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(-) Description

Title :  CRYSTAL STRUCTURE OF C05 VPGSGW MUTANT BOUND TO H3 INFLUENZA HEMAGGLUTININ, HA1 SUBUNIT
 
Authors :  N. C. Wu, I. A. Wilson
Date :  27 Jan 17  (Deposition) - 24 May 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,E,F  (1x)
Biol. Unit 2:  B,C,D  (1x)
Keywords :  Influenza, Fab, Hemagglutinin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. C. Wu, G. Grande, H. L. Turner, A. B. Ward, J. Xie, R. A. Lerner, I. A. Wilson
In Vitro Evolution Of An Influenza Broadly Neutralizing Antibody Is Modulated By Hemagglutinin Receptor Specificity
Nat Commun V. 8 15371 2017
PubMed-ID: 28504265  |  Reference-DOI: 10.1038/NCOMMS15371

(-) Compounds

Molecule 1 - HEMAGGLUTININ
    Chains: A, B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: HA
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 506350
    Strain: A/HONG KONG/1/1968 H3N2
 
Molecule 2 - ANTIBODY C05 VPGSGW MUTANT, HEAVY CHAIN
    Chains: C, E
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - ANTIBODY C05, LIGHT CHAIN
    Chains: D, F
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A   EF
Biological Unit 2 (1x):  BCD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
2FLC2Ligand/IonCITRATE ANION
3NA1Ligand/IonSODIUM ION
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2FLC-1Ligand/IonCITRATE ANION
3NA-1Ligand/IonSODIUM ION
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
11PE3Ligand/IonPENTAETHYLENE GLYCOL
2FLC2Ligand/IonCITRATE ANION
3NA-1Ligand/IonSODIUM ION
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:80 , ARG A:141 , SER A:149 , ARG A:255 , HOH A:652binding site for residue 1PE A 403
02AC2SOFTWAREGLN B:80 , ASN B:133 , ARG B:141 , SER B:149 , ARG B:255binding site for residue 1PE B 403
03AC3SOFTWAREPHE A:94 , ASN A:96 , ASN B:137 , ARG B:224 , HOH B:525 , GLN C:100binding site for residue 1PE B 404
04AC4SOFTWARESER B:95 , TYR B:100 , TYR B:105 , VAL B:223binding site for residue 1PE B 405
05AC5SOFTWAREHIS B:183 , PRO B:185 , GLU B:190 , SER B:228 , SER C:100Dbinding site for residue NA B 406
06AC6SOFTWAREVAL A:309 , ASP C:61 , GLU C:64 , HOH C:412binding site for residue FLC C 301
07AC7SOFTWARELYS B:156 , PHE C:27B , TYR C:32 , MET C:96 , MET C:98 , HOH C:432 , HOH C:460binding site for residue FLC C 302
08AC8SOFTWAREASN A:165 , ASN A:246binding site for Mono-Saccharide NAG A 401 bound to ASN A 165
09AC9SOFTWARESER A:45 , ASN A:285 , VAL A:297 , ASN A:298binding site for Mono-Saccharide NAG A 402 bound to ASN A 285
10AD1SOFTWAREGLN B:80 , ASN B:81 , GLU B:119 , PHE B:120binding site for Mono-Saccharide NAG B 402 bound to ASN B 81
11AD2SOFTWAREASN B:165binding site for Mono-Saccharide NAG B 401 bound to ASN B 165

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:52 -A:277
2A:64 -A:76
3A:97 -A:139
4A:281 -A:305
5B:52 -B:277
6B:64 -B:76
7B:97 -B:139
8B:281 -B:305
9C:22 -C:92
10C:140 -C:196
11D:23 -D:88
12D:134 -D:194
13E:22 -E:92
14E:140 -E:196
15F:23 -F:88
16F:134 -F:194

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Asn A:54 -Pro A:55
2Asn B:54 -Pro B:55
3Phe C:146 -Pro C:147
4Glu C:148 -Pro C:149
5Ser D:7 -Pro D:8
6Leu D:94 -Pro D:95
7Tyr D:140 -Pro D:141
8Phe E:146 -Pro E:147
9Glu E:148 -Pro E:149
10Ser F:7 -Pro F:8
11Leu F:94 -Pro F:95
12Tyr F:140 -Pro F:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UMN)

(-) 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:267
                                                                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee...eee....hhhhhhhhhhhhhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.......eeeee.eeeeee..eee....eeeeee.......eeeeee......eeeeeeeee..hhhhhhhhhh....eeeee....eeee...............eeeeeeeee....eeeeeeee.eeee.eeee......eeee....eeeee..eee..eee.....ee...........ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5umn A   43 VQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYV  309
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       


Chain B from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee....hhhhhhhhhhhhhhhh.....eeee..........ee..hhhhhhhhhhhhh...eee.......eeeee.eeeeee..eee....eeeeee.......eeeeee......eeeeeeeee..hhhhhhhhhh....eeeee....eeee...............eeeeeeeee....eeeeeeee.eeee.eeee......eeee........................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5umn B   51 ICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNNKITYGAC  305
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280    || 302   
                                                                                                                                                                                                                                                                    285|       
                                                                                                                                                                                                                                                                     298       


Chain C from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee..hhhhhhhh.eeeeeeee.....eeeeeee.......ee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeee.ee....ee........eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5umn C    2 VQLQESGGGLVQPGESLRLSCVGSGSSFGESTLSYYAVSWVRQAPGKGLEWLSIINAGGGDIDYADSVEGRFTISRDNSKETLYLQMTNLRVEDTGVYYCAKHMSMQQVPGSGWERADLVGDAFDVWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    11        21      |27D|       36        46      | 55        65        75       82C        92      100B||||||100L||||   106       116       126       136       146       156       166       176       186       196       206        
                                                    27A||||                       52A                            82A||               100A|||||100J||||||                                                                                                                  
                                                     27B|||                                                       82B|                100B|||||100K|||||                                                                                                                  
                                                      27C||                                                        82C                 100C|||||100L||||                                                                                                                  
                                                       27D|                                                                             100D|||||100M|||                                                                                                                  
                                                        27E                                                                              100E|||| 100N||                                                                                                                  
                                                                                                                                          100F|||  100O|                                                                                                                  
                                                                                                                                           100G||   100P                                                                                                                  
                                                                                                                                            100H|                                                                                                                         
                                                                                                                                             100I                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5umn D    1 DIQLTQSPSSLSASVGDRVTLTCQASQDIRKFLNWYQQKPGKGPKLLIYDASNLQRGVPSRFSGGGSGTDFTLIISSLQPEDVGTYYCQQYDGLPFTFGGGTKVVIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain E from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......hhh.eeeeeeee.....eeeeeee.......ee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeee.ee....ee........eeee...eeeee........eeeee......hhh.eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5umn E    2 VQLQESGGGLVQPGESLRLSCVGSGSSFGESTLSYYAVSWVRQAPGKGLEWLSIINAGGGDIDYADSVEGRFTISRDNSKETLYLQMTNLRVEDTGVYYCAKHMSMQQVPGSGWERADLVGDAFDVWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    11        21      |27D|       36        46      | 55        65        75       82C        92      100B||||||100L||||   106       116       126       136       146       156       166       176       186       196       206        
                                                    27A||||                       52A                            82A||               100A|||||100J||||||                                                                                                                  
                                                     27B|||                                                       82B|                100B|||||100K|||||                                                                                                                  
                                                      27C||                                                        82C                 100C|||||100L||||                                                                                                                  
                                                       27D|                                                                             100D|||||100M|||                                                                                                                  
                                                        27E                                                                              100E|||| 100N||                                                                                                                  
                                                                                                                                          100F|||  100O|                                                                                                                  
                                                                                                                                           100G||   100P                                                                                                                  
                                                                                                                                            100H|                                                                                                                         
                                                                                                                                             100I                                                                                                                         


Chain F from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5umn F    1 DIQLTQSPSSLSASVGDRVTLTCQASQDIRKFLNWYQQKPGKGPKLLIYDASNLQRGVPSRFSGGGSGTDFTLIISSLQPEDVGTYYCQQYDGLPFTFGGGTKVVIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
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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 5UMN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

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        HEMA_I68A4 | Q91MA7: 3sdy 3ztj 4fnk 4fp8 4fqr 4fqy 4nm8 4ubd 4we4 4zcj 5k9k 5k9q 5kan 5kuy 5t6n 5thf 5vtq 5vtr 5vtu 5vtv 5vtw 5vtx 5vty 5vtz 5vu4

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