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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 2009 PANDEMIC H1N1 INFLUENZA VIRUS NEURAMINIDASE WITH A NEUTRALIZING ANTIBODY
 
Authors :  H. Q. Wan, H. Yang, D. A. Shore, R. J. Garten, L. Couzens, J. Gao, L. L. Jian P. J. Carney, J. Villanueva, J. Stevens, M. C. Eichelberger
Date :  18 Jun 14  (Deposition) - 11 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,E,F,H,L
Biol. Unit 1:  A,B,E,F,H,L  (4x)
Keywords :  Influenza, Neuraminidase, Antibody, Neutralizing Antibody, Hydrolase- Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wan, H. Yang, D. A. Shore, R. J. Garten, L. Couzens, J. Gao, L. Jiang, P. J. Carney, J. Villanueva, J. Stevens, M. C. Eichelberger
Structural Characterization Of A Protective Epitope Spannin A(H1N1)Pdm09 Influenza Virus Neuraminidase Monomers.
Nat Commun V. 6 6114 2015
PubMed-ID: 25668439  |  Reference-DOI: 10.1038/NCOMMS7114

(-) Compounds

Molecule 1 - NEURAMINIDASE
    Chains: A, B
    EC Number: 3.2.1.18
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 82-467
    Gene: NA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
 
Molecule 2 - NEUTRALIZING ANTIBODY, LIGHT CHAIN
    Cell: HYBRIDOMA
    Chains: F, L
    Engineered: YES
    Fragment: FAB
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 3 - NEUTRALIZING ANTIBODY, HEAVY CHAIN
    Cell: HYBRIDOMA
    Chains: E, H
    Engineered: YES
    Fragment: FAB
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABEFHL
Biological Unit 1 (4x): ABEFHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 32)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NAG32Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:294 , GLY A:298 , ASP A:324 , GLY A:342 , ASN A:344 , HOH A:635BINDING SITE FOR RESIDUE CA A 505
02AC2SOFTWAREASP A:376 , ASN A:378 , ASP A:384 , ASN A:386BINDING SITE FOR RESIDUE CA A 506
03AC3SOFTWAREASP B:294 , GLY B:298 , ASP B:324 , GLY B:342 , ASN B:344 , HOH B:611BINDING SITE FOR RESIDUE CA B 505
04AC4SOFTWAREASP B:376 , ASN B:378 , ASP B:384 , ASN B:386BINDING SITE FOR RESIDUE CA B 506
05AC5SOFTWAREASN A:88BINDING SITE FOR MONO-SACCHARIDE NAG A 504 BOUND TO ASN A 88
06AC6SOFTWAREASN A:146 , THR A:148BINDING SITE FOR MONO-SACCHARIDE NAG A 503 BOUND TO ASN A 146
07AC7SOFTWAREASN A:235 , GLN A:308BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 235 RESIDUES 501 TO 502
08AC8SOFTWAREASN B:88 , SER B:89 , HOH B:624 , HOH B:645 , HOH B:646BINDING SITE FOR MONO-SACCHARIDE NAG B 502 BOUND TO ASN B 88
09AC9SOFTWAREASN B:146 , HOH B:625BINDING SITE FOR MONO-SACCHARIDE NAG B 501 BOUND TO ASN B 146
10BC1SOFTWAREASN B:235 , GLN B:308BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 235 RESIDUES 503 TO 504

(-) SS Bonds  (24, 24)

Asymmetric Unit
No.Residues
1A:92 -A:417
2A:124 -A:129
3A:184 -A:231
4A:233 -A:238
5A:279 -A:292
6A:281 -A:290
7A:318 -A:335
8A:421 -A:446
9B:92 -B:417
10B:124 -B:129
11B:184 -B:231
12B:233 -B:238
13B:279 -B:292
14B:281 -B:290
15B:318 -B:335
16B:421 -B:446
17E:22 -E:98
18E:151 -E:206
19F:23 -F:87
20F:133 -F:193
21H:22 -H:98
22H:151 -H:206
23L:23 -L:87
24L:133 -L:193

(-) Cis Peptide Bonds  (18, 18)

Asymmetric Unit
No.Residues
1Asn A:325 -Pro A:326
2Arg A:430 -Pro A:431
3Leu A:463 -Pro A:464
4Asn B:325 -Pro B:326
5Arg B:430 -Pro B:431
6Leu B:463 -Pro B:464
7Ser F:7 -Pro F:8
8Asn F:93 -Pro F:94
9Tyr F:139 -Pro F:140
10Phe E:157 -Pro E:158
11Glu E:159 -Pro E:160
12Trp E:199 -Pro E:200
13Ser L:7 -Pro L:8
14Asn L:93 -Pro L:94
15Tyr L:139 -Pro L:140
16Phe H:157 -Pro H:158
17Glu H:159 -Pro H:160
18Trp H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QNP)

(-) 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhh....eeee...eee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeeee....eeeee.................................eeee..eeeeee.......eeeeeeee............eeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee........eeeeeeeeeee................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qnp A  82 SVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTI 467
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461      


Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhh....eeee...eee....eeeeeeeeeee..hhhhh..........eeeeee..........eeeee..eeeeee....eeeeeee......eeeeee..eeeeeee..............eee..eeeeeeee.......eeeeeeee..eeeeeee........eeeeeeee..eeeeeee........eeeeee....eeeee.................................eeee..eeeeee.......eeeeeeee............eeeeeeeeeee...eeeeeehhhhhh....eeeeeeeeeee........eeeeeeeeeee................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qnp B  82 SVKLAGNSSLCPVSGWAIYSKDNSVRIGSKGDVFVIREPFISCSPLECRTFFLTQGALLNDKHSNGTIKDRSPYRTLMSCPIGEVPSPYNSRFESVAWSASACHDGINWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTVMTDGPSNGQASYKIFRIEKGKIVKSVEMNAPNYHYEECSCYPDSSEITCVCRDNWHGSNRPWVSFNQNLEYQIGYICSGIFGDNPRPNDKTGSCGPVSSNGANGVKGFSFKYGNGVWIGRTKSISSRNGFEMIWDPNGWTGTDNNFSIKQDIVGINEWSGYSGSFVQHPELTGLDCIRPCFWVELIRGRPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFTI 467
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461      


Chain E from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhhh..eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee..hhhhh..eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qnp E   1 QVKLQESGGGLVQPKGSLKLSCAASGFTFNTYAMNWVRQAPGKGLEWVARIRSKSNNYATFYADSVKDRFTISRDDSQSMLYLQMHNLKTDDTAMYYCVRPSIYYYASGYLDVWGAGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    


Chain F from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qnp F   1 QIVLSQSPAILSASPGEKVTMTCRTSSSVSYMHWYQQKPGSSPKPWIYATSNLASGVPFRFSGSGSGTSYSLTISRVEAEDAATYYCQQWNSNPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  


Chain H from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhhh..eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee..hhhhh..eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qnp H   1 QVKLQESGGGLVQPKGSLKLSCAASGFTFNTYAMNWVRQAPGKGLEWVARIRSKSNNYATFYADSVKDRFTISRDDSQSMLYLQMHNLKTDDTAMYYCVRPSIYYYASGYLDVWGAGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qnp L   1 QIVLSQSPAILSASPGEKVTMTCRTSSSVSYMHWYQQKPGSSPKPWIYATSNLASGVPFRFSGSGSGTSYSLTISRVEAEDAATYYCQQWNSNPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 211
                                    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)
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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  (0, 0)

(no "SCOP Domain" information available for 4QNP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 44)

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_MOUSE | P01837: 15c8 1a0q 1a3l 1ahw 1ai1 1aif 1c12 1cf8 1cfn 1cfq 1cfs 1cft 1cic 1ck0 1ct8 1dqj 1dqm 1dqq 1e4w 1e4x 1ehl 1emt 1f11 1fai 1fbi 1fdl 1fe8 1fgn 1fj1 1fl3 1fns 1frg 1fsk 1gpo 1hh6 1hh9 1hi6 1i8m 1iai 1igy 1jnl 1jnn 1jrh 1k4c 1k4d 1kb5 1kc5 1kcr 1kcs 1kcu 1kcv 1ken 1kno 1lo0 1mf2 1mh5 1mlb 1mlc 1n5y 1n6q 1nby 1nbz 1ndg 1ndm 1oak 1ob1 1orq 1ors 1osp 1ots 1ott 1otu 1p2c 1p7k 1psk 1q9o 1q9w 1qgc 1r0a 1r24 1r3i 1r3j 1r3k 1r3l 1rih 1ruq 1rur 1s5h 1seq 1t03 1t4k 1ub5 1ub6 1uwx 1xf2 1xf3 1xf4 1xgp 1xgq 1xgu 25c8 2a6d 2a6k 2adf 2adj 2ajs 2aju 2ajv 2ajx 2ajy 2ajz 2ak1 2bob 2boc 2ck0 2f19 2fr4 2g5b 2h8p 2hg5 2hrp 2mpa 2nr6 2q76 2r1w 2r1y 2r23 2r2b 2uyl 2v17 2v7h 2vc2 2vdk 2vdl 2vdm 2vdn 2vdo 2vdp 2vdq 2vdr 2vl5 2vq1 2vwe 2w60 2w65 2w9d 2w9e 2z91 2z92 2z93 2zjs 35c8 3bae 3bgf 3bkc 3bkj 3bkm 3bpc 3bqu 3bsz 3bt2 3bz4 3c5s 3c6s 3cfb 3cfc 3cfd 3cfe 3ck0 3cle 3clf 3cmo 3cvh 3cvi 3d9a 3ejz 3eot 3f7v 3f7y 3fb6 3hfm 4kk5 4kk8 4zxb 6fab

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4QNP)