4C99 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   MOUSE ZNRF3 ECTODOMAIN IN COMPLEX WITH MOUSE RSPO2 FU1-FU2 CRYSTAL FORM I

Authors :   M. Zebisch, E. Y. Jones

Date :   02 Oct 13 (Deposition) - 20 Nov 13 (Release) - 27 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Ligase-Signaling Protein Complex, Wnt, Rnf43, Lgr4, Lgr5, Lgr6, Rspo, R-Spondin, R-Spo, Rspo1, Rspo3, Rspo4, Receptor, Membrane, Signalling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Zebisch, Y. Xu, C. Krastev, B. T. Macdonald, M. Chen, R. J. C. Gilbert X. He, E. Y. Jones
Structural And Molecular Basis Of Znrf3/Rnf43 Transmembrane Ubiquitin Ligase Inhibition By The Wnt Agonist R-Spondin.
Nat. Commun. V. 4 2787 2013
PubMed-ID: 24225776 | Reference-DOI: 10.1038/NCOMMS3787

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
	Chains	:	A, C
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293T
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Expression System Vector	:	TRANSIENT
	Fragment	:	ECTODOMAIN, RESIDUES 53-205
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	ZINC/RING FINGER PROTEIN 3, ZNRF3

Molecule 2 - R-SPONDIN-2
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293T
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PHLSEC
	Expression System Taxid	:	9606
	Expression System Vector	:	TRANSIENT
	Fragment	:	FU1-FU2, RESIDUES 37-144
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	CYSTEINE-RICH AND SINGLE THROMBOSPONDIN DOMAIN-CONTAINING PR

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:199 , ARG C:199	BINDING SITE FOR RESIDUE CL A1206

Asymmetric/Biological Unit

No.	Residues
1	A:104	-	A:133
2	B:40	-	B:46
3	B:43	-	B:52
4	B:55	-	B:74
5	B:78	-	B:93
6	B:96	-	B:104
7	B:101	-	B:110
8	B:113	-	B:124
9	B:128	-	B:141
10	C:104	-	C:133
11	D:40	-	D:46
12	D:43	-	D:52
13	D:55	-	D:74
14	D:78	-	D:93
15	D:96	-	D:104
16	D:101	-	D:110
17	D:113	-	D:124
18	D:128	-	D:141

(no "Cis Peptide Bond" information available for 4C99)

(no "SAP(SNP)/Variant" information available for 4C99)

(no "PROSITE Motif" information available for 4C99)

(no "Exon" information available for 4C99)

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:153
 aligned with ZNRF3_MOUSE | Q5SSZ7 from UniProtKB/Swiss-Prot  Length:913

    Alignment length:153
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   
          ZNRF3_MOUSE    53 KETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHL 205
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeeee.hhhhh..............eeeee..hhhhh.....hhhhhhhhhhhh...eeeee....hhhhhhhhh.........eeeehhhhhhhhhhhhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c99 A  53 KETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHL 205
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with RSPO2_MOUSE | Q8BFU0 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:103
                                    48        58        68        78        88        98       108       118       128       138   
          RSPO2_MOUSE    39 ICKGCLSCSKDNGCSRCQQKLFFFLRREGMRQYGECLHSCPSGYYGHRAPDMNRCARCRIENCDSCFSKDFCTKCKVGFYLHRGRCFDECPDGFAPLDETMEC 141
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.......eee....eeeeeee..eeeeeee......ee..........ee......................eee..eee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4c99 B  39 ICKGCLSCSKDNGCSRCQQKLFFFLRREGMRQYGECLHSCPSGYYGHRAPDMNRCARCRIENCDSCFSKDFCTKCKVGFYLHRGRCFDECPDGFAPLDETMEC 141
                                    48        58        68        78        88        98       108       118       128       138

Chain C from PDB  Type:PROTEIN  Length:153
 aligned with ZNRF3_MOUSE | Q5SSZ7 from UniProtKB/Swiss-Prot  Length:913

    Alignment length:153
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   
          ZNRF3_MOUSE    53 KETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHL 205
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeeeeeeee........eeeeeee.hhhhh.............eeeeee..hhhhh.....hhhhhhhhhhhh.eeeeeee.....hhhhhhhhhh.......eeeehhhhhhhhhhhhhhh...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c99 C  53 KETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHL 205
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

Chain D from PDB  Type:PROTEIN  Length:105
 aligned with RSPO2_MOUSE | Q8BFU0 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:105
                                    48        58        68        78        88        98       108       118       128       138     
          RSPO2_MOUSE    39 ICKGCLSCSKDNGCSRCQQKLFFFLRREGMRQYGECLHSCPSGYYGHRAPDMNRCARCRIENCDSCFSKDFCTKCKVGFYLHRGRCFDECPDGFAPLDETMECVE 143
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeeee....ee..eee..eee..ee......eeeee....eeeee.....eeeeee..eeeee....eee..eee.......eee....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4c99 D  39 ICKGCLSCSKDNGCSRCQQKLFFFLRREGMRQYGECLHSCPSGYYGHRAPDMNRCARCRIENCDSCFSKDFCTKCKVGFYLHRGRCFDECPDGFAPLDETMECVE 143
                                    48        58        68        78        88        98       108       118       128       138

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 '\|'

(no "SCOP Domain" information available for 4C99)

(no "CATH Domain" information available for 4C99)

(no "Pfam Domain" information available for 4C99)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (ZNRF3_MOUSE | Q5SSZ7)

molecular function
	GO:0005109	frizzled binding	Interacting selectively and non-covalently with the frizzled (fz) receptor.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0038018	Wnt receptor catabolic process	The chemical reactions and pathways resulting in the breakdown of a Wnt receptor. Internalized Wnt receptors can be recycled to the plasma membrane or sorted to lysosomes for protein degradation.
	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:0060071	Wnt signaling pathway, planar cell polarity pathway	The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity.
	GO:0060070	canonical 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, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
	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:0090090	negative regulation of canonical Wnt signaling pathway	Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
	GO:2000051	negative regulation of non-canonical Wnt signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of non-canonical Wnt signaling pathway.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0072089	stem cell proliferation	The multiplication or reproduction of stem cells, resulting in the expansion of a stem cell population. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
	GO:0006511	ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B,D (RSPO2_MOUSE | Q8BFU0)

molecular function
	GO:0008201	heparin binding	Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
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:0030282	bone mineralization	The deposition of hydroxyapatite, a form of calcium phosphate with the formula Ca10(PO4)6(OH)2, in bone tissue.
	GO:0071542	dopaminergic neuron differentiation	The process in which a neuroblast acquires the specialized structural and functional features of a dopaminergic neuron, a neuron that secretes dopamine.
	GO:0035115	embryonic forelimb morphogenesis	The process, occurring in the embryo, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human.
	GO:0035116	embryonic hindlimb morphogenesis	The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.
	GO:0060441	epithelial tube branching involved in lung morphogenesis	The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units.
	GO:0060437	lung growth	The increase in size or mass of a lung. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
	GO:0042489	negative regulation of odontogenesis of dentin-containing tooth	Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx.
	GO:0001649	osteoblast differentiation	The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
	GO:0090263	positive regulation of canonical Wnt signaling pathway	Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
	GO:0050896	response to 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 stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0060535	trachea cartilage morphogenesis	The process in which the anatomical structures of cartilage in the trachea are generated and organized.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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.

Asymmetric/Biological Unit
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	4c99
		Family and Domain Information	:	ProDom \| SYSTERS
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		Orientation in Membranes	:	OPM
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	RSPO2_MOUSE \| Q8BFU0
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	ZNRF3_MOUSE \| Q5SSZ7
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	6.3.2.-
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		Pathway	:	KEGG \| MetaCyc

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	RSPO2_MOUSE \| Q8BFU0
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	ZNRF3_MOUSE \| Q5SSZ7
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UniProtKB/Swiss-Prot
	RSPO2_MOUSE \| Q8BFU0	:	4ufr 4ufs
	ZNRF3_MOUSE \| Q5SSZ7	:	4c86 4c8a 4c8c 4c8f 4c8p 4c9a 4c9e 4cdj 4cdk 4ufs

4c84	ZEBRAFISH ZNRF3 ECTODOMAIN CRYSTAL FORM I
4c85	ZEBRAFISH ZNRF3 ECTODOMAIN CRYSTAL FORM II
4c86	MOUSE ZNRF3 ECTODOMAIN CRYSTAL FORM I
4c8a	MOUSE ZNRF3 ECTODOMAIN CRYSTAL FORM II
4c8c	MOUSE ZNRF3 ECTODOMAIN CRYSTAL FORM III
4c8f	MOUSE ZNRF3 ECTODOMAIN CRYSTAL FORM IV
4c8p	MOUSE ZNRF3 ECTODOMAIN CRYSTAL FORM V, DISULFIDE-BRIDGED S90C VARIANT
4c8t	XENOPUS ZNRF3 ECTODOMAIN CRYSTAL FORM I
4c8u	XENOPUS ZNRF3 ECTODOMAIN CRYSTAL FORM II
4c8v	XENOPUS RSPO2 FU1-FU2 CRYSTAL FORM I
4c8w	XENOPUS RSPO2 FU1-FU2 CRYSTAL FORM II
4c9a	MOUSE ZNRF3 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2 (SELENO MET) CRYSTAL FORM I
4c9e	MOUSE ZNRF3 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2 (SELENO MET) CRYSTAL FORM II
4c9r	XENOPUS ZNRF3 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2 CRYSTAL FORM I
4c9u	XENOPUS ZNRF3 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2 CRYSTAL FORM II
4c9v	XENOPUS RNF43 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (18, 18)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (34, 35)

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