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(-) Description

Title :  CRYSTAL STRUCTURE OF BROADLY NEUTRALIZING ANTIBODY CR8043
 
Authors :  P. S. Lee, I. A. Wilson
Date :  14 Nov 13  (Deposition) - 25 Dec 13  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  H,I,L,M
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  I,M  (1x)
Keywords :  Immune System, Immune Recognition, Antibody, Fab, Immunoglobulin, Influenza Hemagglutinin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. H. Friesen, P. S. Lee, E. J. Stoop, R. M. Hoffman, D. C. Ekiert, G. Bhabha, W. Yu, J. Juraszek, W. Koudstaal, M. Jongeneelen, H. J. Korse, C. Ophorst, E. C. Brinkman-Van Der Linden, M. Throsby, M. J. Kwakkenbos, A. Q. Bakker, T. Beaumont, H. Spits, T. Kwaks, R. Vogels, A. B. Ward, J. Goudsmit, I. A. Wilson
A Common Solution To Group 2 Influenza Virus Neutralization
Proc. Natl. Acad. Sci. Usa V. 111 445 2014
PubMed-ID: 24335589  |  Reference-DOI: 10.1073/PNAS.1319058110

(-) Compounds

Molecule 1 - ANTIBODY CR8043, LIGHT CHAIN
    Chains: L, M
    Organism Common: HUMAN, HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IMMUNOGLOBULIN KAPPA LIGHT CHAIN EU
 
Molecule 2 - ANTIBODY CR8043, HEAVY CHAIN
    Chains: H, I
    Organism Common: HUMAN, HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : HILM
Biological Unit 1 (1x): H L 
Biological Unit 2 (1x):  I M

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN L:37 , LYS L:45 , ALA L:81 , ASP L:82BINDING SITE FOR RESIDUE PEG L 301
2AC2SOFTWAREPHE H:166 , PRO H:167 , ALA H:168 , SER H:177 , LEU H:178 , SER H:179 , GLN L:160 , SER L:162 , SER L:176 , SER L:177 , THR L:178BINDING SITE FOR RESIDUE PEG L 302
3AC3SOFTWAREGLY I:42 , GLN I:43 , GLN M:38 , PRO M:40 , GLY M:41 , GLN M:42BINDING SITE FOR RESIDUE PEG I 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3I:22 -I:92
4I:140 -I:196
5L:23 -L:88
6L:134 -L:194
7M:23 -M:88
8M:134 -M:194

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Ala L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149
6Ser M:7 -Pro M:8
7Ala M:94 -Pro M:95
8Tyr M:140 -Pro M:141
9Phe I:146 -Pro I:147
10Glu I:148 -Pro I:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NM4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NM4)

(-) Exons   (0, 0)

(no "Exon" information available for 4NM4)

(-) 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 H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nm4 H    1 QVQLVQSGAEVKKPGASVKLSCKASGYTFTAYSMHWVRQAPGQSLEWLGWINTAIGNTQYSQKFQDRVTITRDTSARTSYMELSSLRSGDTAVYFCARGASWDARGWSGYWGKGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122     ||136       146       156       166       176       186       196       206         
                                                                              52A                            82A||               100A|||                         128|                                                                                  
                                                                                                              82B|                100B||                          133                                                                                  
                                                                                                               82C                 100C|                                                                                                               
                                                                                                                                    100D                                                                                                               


Chain I from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nm4 I    1 QVQLVQSGAEVKKPGASVKLSCKASGYTFTAYSMHWVRQAPGQSLEWLGWINTAIGNTQYSQKFQDRVTITRDTSARTSYMELSSLRSGDTAVYFCARGASWDARGWSGYWGKGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122       132       142       152       162       172       182       192       202       212   
                                                                              52A                            82A||               100A|||                                                                                                                   
                                                                                                              82B|                100B||                                                                                                                   
                                                                                                               82C                 100C|                                                                                                                   
                                                                                                                                    100D                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d4nm4l1 L:1-107 automated matches                                                                                d4nm4l2 L:108-213 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..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nm4 L    1 DIQMTQSPDSLAVSLGERATINCKSSQSVFSSSTNKNYLAWYQQKPGQPPKVLIYWSSTRESGVPDRFSASGSGTDFTLTISSLQAADVAVYYCHQYYTAPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
                                                     27A|||||                                                                                                                                                                                          
                                                      27B||||                                                                                                                                                                                          
                                                       27C|||                                                                                                                                                                                          
                                                        27D||                                                                                                                                                                                          
                                                         27E|                                                                                                                                                                                          
                                                          27F                                                                                                                                                                                          


Chain M from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d4nm4m1 M:1-107 automated matches                                                                                d4nm4m2 M: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..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nm4 M    1 DIQMTQSPDSLAVSLGERATINCKSSQSVFSSSTNKNYLAWYQQKPGQPPKVLIYWSSTRESGVPDRFSASGSGTDFTLTISSLQAADVAVYYCHQYYTAPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20       27C|||     34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
                                                     27A|||||                                                                                                                                                                                          
                                                      27B||||                                                                                                                                                                                          
                                                       27C|||                                                                                                                                                                                          
                                                        27D||                                                                                                                                                                                          
                                                         27E|                                                                                                                                                                                          
                                                          27F
   Legend:   → Mismatch (orange background)
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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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NM4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NM4)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IGKC_HUMAN | P01834: 1a4j 1a4k 1cly 1d5b 1d5i 1d6v 1dfb 1gaf 1hez 1hkl 1hzh 1i7z 1mim 1n0x 1om3 1op3 1op5 1ucb 2ny7 2o5x 2o5y 2o5z 2qqk 2qql 2qqn 2qsc 2r56 2rfx 2vxq 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3cfj 3cfk 3csy 3d0l 3d85 3dvg 3dvn 3eyf 3eyo 3eyq 3iu3 3o11 3qct 3qcu 3qcv 3ru8 3u0w 3u7w 3u7y 3vh8 3wuw 3x11 3x12 4d3c 4d9r 4hix 4nm8 4xmp 4xny 4xnz 4xxd 4ydv 5b38 5b39 5c7k 5esv 5esz 5ewi 5veb 5viy
        IGK_HUMAN | P0DOX7: 4nm8 5vic 5vig
        Q6N089_HUMAN | Q6N089: 2oqj 3mnv 3qct 3qcu 3qcv 4nm8 4nuj 5ewi 5ug0
        S6C4S0_HUMAN | S6C4S0: 4o58 4o5i 5ugy
UniProtKB/TrEMBL
        Q6N089_HUMAN | Q6N089: 1u6a 3cfj 3cfk 4hpy
        S6C4S0_HUMAN | S6C4S0: 4nm8

(-) Related Entries Specified in the PDB File

4mn8