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(-) Description

Title :  HUMAN ANTIBODY H2897 IN COMPLEX WITH INFLUENZA HEMAGGLUTININ H1 SOLOMON ISLANDS/03/2006
 
Authors :  D. D. Raymond, T. Caradonna, A. G. Schmidt, S. C. Harrison
Date :  06 Jan 17  (Deposition) - 31 May 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Influenza Ha, Antibody, Complex, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, J. Pan, S. Jenni, D. D. Raymond, T. Caradonna, K. T. Do, A. G. Schmidt, S. C. Harrison, N. Grigorieff
Cryoem Structure Of An Influenza Virus Receptor-Binding Sit Antibody-Antigen Interface.
J. Mol. Biol. V. 429 1829 2017
PubMed-ID: 28506635  |  Reference-DOI: 10.1016/J.JMB.2017.05.011

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 18-343
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS (A/SOLOMON ISLANDS/3/2006(H1N1))
    Organism Taxid: 464623
    Strain: A/SOLOMON ISLANDS/3/2006(H1N1)
 
Molecule 2 - HEMAGGLUTININ HA2
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 344-519
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS (A/SOLOMON ISLANDS/3/2006(H1N1))
    Organism Taxid: 464623
    Strain: A/SOLOMON ISLANDS/3/2006(H1N1)
 
Molecule 3 - 2897 LIGHT CHAIN
    Chains: C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: IGK@
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - 2897 HEAVY CHAIN
    Chains: D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: DKFZP686P15220
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 39)
No.NameCountTypeFull Name
1BMA6Ligand/IonBETA-D-MANNOSE
2NAG33Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARENAG A:402binding site for residue NAG A 407
2AC2SOFTWAREASN A:15 , NAG A:407binding site for Mono-Saccharide NAG A 402 bound to ASN A 15
3AC3SOFTWARETHR A:19 , ASN A:27binding site for Mono-Saccharide NAG A 406 bound to ASN A 27
4AC4SOFTWAREASN A:58 , GLU A:90binding site for Mono-Saccharide NAG A 401 bound to ASN A 58
5AC5SOFTWAREASN A:68 , GLU A:90 , ASN A:91 , SER A:140 , ARG A:224binding site for Poly-Saccharide residues BMA A 403 through NAG A 405 bound to ASN A 91
6AC6SOFTWAREPRO A:128 , ASN A:129 , SER A:165binding site for Poly-Saccharide residues NAG A 408 through NAG A 409 bound to ASN A 129
7AC7SOFTWAREASN A:163 , ARG A:192 , TYR A:201binding site for Poly-Saccharide residues BMA A 410 through NAG A 412 bound to ASN A 163
8AC8SOFTWAREGLU B:147 , ASN B:154 , THR B:156binding site for Mono-Saccharide NAG B 201 bound to ASN B 154

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:8 -B:137
2A:46 -A:278
3A:59 -A:71
4A:94 -A:139
5A:282 -A:306
6B:144 -B:148
7C:23 -C:89
8C:136 -C:196
9D:22 -D:95
10D:154 -D:210

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser C:7 -Pro C:8
2Ser C:95 -Pro C:96
3Phe D:160 -Pro D:161
4Glu D:162 -Pro D:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5UG0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5UG0)

(-) Exons   (0, 0)

(no "Exon" information available for 5UG0)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......ee...eee.ee......eeee.....ee....hhhhhhhh...............eee...............hhhhhhhhhhh.....ee...hhhhhh........eeeeee..eee....eee..........eeeeee.....eeeeeeeeee..hhhhhhhhh......eeeee..eeeee...............eeeeeeeee....eeeeee...eeee..eeee.......eee....eeeeee.eee..eee.....ee......eeee.........eee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ug0 A   4 EDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCLLKGIAPLQLGNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDREGRINYYWTLLEPGDTIIFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAKLRMVTGLRNIPSIQS 329
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323      


Chain B from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eee..........eehhhhhhhhhhhhhhhhhhhhhhh..ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....eeee....hhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ug0 B   4 GAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMNTQFTAVGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNREKI 173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173


Chain C from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...........eeeeeee........eeee.........eee.............eeeeee..eeeeee...........eeee..........................ee.....hhhhh..eee.eeeeee.....eeeeee......................eee...eeehhhhhh....eeeeee........eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ug0 C   1 EIVLTQSPGTLSLSPGEKATLSCRASQSVSSYYLGWYQQKPGQAPRLLIYETSRRATGIPDRFSGSGSGTDFTLTISGLEPEDFAVYYCQHYGVSPVITFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFN 212
                                    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:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee.....ee........eeeeee....eeeeee........eeeeeeeeee.............eeee...eeeee........ee................eeeeeeee....eeeee........eee...ee.....eeeeeee.............eeeee....eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ug0 D   1 EVQLVESGGGLVQPGGSLRLSCAASGFTFNIYDMHWVRQAPGKGLEWVSSITTAGDTYYPGSVKGRFTTSRENAKNSLYLQMNSLRAGDTGVYYCTRGVREVGATGDDPFYYGMYVWGQGTTVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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 5UG0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5UG0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5UG0)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        A7UPX0_9INFA | A7UPX0: 5ugy 5ujz 5uk0 5uk1 5uk2
        Q6N089_HUMAN | Q6N089: 2oqj 3mnv 3qct 3qcu 3qcv 4nm4 4nm8 4nuj 5ewi
UniProtKB/TrEMBL
        A7UPX0_9INFA | A7UPX0: 3sm5 4hkx 4yjz 4yk4
        Q6N089_HUMAN | Q6N089: 1u6a 3cfj 3cfk 4hpy
        Q6PIL8_HUMAN | Q6PIL8: 1u6a 3dvg 3dvn 3eyq 3hi1 4oqt

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5UG0)