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(-) Description

Title :  CRYSTAL STRUCTURE OF BIRCH POLLEN ALLERGEN BET V 1 MUTANT G26L, D69I, P90L, K97I
 
Authors :  R. Freier, H. Brandstetter
Date :  31 Mar 15  (Deposition) - 25 Nov 15  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  E  (1x)
Biol. Unit 5:  F  (1x)
Biol. Unit 6:  D  (1x)
Keywords :  Allergen, Fold Stability (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Machado, R. Freier, S. Scheiblhofer, T. Thalhamer, M. Mayr, P. Briza, S. Grutsch, L. Ahammer, J. E. Fuchs, H. G. Wallnoefer, A. Isakovic, V. Kohlbauer, A. Hinterholzer, M. Steiner, M. Danzer, J. Horejs-Hoeck, F. Ferreira, K. R. Liedl, M. Tollinger, P. Lackner, C. M. Johnson, H. Brandstetter, J. Thalhamer, R. Weiss
Fold Stability During Endolysosomal Acidification Is A Key Factor For Allergenicity And Immunogenicity Of The Major Birch Pollen Allergen.
J. Allergy Clin. Immunol. V. 137 1525 2016
PubMed-ID: 26559323  |  Reference-DOI: 10.1016/J.JACI.2015.09.026

(-) Compounds

Molecule 1 - MAJOR POLLEN ALLERGEN BET V 1-A
    Chains: A, B, C, E, F, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: BETVIA, BETVI
    Mutation: YES
    Organism Common: EUROPEAN WHITE BIRCH
    Organism Scientific: BETULA PENDULA
    Organism Taxid: 3505
    Synonym: ALLERGEN BET V I-A

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):     E 
Biological Unit 5 (1x):      F
Biological Unit 6 (1x):    D  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1SO414Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 5 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:74 , ASP A:75 , HIS A:76 , THR A:77 , GLN E:36binding site for residue SO4 A 201
02AC2SOFTWAREPHE A:64 , LYS A:65binding site for residue SO4 A 202
03AC3SOFTWAREGLY A:48 , GLY A:49 , HIS A:76 , HOH A:312binding site for residue SO4 A 203
04AC4SOFTWAREASN B:47 , GLY B:48 , GLY B:49 , HOH B:303 , HOH B:304binding site for residue SO4 B 201
05AC5SOFTWAREVAL B:133 , VAL E:133binding site for residue SO4 B 202
06AC6SOFTWAREPHE B:64 , LYS B:65 , TYR B:66binding site for residue SO4 B 203
07AC7SOFTWAREGLU A:45 , GLY A:46 , HOH A:324 , HIS B:154 , SER B:155 , ASP B:156binding site for residue SO4 B 204
08AC8SOFTWARELEU C:26 , PHE C:30 , TYR C:81 , TYR C:83 , ILE C:102binding site for residue SO4 C 201
09AC9SOFTWAREGLU E:45 , GLY E:46binding site for residue SO4 E 201
10AD1SOFTWAREVAL B:74 , ASP B:75 , HIS B:76 , THR B:77 , GLN F:36binding site for residue SO4 F 201
11AD2SOFTWAREGLY F:46 , ASN F:47 , GLY F:48 , GLY F:49binding site for residue SO4 F 202
12AD3SOFTWARETYR F:158 , ASN F:159binding site for residue SO4 F 203
13AD4SOFTWAREPHE F:64 , GLY F:89 , LEU F:90 , GLN F:132binding site for residue SO4 F 204
14AD5SOFTWAREILE E:44 , ILE E:53 , LYS E:68 , GLU F:45 , ILE F:53 , HOH F:303binding site for residue SO4 F 205
15AD6SOFTWAREGLY C:1 , VAL C:2 , ASN C:4 , GLU C:6 , THR C:7 , ASN C:118 , LYS C:119 , TYR C:120 , THR C:122 , GLY D:1 , VAL D:2 , ASN D:4 , GLU D:6 , THR D:7 , ASN D:118 , LYS D:119 , TYR D:120 , THR D:122 , VAL D:128 , VAL D:133 , LYS D:137binding site for Di-peptide PHE C 3 and TYR D 5
16AD7SOFTWAREGLY C:1 , VAL C:2 , ASN C:4 , TYR C:5 , ASN C:118 , LYS C:119 , TYR C:120 , THR C:122 , GLY D:1 , VAL D:2 , ASN D:4 , TYR D:5 , ASN D:118 , LYS D:119 , TYR D:120 , THR D:122 , VAL D:128 , VAL D:133binding site for Di-peptide PHE C 3 and PHE D 3
17AD8SOFTWAREGLY C:1 , VAL C:2 , ASN C:4 , GLU C:6 , THR C:7 , ASN C:118 , LYS C:119 , TYR C:120 , THR C:122 , GLY D:1 , VAL D:2 , ASN D:4 , GLU D:6 , THR D:7 , ASN D:118 , LYS D:119 , TYR D:120 , THR D:122 , VAL D:128 , VAL D:133 , LYS D:137binding site for Di-peptide PHE C 3 and TYR D 5
18AD9SOFTWAREGLY C:1 , VAL C:2 , ASN C:4 , TYR C:5 , ASN C:118 , LYS C:119 , TYR C:120 , THR C:122 , GLY D:1 , VAL D:2 , ASN D:4 , TYR D:5 , ASN D:118 , LYS D:119 , TYR D:120 , THR D:122 , VAL D:128 , VAL D:133binding site for Di-peptide PHE C 3 and PHE D 3
19AE1SOFTWAREGLY C:1 , VAL C:2 , ASN C:4 , TYR C:5 , ASN C:118 , LYS C:119 , TYR C:120 , THR C:122 , GLY D:1 , VAL D:2 , ASN D:4 , TYR D:5 , ASN D:118 , LYS D:119 , TYR D:120 , THR D:122 , VAL D:128 , VAL D:133binding site for Di-peptide PHE C 3 and PHE D 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z3L)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly E:124 -Asp E:125
2Gly F:124 -Asp F:125
3Gly D:124 -Asp D:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z3L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z3L)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z3L)

(-) 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:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhh.hhhhhhhhhh.....eeeeee.......eeeee........eeeeeeeeee....eeeeeeee.......eeeeeeeeeeee.....eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z3l A   1 GVFNYETETTSVIPAARLFKAFILDLDNLFPKVAPQAISSVENIEGNGGPGTIKKISFPEGFPFKYVKIRVDEVDHTNFKYNYSVIEGGLIGDTLEIISNEIKIVATPDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain B from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhh.hhhhhhhhhh.....eeeeee.......eeeee........eeeeeeeeee....eeeeeeeee......eeeeeeeeeeee.....eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z3l B   1 GVFNYETETTSVIPAARLFKAFILDLDNLFPKVAPQAISSVENIEGNGGPGTIKKISFPEGFPFKYVKIRVDEVDHTNFKYNYSVIEGGLIGDTLEIISNEIKIVATPDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain C from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhh.hhhhhhhhhh.....eeeeee.......eeeee........eeeeeeeeee....eeeeeeee.......eeeeeeeeeeee.....eeeeeeeeeee....eehhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z3l C   1 GVFNYETETTSVIPAARLFKAFILDLDNLFPKVAPQAISSVENIEGNGGPGTIKKISFPEGFPFKYVKIRVDEVDHTNFKYNYSVIEGGLIGDTLEIISNEIKIVATPDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain D from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhh.hhhhhhhhhh.....eeeeee.......eeeee........eeeeeeeeee....eeeeeeee.......eeeeeeeeeeee.....eeeeeeeeeee....eehhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z3l D   1 GVFNYETETTSVIPAARLFKAFILDLDNLFPKVAPQAISSVENIEGNGGPGTIKKISFPEGFPFKYVKIRVDEVDHTNFKYNYSVIEGGLIGDTLEIISNEIKIVATPDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain E from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhh.hhhhhhhhhh.....eeeeee.......eeeee........eeeeeeeeee....eeeeeeee.......eeeeeeeeeeee.....eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z3l E   1 GVFNYETETTSVIPAARLFKAFILDLDNLFPKVAPQAISSVENIEGNGGPGTIKKISFPEGFPFKYVKIRVDEVDHTNFKYNYSVIEGGLIGDTLEIISNEIKIVATPDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain F from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee..hhhhhhhhhh.hhhhhhhhhh.....eeeeee.......eeeee........eeeeeeeeee....eeeeeeee.......eeeeeeeeeeee.....eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z3l F   1 GVFNYETETTSVIPAARLFKAFILDLDNLFPKVAPQAISSVENIEGNGGPGTIKKISFPEGFPFKYVKIRVDEVDHTNFKYNYSVIEGGLIGDTLEIISNEIKIVATPDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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 4Z3L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z3L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z3L)

(-) Gene Ontology  (3, 3)

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 Related Entries

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UniProtKB/Swiss-Prot
        BEV1A_BETPN | P15494: 1b6f 1btv 1bv1 1fsk 1llt 1qmr 4a80 4a81 4a83 4a84 4a85 4a86 4a87 4a88 4a8g 4b9r 4bk6 4bk7 4bkc 4bkd 4btz 4mns 4qip

(-) Related Entries Specified in the PDB File

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