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(-) Description

Title :  ELECTRON CRYO-MICROSCOPY OF CHIKUNGUNYA VLP IN COMPLEX WITH NEUTRALIZING ANTIBODY FAB M242
 
Authors :  S. Sun, Y. Xiang, M. G. Rossmann
Date :  28 Jan 13  (Deposition) - 24 Apr 13  (Release) - 24 Apr 13  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  15.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D,E,F,G,H  (60x)
Keywords :  Alpha Virus, Chikungunya Vlp, Neutralizing Antibody M242, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sun, Y. Xiang, W. Akahata, H. Holdaway, P. Pal, X. Zhang, M. S. Diamond, G. J. Nabel, M. G. Rossmann
Structural Analyses At Pseudo Atomic Resolution Of Chikungunya Virus And Antibodies Show Mechanisms Of Neutralization.
Elife V. 2 00435 2013
PubMed-ID: 23577234  |  Reference-DOI: 10.7554/ELIFE.00435

(-) Compounds

Molecule 1 - M242 LIGHT CHAIN
    Chains: A, C, E, G
    Fragment: FAB
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - M242 HEAVY CHAIN
    Chains: B, D, F, H
    Fragment: FAB
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (60x): ABCDEFGH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3J2X)

(-) Sites  (0, 0)

(no "Site" information available for 3J2X)

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:23 -A:92
2A:138 -A:198
3B:522 -B:596
4B:644 -B:699
5C:1023 -C:1092
6C:1138 -C:1198
7D:1522 -D:1596
8D:1644 -D:1699
9E:2023 -E:2092
10E:2138 -E:2198
11F:2522 -F:2596
12F:2644 -F:2699
13G:3023 -G:3092
14G:3138 -G:3198
15H:3522 -H:3596
16H:3644 -H:3699

(-) Cis Peptide Bonds  (36, 36)

Asymmetric Unit
No.Residues
1Ser A:7 -Pro A:8
2Asn A:80 -Pro A:81
3Glu A:97 -Asp A:98
4Tyr A:144 -Pro A:145
5Gly B:601 -Tyr B:602
6Val B:615 -Ser B:616
7Phe B:650 -Pro B:651
8Glu B:652 -Pro B:653
9Trp B:692 -Pro B:693
10Ser C:1007 -Pro C:1008
11Asn C:1080 -Pro C:1081
12Glu C:1097 -Asp C:1098
13Tyr C:1144 -Pro C:1145
14Gly D:1601 -Tyr D:1602
15Val D:1615 -Ser D:1616
16Phe D:1650 -Pro D:1651
17Glu D:1652 -Pro D:1653
18Trp D:1692 -Pro D:1693
19Ser E:2007 -Pro E:2008
20Asn E:2080 -Pro E:2081
21Glu E:2097 -Asp E:2098
22Tyr E:2144 -Pro E:2145
23Gly F:2601 -Tyr F:2602
24Val F:2615 -Ser F:2616
25Phe F:2650 -Pro F:2651
26Glu F:2652 -Pro F:2653
27Trp F:2692 -Pro F:2693
28Ser G:3007 -Pro G:3008
29Asn G:3080 -Pro G:3081
30Glu G:3097 -Asp G:3098
31Tyr G:3144 -Pro G:3145
32Gly H:3601 -Tyr H:3602
33Val H:3615 -Ser H:3616
34Phe H:3650 -Pro H:3651
35Glu H:3652 -Pro H:3653
36Trp H:3692 -Pro H:3693

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3J2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3J2X)

(-) Exons   (0, 0)

(no "Exon" information available for 3J2X)

(-) 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:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....hhhhh..eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j2x A    1 DIVLTQSPASLAVSLGQRATISCRASESVDSYGNSFMNWYQQKPGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPFTFGSGTKLEIKRADAAPTVSIFPPSSKLGTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  217
                                    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:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...ee......eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhh.eeeeeeee..eeeee...eeee.........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j2x B  501 QVQLQQSGPELVKPGVSVKISCKASGYSFTSFYIYWVKQRPGQGLEWIGWIFPGSTNTKYNEKFKGKATLTADTSSSTASMQLSSLTSEDSAVYFCARVDGYAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  717
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       


Chain C from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....hhhhh..eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j2x C 1001 DIVLTQSPASLAVSLGQRATISCRASESVDSYGNSFMNWYQQKPGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPFTFGSGTKLEIKRADAAPTVSIFPPSSKLGTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 1217
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210       


Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...ee......eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhh.eeeeeeee..eeeee...eeee.........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j2x D 1501 QVQLQQSGPELVKPGVSVKISCKASGYSFTSFYIYWVKQRPGQGLEWIGWIFPGSTNTKYNEKFKGKATLTADTSSSTASMQLSSLTSEDSAVYFCARVDGYAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 1717
                                  1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610      1620      1630      1640      1650      1660      1670      1680      1690      1700      1710       


Chain E from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....hhhhh..eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j2x E 2001 DIVLTQSPASLAVSLGQRATISCRASESVDSYGNSFMNWYQQKPGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPFTFGSGTKLEIKRADAAPTVSIFPPSSKLGTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 2217
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210       


Chain F from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...ee......eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhh.eeeeeeee..eeeee...eeee.........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j2x F 2501 QVQLQQSGPELVKPGVSVKISCKASGYSFTSFYIYWVKQRPGQGLEWIGWIFPGSTNTKYNEKFKGKATLTADTSSSTASMQLSSLTSEDSAVYFCARVDGYAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 2717
                                  2510      2520      2530      2540      2550      2560      2570      2580      2590      2600      2610      2620      2630      2640      2650      2660      2670      2680      2690      2700      2710       


Chain G from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....hhhhh..eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j2x G 3001 DIVLTQSPASLAVSLGQRATISCRASESVDSYGNSFMNWYQQKPGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPFTFGSGTKLEIKRADAAPTVSIFPPSSKLGTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 3217
                                  3010      3020      3030      3040      3050      3060      3070      3080      3090      3100      3110      3120      3130      3140      3150      3160      3170      3180      3190      3200      3210       


Chain H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...ee......eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhh.eeeeeeee..eeeee...eeee.........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3j2x H 3501 QVQLQQSGPELVKPGVSVKISCKASGYSFTSFYIYWVKQRPGQGLEWIGWIFPGSTNTKYNEKFKGKATLTADTSSSTASMQLSSLTSEDSAVYFCARVDGYAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 3717
                                  3510      3520      3530      3540      3550      3560      3570      3580      3590      3600      3610      3620      3630      3640      3650      3660      3670      3680      3690      3700      3710
   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 3J2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3J2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3J2X)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3J2X)

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Asymmetric Unit
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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 3j2x)
 
  Cis Peptide Bonds
    Asn A:80 - Pro A:81   [ RasMol ]  
    Asn C:1080 - Pro C:1081   [ RasMol ]  
    Asn E:2080 - Pro E:2081   [ RasMol ]  
    Asn G:3080 - Pro G:3081   [ RasMol ]  
    Glu A:97 - Asp A:98   [ RasMol ]  
    Glu B:652 - Pro B:653   [ RasMol ]  
    Glu C:1097 - Asp C:1098   [ RasMol ]  
    Glu D:1652 - Pro D:1653   [ RasMol ]  
    Glu E:2097 - Asp E:2098   [ RasMol ]  
    Glu F:2652 - Pro F:2653   [ RasMol ]  
    Glu G:3097 - Asp G:3098   [ RasMol ]  
    Glu H:3652 - Pro H:3653   [ RasMol ]  
    Gly B:601 - Tyr B:602   [ RasMol ]  
    Gly D:1601 - Tyr D:1602   [ RasMol ]  
    Gly F:2601 - Tyr F:2602   [ RasMol ]  
    Gly H:3601 - Tyr H:3602   [ RasMol ]  
    Phe B:650 - Pro B:651   [ RasMol ]  
    Phe D:1650 - Pro D:1651   [ RasMol ]  
    Phe F:2650 - Pro F:2651   [ RasMol ]  
    Phe H:3650 - Pro H:3651   [ RasMol ]  
    Ser A:7 - Pro A:8   [ RasMol ]  
    Ser C:1007 - Pro C:1008   [ RasMol ]  
    Ser E:2007 - Pro E:2008   [ RasMol ]  
    Ser G:3007 - Pro G:3008   [ RasMol ]  
    Trp B:692 - Pro B:693   [ RasMol ]  
    Trp D:1692 - Pro D:1693   [ RasMol ]  
    Trp F:2692 - Pro F:2693   [ RasMol ]  
    Trp H:3692 - Pro H:3693   [ RasMol ]  
    Tyr A:144 - Pro A:145   [ RasMol ]  
    Tyr C:1144 - Pro C:1145   [ RasMol ]  
    Tyr E:2144 - Pro E:2145   [ RasMol ]  
    Tyr G:3144 - Pro G:3145   [ RasMol ]  
    Val B:615 - Ser B:616   [ RasMol ]  
    Val D:1615 - Ser D:1616   [ RasMol ]  
    Val F:2615 - Ser F:2616   [ RasMol ]  
    Val H:3615 - Ser H:3616   [ RasMol ]  
 
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  3j2x
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

3j2w 3j2y 3j2z 3j30 4gq8