L:7 -Pro L:8
23Tyr L:94 -Pro L:95
24Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R06)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R06)

(-) Exons   (0, 0)

(no "Exon" information available for 3R06)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains d3r06a1 A:1-107 automated matches                                                                          d3r06a2 A:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r06 A   1 DIQMTQSPSSLPASLGDRVTINCQASQDISNYLNWYQQKPGKAPKLLIYYTNKLADGVPSRFSGSGSGRDSSFTISSLESEDIGSYYCQQYYNYPWTFGPGTKLEIKRADAKPTVSIFPPSSEQLGTGSATLVCFVNNFYPKDINVKWKVDGSEKRDGVLQSVTDQDSKDSTYSLSSTLSLTKADYERHNLYTCEVTHKTSTAAIVKTLNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee....eee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r06 B   1 EVQLVESGGGLVQPGKSLKLSCEASGFTFSGYGMHWVRQAPGRGLESVAYITSSSINIKYADAVKGRFTVSRDNAKNLLFLQMNILKSEDTAMYYCARFDWDKNYWGQGTMVTVSSAKTTAPSVYPLAPATTNTVTLGCLVKGYFPEPVTVIWNSGALTSGVHTFPSVLHSGLYSLSSSVTVPSSTWPSQTVTCNVAHPASSTTVDLKIE 226
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127|      143       153||||   168||     179||     191    |||204       214       226
                                                                              52A                            82A||               99|                       127|                 154|||    169|      180|          196|||                  223|
                                                                                                              82B|               101                        134                  156||     171       183           199||                   226
                                                                                                               82C                                                                157|                              200|                      
                                                                                                                                                                                   162                               202                      


Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d3r06c1 C:1-107 automated matches                                                                          d3r06c2 C:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r06 C   1 DIQMTQSPSSLPASLGDRVTINCQASQDISNYLNWYQQKPGKAPKLLIYYTNKLADGVPSRFSGSGSGRDSSFTISSLESEDIGSYYCQQYYNYPWTFGPGTKLEIKRADAKPTVSIFPPSSEQLGTGSATLVCFVNNFYPKDINVKWKVDGSEKRDGVLQSVTDQDSKDSTYSLSSTLSLTKADYERHNLYTCEVTHKTSTAAIVKTLNRNE 213
                                    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:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee....eee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r06 D   1 EVQLVESGGGLVQPGKSLKLSCEASGFTFSGYGMHWVRQAPGRGLESVAYITSSSINIKYADAVKGRFTVSRDNAKNLLFLQMNILKSEDTAMYYCARFDWDKNYWGQGTMVTVSSAKTTAPSVYPLAPACTTNTVTLGCLVKGYFPEPVTVIWNSGALTSGVHTFPSVLHSGLYSLSSSVTVPSSTWPSQTVTCNVAHPASSTTVDLKIE 226
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127||     142       152 ||||  167 ||    178 ||    190     ||203       213       223|
                                                                              52A                            82A||               99|                        128|                 154|||    169|      180|          196|||                  223|
                                                                                                              82B|               101                         134                  156||     171       183           199||                   226
                                                                                                               82C                                                                 157|                              200|                      
                                                                                                                                                                                    162                               202                      


Chain E from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d3r06e1 E:1-107 automated matches                                                                          d3r06e2 E:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r06 E   1 DIQMTQSPSSLPASLGDRVTINCQASQDISNYLNWYQQKPGKAPKLLIYYTNKLADGVPSRFSGSGSGRDSSFTISSLESEDIGSYYCQQYYNYPWTFGPGTKLEIKRADAKPTVSIFPPSSEQLGTGSATLVCFVNNFYPKDINVKWKVDGSEKRDGVLQSVTDQDSKDSTYSLSSTLSLTKADYERHNLYTCEVTHKTSTAAIVKTLNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain F from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee....eee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r06 F   1 EVQLVESGGGLVQPGKSLKLSCEASGFTFSGYGMHWVRQAPGRGLESVAYITSSSINIKYADAVKGRFTVSRDNAKNLLFLQMNILKSEDTAMYYCARFDWDKNYWGQGTMVTVSSAKTTAPSVYPLAPACTTNTVTLGCLVKGYFPEPVTVIWNSGALTSGVHTFPSVLHSGLYSLSSSVTVPSSTWPSQTVTCNVAHPASSTTVDLKIE 226
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127||     142       152 ||||  167 ||    178 ||    190     ||203       213       223|
                                                                              52A                            82A||               99|                        128|                 154|||    169|      180|          196|||                  223|
                                                                                                              82B|               101                         134                  156||     171       183           199||                   226
                                                                                                               82C                                                                 157|                              200|                      
                                                                                                                                                                                    162                               202                      


Chain H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee....eee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r06 H   1 EVQLVESGGGLVQPGKSLKLSCEASGFTFSGYGMHWVRQAPGRGLESVAYITSSSINIKYADAVKGRFTVSRDNAKNLLFLQMNILKSEDTAMYYCARFDWDKNYWGQGTMVTVSSAKTTAPSVYPLAPACTTNTVTLGCLVKGYFPEPVTVIWNSGALTSGVHTFPSVLHSGLYSLSSSVTVPSSTWPSQTVTCNVAHPASSTTVDLKIE 226
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   107       117       127||     142       152 ||||  167 ||    178 ||    190     ||203       213       223|
                                                                              52A                            82A||               99|                        128|                 154|||    169|      180|          196|||                  223|
                                                                                                              82B|               101                         134                  156||     171       183           199||                   226
                                                                                                               82C                                                                 157|                              200|                      
                                                                                                                                                                                    162                               202                      


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d3r06l1 L:1-107 automated matches                                                                          d3r06l2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r06 L   1 DIQMTQSPSSLPASLGDRVTINCQASQDISNYLNWYQQKPGKAPKLLIYYTNKLADGVPSRFSGSGSGRDSSFTISSLESEDIGSYYCQQYYNYPWTFGPGTKLEIKRADAKPTVSIFPPSSEQLGTGSATLVCFVNNFYPKDINVKWKVDGSEKRDGVLQSVTDQDSKDSTYSLSSTLSLTKADYERHNLYTCEVTHKTSTAAIVKTLNRNE 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)
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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  (1, 8)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R06)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R06)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3R06)

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  Cis Peptide Bonds
    Glu B:150 - Pro B:151   [ RasMol ]  
    Glu D:150 - Pro D:151   [ RasMol ]  
    Glu F:150 - Pro F:151   [ RasMol ]  
    Glu H:150 - Pro H:151   [ RasMol ]  
    Phe B:148 - Pro B:149   [ RasMol ]  
    Phe D:148 - Pro D:149   [ RasMol ]  
    Phe F:148 - Pro F:149   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Ser C:7 - Pro C:8   [ RasMol ]  
    Ser E:7 - Pro E:8   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp B:200 - Pro B:202   [ RasMol ]  
    Trp D:200 - Pro D:202   [ RasMol ]  
    Trp F:200 - Pro F:202   [ RasMol ]  
    Trp H:200 - Pro H:202   [ RasMol ]  
    Tyr A:140 - Pro A:141   [ RasMol ]  
    Tyr A:94 - Pro A:95   [ RasMol ]  
    Tyr C:140 - Pro C:141   [ RasMol ]  
    Tyr C:94 - Pro C:95   [ RasMol ]  
    Tyr E:140 - Pro E:141   [ RasMol ]  
    Tyr E:94 - Pro E:95   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Tyr L:94 - Pro L:95   [ RasMol ]  
 
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  3r06
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 Related Entries

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3r08