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Description

Title :   WIF DOMAIN OF HUMAN WNT INHIBITORY FACTOR 1 IN COMPLEX WITH 1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE

Authors :   T. Malinauskas, A. R. Aricescu, W. Lu, C. Siebold, E. Y. Jones

Date :   19 Apr 11 (Deposition) - 20 Jul 11 (Release) - 17 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Signaling Protein, Wnt Signaling Pathway, Wnt Antagonist, Morphogen, Cancer, Glycosaminoglycan (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Malinauskas, A. R. Aricescu, W. Lu, C. Siebold, E. Y. Jones
Modular Mechanism Of Wnt Signaling Inhibition By Wnt Inhibitory Factor 1
Nat. Struct. Mol. Biol. V. 18 886 2011
PubMed-ID: 21743455 | Reference-DOI: 10.1038/NSMB.2081

Compounds

Molecule 1 - WNT INHIBITORY FACTOR 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	N-ACETYLGLUCOSAMINYLTRANSFERASE I-NEGATIVE HEK 293S GNTI(-)CELLS
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Expression System Vector	:	PHLSEC
	Expression System Vector Type	:	PLASMID
	Fragment	:	WIF DOMAIN, RESIDUES 35-178
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	WIF-1

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 9)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	MLY	6	Mod. Amino Acid	N-DIMETHYL-LYSINE
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PCF	1	Ligand/Ion	1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

Biological Unit 1 (4, 18)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	MLY	12	Mod. Amino Acid	N-DIMETHYL-LYSINE
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	PCF	2	Ligand/Ion	1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:48 , ILE A:49 , PHE A:66 , ARG A:76 , MET A:77 , PRO A:78 , MET A:87 , VAL A:152 , VAL A:156 , PHE A:173 , GLN A:178 , HOH A:2027	BINDING SITE FOR RESIDUE PCF A1179
2	AC2	SOFTWARE	HIS A:43 , GLN A:44 , GLU A:52 , ASN A:88 , GLN A:135 , HOH A:2008 , HOH A:2016 , HOH A:2083	BINDING SITE FOR RESIDUE NAG A1180
3	AC3	SOFTWARE	TYR A:101 , THR A:126 , HOH A:2038	BINDING SITE FOR RESIDUE ACT A1181

SS Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	A:140	-	A:177

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2YGN)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2YGN)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	WIF	PS50814	WIF domain profile.	WIF1_HUMAN	38-177	1	A:38-177
2	EGF_3	PS50026	EGF-like domain profile.	WIF1_HUMAN	178-210 274-306 211-242 243-271 307-338	1	A:178-178 - - - -

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	WIF	PS50814	WIF domain profile.	WIF1_HUMAN	38-177	2	A:38-177
2	EGF_3	PS50026	EGF-like domain profile.	WIF1_HUMAN	178-210 274-306 211-242 243-271 307-338	2	A:178-178 - - - -

Exons (4, 4)

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000286574	1	ENSE00001313678	chr12:65515116-65514824	293	WIF1_HUMAN	1-50	50	1	A:33-50 (gaps)	23
1.2	ENST00000286574	2	ENSE00001291687	chr12:65514336-65514197	140	WIF1_HUMAN	50-96	47	1	A:50-96	47
1.3	ENST00000286574	3	ENSE00001309501	chr12:65471634-65471526	109	WIF1_HUMAN	97-133	37	1	A:97-133	37
1.4	ENST00000286574	4	ENSE00001297646	chr12:65462684-65462544	141	WIF1_HUMAN	133-180	48	1	A:133-178	46
1.5	ENST00000286574	5	ENSE00001305730	chr12:65461570-65461475	96	WIF1_HUMAN	180-212	33	0	-	-
1.6	ENST00000286574	6	ENSE00001292676	chr12:65460516-65460421	96	WIF1_HUMAN	212-244	33	0	-	-
1.7	ENST00000286574	7	ENSE00001313446	chr12:65456356-65456261	96	WIF1_HUMAN	244-276	33	0	-	-
1.8	ENST00000286574	8	ENSE00001024346	chr12:65449906-65449811	96	WIF1_HUMAN	276-308	33	0	-	-
1.9	ENST00000286574	9	ENSE00001024351	chr12:65448993-65448898	96	WIF1_HUMAN	308-340	33	0	-	-
1.10	ENST00000286574	10	ENSE00001297515	chr12:65445250-65444407	844	WIF1_HUMAN	340-379	40	0	-	-

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:146
 aligned with WIF1_HUMAN | Q9Y5W5 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:151
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177 
           WIF1_HUMAN    28 AGPPQEESLYLWIDAHQARVLIGFEEDILIVSEGKMAPFTHDFRKAQQRMPAIPVNIHSMNFTWQAAGQAEYFYEFLSLRSLDKGIMADPTVNVPLLGTVPHKASVVQVGFPCLGKQDGVAAFEVDVIVMNSEGNTILQTPQNAIFFKTCQ 178
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----.eeeeehhhhhhhhhh....eeeee..ee.hhhhhhhhhhhh.........eeeeeeee.....eeeeeeeeee.........ee....eee.....eeeeee........eeeeeeeeeeeee....eeee......eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------WIF  PDB: A:38-177 UniProt: 38-177                                                                                                          E PROSITE
           Transcript 1 (1) Exon 1.1 UniProt: 1-50 ----------------------------------------------Exon 1.3  PDB: A:97-133              --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.2  PDB: A:50-96 UniProt: 50-96          ------------------------------------Exon 1.4  PDB: A:133-178 UniProt: 133-180      Transcript 1 (2)
                 2ygn A  33 TG-----SLYLWIDAHQARVLIGFEEDILIVSEGkMAPFTHDFRkAQQRMPAIPVNIHSMNFTWQAAGQAEYFYEFLSLRSLDkGIMADPTVNVPLLGTVPHkASVVQVGFPCLGkQDGVAAFEVDVIVMNSEGNTILkTPQNAIFFKTCQ 178
                             |     |37        47        57    |   67    |   77        87        97       107   |   117       127  |    137     | 147       157       167       177 
                             |    35                         62-MLY    72-MLY                                111-MLY            130-MLY      143-MLY                166-MLY        
                            34

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Classification and Annotation

SCOP Domains (0, 0)

(no "SCOP Domain" information available for 2YGN)

CATH Domains (0, 0)

(no "CATH Domain" information available for 2YGN)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2YGN)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (WIF1_HUMAN | Q9Y5W5)

molecular function
	GO:0017147	Wnt-protein binding	Interacting selectively and non-covalently with Wnt-protein, a secreted growth factor involved in signaling.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0016055	Wnt signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0030178	negative regulation of Wnt signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway.
	GO:0045600	positive regulation of fat cell differentiation	Any process that activates or increases the frequency, rate or extent of adipocyte differentiation.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	WIF1_HUMAN \| Q9Y5W5	:	2d3j 2ygo 2ygp 2ygq

Related Entries Specified in the PDB File

2ygo	WIF DOMAIN-EGF-LIKE DOMAIN 1 OF HUMAN WNT INHIBITORY FACTOR 1 IN COMPLEX WITH 1,2- DIPALMITOYLPHOSPHATIDYLCHOLINE
2ygp	WIF DOMAIN-EGF-LIKE DOMAIN 1 MET77TRP OF HUMAN WNT INHIBITORY FACTOR 1 IN COMPLEX WITH 1,2- DIPALMITOYLPHOSPHATIDYLCHOLINE
2ygq	WIF DOMAIN-EPIDERMAL GROWTH FACTOR (EGF)-LIKE DOMAINS 1-3 OF HUMAN WNT INHIBITORY FACTOR 1 IN COMPLEX WITH 1,2-DIPALMITOYLPHOSPHATIDYLCHOLINE