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Description

Title :   CRYSTAL STRUCTURE OF A PHEROMONE BINDING PROTEIN FROM APIS MELLIFERA WITH A SERENDIPITOUS LIGAND SOAKED AT PH 4.0

Authors :   M. E. Pesenti, S. Spinelli, V. Bezirard, L. Briand, J. C. Pernollet, M. T C. Cambillau

Date :   28 Nov 08 (Deposition) - 01 Dec 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Pheromone Binding Protein, Honey Bee, Apis Mellifera, Signal Transduction, Queen Mandibular Protein, Ph (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Pesenti, S. Spinelli, V. Bezirard, L. Briand, J. C. Pernollet, M. Tegoni, C. Cambillau
Queen Bee Pheromone Binding Protein Ph Induced Domain-Swapping Favors Pheromone Release
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - PHEROMONE-BINDING PROTEIN ASP1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PHIL_D2
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 26-144
	Organism Common	:	HONEYBEE
	Organism Scientific	:	APIS MELLIFERA
	Organism Taxid	:	7460

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 3)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	CMJ	1	Ligand/Ion	(20S)-20-METHYLDOTETRACONTANE
3	GOL	1	Ligand/Ion	GLYCEROL

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:9 , LEU A:53 , PHE A:56 , MET A:70 , LEU A:73 , MET A:86 , VAL A:115 , PHE A:117 , GOL A:121	BINDING SITE FOR RESIDUE CMJ A 120
2	AC2	SOFTWARE	GLY A:72 , CMJ A:120 , HOH A:264 , HOH A:274	BINDING SITE FOR RESIDUE GOL A 121
3	AC3	SOFTWARE	ASN A:64 , VAL A:65 , PRO A:91 , THR A:92	BINDING SITE FOR RESIDUE CL A 122

SS Bonds (3, 3)

Asymmetric/Biological Unit

No.	Residues
1	A:20	-	A:51
2	A:47	-	A:98
3	A:89	-	A:107

Cis Peptide Bonds (1, 1)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:90	-	Pro A:91

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 3FE8)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 3FE8)

Exons (0, 0)

(no "Exon" information available for 3FE8)

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:119
 aligned with Q9U9J6_APIME | Q9U9J6 from UniProtKB/TrEMBL  Length:144

    Alignment length:119
                                    35        45        55        65        75        85        95       105       115       125       135         
         Q9U9J6_APIME    26 APDWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 144
               SCOP domains d3fe8a_ A: Pheromone-binding protein asp1                                                                               SCOP domains
               CATH domains 3fe8A00 A:1-119  [code=1.10.238.20, no name defined]                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3fe8 A   1 APDWVPPEVFDLVAEDKARCMSEHGTTQAQIDDVDKGNLVNEPSITCYMYCLLEAFSLVDDEANVDEDIMLGLLPDQLQERAQSVMGKCLPTSGSDNCNKIYNLAKCVQESAPDVWFVI 119
                                    10        20        30        40        50        60        70        80        90       100       110

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 (1, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: Insect pheromone/odorant-binding proteins (68)

Family: Insect pheromone/odorant-binding proteins (50)

Protein domain: Pheromone-binding protein asp1 (14)

Honeybee (Apis mellifera) [TaxId: 7460] (14)

d3fe8a_

CATH Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: [code=1.10.238.20, no name defined] (55)

Honeybee (Apis mellifera) (19)

3fe8A00

A:1-119

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 3FE8)

Gene Ontology (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q9U9J6_APIME | Q9U9J6)

molecular function
	GO:0005549		odorant binding		Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell.

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Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Leu A:90 - Pro A:91	[ RasMol ]

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	3fe8
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	Q9U9J6_APIME \| Q9U9J6	:	2h8v 3bfa 3bjh 3cab 3cdn
UniProtKB/TrEMBL
	Q9U9J6_APIME \| Q9U9J6	:	3bfb 3bfh 3cyz 3cz0 3cz1 3cz2 3d73 3d74 3d75 3d76 3d77 3d78 3fe6 3fe9

Related Entries Specified in the PDB File

2h8v	THE SAME PROTEIN IN THE APO FORM AT PH 5.5
3bfa	THE SAME PROTEIN IN COMPLEX WITH THE QMP AT PH 5.5
3bfb	THE SAME PROTEIN IN COMPLEX WITH THE 9-ODA AT PH 5.5
3bfh	THE SAME PROTEIN IN COMPLEX WITH THE HDOA AT PH 5.5
3bjh	THE SAME PROTEIN IN COMPLEX WITH THE NBBSA AT PH 5.5
3cab	THE SAME PROTEIN IN COMPLEX WITH THE NBBSA SOAKED AT PH 7.0
3cdn	THE SAME PROTEIN IN THE APO FORM SOAKED AT PH 4.0
3cyz	THE SAME PROTEIN IN COMPLEX WITH THE 9-ODA AT PH 7.0
3cz0	THE SAME PROTEIN IN COMPLEX WITH THE QMP AT PH 7.0
3cz1	THE SAME PROTEIN IN COMPLEX WITH THE NBBSA AT PH 7.0
3cz2	THE SAME PROTEIN IN THE APO FORM AT PH 7.0
3d73	THE MUTANT D35A OF THE SAME PROTEIN IN COMPLEX WITH HE NBBSA AT PH 7.0
3d74	THE MUTANT D35A OF THE SAME PROTEIN IN COMPLEX WITH HE NBBSA SOAKED AT PH 5.5
3d75	THE MUTANT D35N OF THE SAME PROTEIN IN COMPLEX WITH HE NBBSA AT PH 5.5
3d76	THE MUTANT D35N OF THE SAME PROTEIN IN COMPLEX WITH HE NBBSA SOAKED AT PH 7.0
3d77	THE MUTANT D35N OF THE SAME PROTEIN IN COMPLEX WITH HE NBBSA SOAKED AT PH 4.0
3d78	THE MUTANT D35N OF THE SAME PROTEIN IN COMPLEX WITH HE NBBSA AT PH 7.0
3fe6	THE SAME PROTEIN IN COMPLEX WITH A SERENDIPITOUS LIGAND AT PH 5.5
3fe9	THE SAME PROTEIN IN COMPLEX WITH A SERENDIPITOUS LIGAND SOAKED AT PH 7.0