4BKC - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A UNUSUALLY LINKED DIMERIC VARIANT OF BET V 1

Authors :   S. G. Kofler, H. Brandstetter

Date :   23 Apr 13 (Deposition) - 27 Nov 13 (Release) - 15 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

Chains :   Asym./Biol. Unit : A,B

Keywords :   Allergen, Dimerisation, Polysulfide, Sulfur Incorporation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. G. Kofler, C. Ackaert, M. Samonig, C. Asam, P. Briza, J. Horeis-Hoeck, C. Cabrele, F. Ferreira, A. Duschl, C. Huber, H. Brandstetter
Stabilization Of The Dimeric Birch Pollen Allergen Bet V 1 Impacts Its Immunological Properties
J. Biol. Chem. V. 289 540 2014
PubMed-ID: 24253036 | Reference-DOI: 10.1074/JBC.M113.518795

Molecule 1 - MAJOR POLLEN ALLERGEN BET V 1-A
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET-28B
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	EUROPEAN WHITE BIRCH
	Organism Scientific	:	BETULA PENDULA
	Organism Taxid	:	3505
	Other Details	:	BOTH MONOMERS ARE LINKED VIA A POLYSULFIDE BRIDGE BETWEEN CYS5A AND CYS5B. DUE TO OCCUPANCY REASONS, THE MODIFIED CYSTEINE RESIDUES ARE INTRODUCED AS DISCRETE COMPOUNDS.
	Synonym	:	ALLERGEN BET V I-A, BET V 1-A BET V 1
	Tissue	:	POLLEN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	TSY	2	Mod. Amino Acid	(2S)-2-AMINO-3-TRISULFANYLPROPANOIC ACID

(no "Site" information available for 4BKC)

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

(no "Cis Peptide Bond" information available for 4BKC)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_BEV1A_BETPN_001 *	F	63	L	BEV1A_BETPN	---	---	A/B	F	62	L
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PATHOGENESIS_BETVI	PS00451	Pathogenesis-related proteins Bet v I family signature.	BEV1A_BETPN	89-121	2	A:88-120 B:88-120

(no "Exon" information available for 4BKC)

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:159
 aligned with BEV1A_BETPN | P15494 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151         
          BEV1A_BETPN     2 GVFNYETETTSVIPAARLFKAFILDGDNLFPKVAPQAISSVENIEGNGGPGTIKKISFPEGFPFKYVKDRVDEVDHTNFKYNYSVIEGGPIGDTLEKISNEIKIVATPDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 160
               SCOP domains d4bkca_ A: Major tree pollen allergen                                                                                                                           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) -------------------------------------------------------------L------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------PATHOGENESIS_BETVI  PDB: A:88-120--------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bkc A   1 GVFNcETETTSVIPAARLFKAFILDGDNLFPKVAPQAISSVENIEGNGGPGTIKKISFPEGFPFKYVKDRVDEVDHTNFKYNYSVIEGGPIGDTLEKISNEIKIVATPDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 159
                                |   10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
                                |                                                                                                                                                          
                                5-TSY

Chain B from PDB  Type:PROTEIN  Length:159
 aligned with BEV1A_BETPN | P15494 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151         
          BEV1A_BETPN     2 GVFNYETETTSVIPAARLFKAFILDGDNLFPKVAPQAISSVENIEGNGGPGTIKKISFPEGFPFKYVKDRVDEVDHTNFKYNYSVIEGGPIGDTLEKISNEIKIVATPDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 160
               SCOP domains d4bkcb_ B: Major tree pollen allergen                                                                                                                           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) -------------------------------------------------------------L------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------PATHOGENESIS_BETVI  PDB: B:88-120--------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bkc B   1 GVFNcETETTSVIPAARLFKAFILDGDNLFPKVAPQAISSVENIEGNGGPGTIKKISFPEGFPFKYVKDRVDEVDHTNFKYNYSVIEGGPIGDTLEKISNEIKIVATPDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 159
                                |   10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
                                5-TSY

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: TBP-like (289)

Superfamily: Bet v1-like (158)

Family: Pathogenesis-related protein 10 (PR10)-like (38)

Protein domain: Major tree pollen allergen (22)

White birch (Betula verrucosa), Bet v 1 [TaxId: 3505] (18)

1a	d4bkca_	A:
1b	d4bkcb_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BEV1A_BETPN | P15494)

biological process
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0009607	response to biotic stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Sites
(no "Sites" information available for 4bkc)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4bkc)

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4bk6	CRYSTAL STRUCTURE OF A DIMERIC VARIANT OF BET V 1
4bk7	CRYSTAL STRUCTURE OF A VARIANT OF THE MAJOR BIRCH POLLEN ALLERGEN BET V 1
4bkd	CRYSTAL STRUCTURE OF AN UNUSUALLY LINKED DIMERIC VARIANT OF BET V 1 (B)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

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Gene Ontology (3, 3)

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