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(-) Description

Title :  INFLUENZA HEMAGGLUTININ IN COMPLEX WITH CH67 FAB
 
Authors :  A. G. Schmidt, S. C. Harrison
Date :  15 Oct 12  (Deposition) - 21 Nov 12  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,E
Keywords :  Fab Fragment, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Schmidt, H. Xu, A. R. Khan, T. O'Donnell, S. Khurana, L. R. King, J. Manischewitz, H. Golding, P. Suphaphiphat, A. Carfi, E. C. Settembre, P. R. Dormitzer, T. B. Kepler, R. Zhang, M. A. Moody, B. F. Haynes, H. X. Liao, D. E. Shaw, S. C. Harrison
Preconfiguration Of The Antigen-Binding Site During Affinit Maturation Of A Broadly Neutralizing Influenza Virus Antibody.
Proc. Natl. Acad. Sci. Usa V. 110 264 2013
PubMed-ID: 23175789  |  Reference-DOI: 10.1073/PNAS.1218256109

(-) Compounds

Molecule 1 - HEMAGGLUTININ HA1
    Chains: E
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PFASTBAC
    Expression System Strain: HI5
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 65-276
    Gene: HA1
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 464623
    Strain: A/SOLOMON ISLANDS/3/2006(H1N1)
 
Molecule 2 - CH67 HEAVY CHAIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - CH67 LIGHT CHAIN
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Fragment: FAB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN E:68 , GLU E:70 , GLU E:90 , ASN E:91 , ARG E:224BINDING SITE FOR RESIDUE NAG E 301
2AC2SOFTWAREASN E:58 , GLU E:90BINDING SITE FOR RESIDUE NAG E 302

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:96
2A:153 -A:209
3B:22 -B:87
4B:136 -B:195
5E:59 -E:71
6E:94 -E:139

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:159 -Pro A:160
2Glu A:161 -Pro A:162
3Tyr B:142 -Pro B:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HKX)

(-) Sequences/Alignments

Asymmetric/Biological 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:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee......eeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeee......hhhhh.....ee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hkx A   1 QVQLVQSGAEVRKPGASVKVSCKASGYTFTDNYIHWVRQAPGQGLEWMGWIHPNSGATKYAQKFEGWVTMTRDTSISTVYMELSRSRSDDTAVYYCARAGLEPRSVDYYFYGLDVWGQGTAVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      


Chain B from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains d4hkxb1 B:1-109 automated matches                                                                  d4hkxb2 B:110-211 automated matches                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee..hhhhh..eeeee......ee.....eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hkx B   1 QSALTQPPSVSVAPGQTATITCGGNNIGRKRVDWFQQKPGQAPVLVVYERFSDSNSGTTATLTISRVEAGDEADYYCQVWDSDSDHVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 211
                                    10        20        30        40       |60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
                                                                          48|                                                                                                                                                        
                                                                           59                                                                                                                                                        


Chain E from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....hhhhhhhhhhhhh..........ee................hhhhhhhhh....eeeee...hhhhhh........eeeeee..eee....eee..........eeeeee.....eeeeeeeeee..hhhhhhhhhh.....eeee....eeee...............eeeeeeeee....eeeeee...eeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hkx E  52 APLQLGNCSVAGWILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPKESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGVHHPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDQEGRINYYWTLLEPGDTIIFEANGNLIAPRYAFALSRG 263
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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  (2, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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    Glu A:161 - Pro A:162   [ RasMol ]  
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  4hkx
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 Related Entries

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

UniProtKB/Swiss-Prot
        A7UPX0_9INFA | A7UPX0: 5ug0 5ugy 5ujz 5uk0 5uk1 5uk2
UniProtKB/TrEMBL
        A7UPX0_9INFA | A7UPX0: 3sm5 4yjz 4yk4

(-) Related Entries Specified in the PDB File

4hk0 4hk3 4hkb