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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE C-TERMINAL REGION OF HUMAN ZFYVE9

Authors :   E. Williams, T. Krojer, M. Vollmar, L. Shrestha, F. Von Delft, C. H. Arr A. M. Edwards, C. Bountra, A. Bullock

Date :   30 Apr 13 (Deposition) - 15 May 13 (Release) - 15 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.53

Chains :   Asym./Biol. Unit : A

Keywords :   Receptor, Protein Interaction Domain, Tgf-Beta And Egfr Signalling, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Williams
Crystal Structure Of The C-Terminal Region Of Human Zfyve9
Ph D Thesis 2013
PubMed: search

Molecule 1 - ZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 9
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	PROTEIN INTERACTING DOMAIN, RESIDUES 895-1425
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	MGM
	Synonym	:	MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG-INTERACTING PROTEIN, MADH-INTERACTING PROTEIN, NOVEL SERINE PROTEASE, NSP, RECEPTOR ACTIVATION ANCHOR, HSARA, SMAD ANCHOR FOR RECEPTOR ACTIVATION, ZFYVE9C

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:1103 , HIS A:1104 , GLY A:1181 , ASN A:1182 , TYR A:1183 , ILE A:1221	BINDING SITE FOR RESIDUE EDO A2366
2	AC2	SOFTWARE	ARG A:1077 , ALA A:1080 , GLU A:1081 , ASN A:1178 , GLN A:1184 , GLN A:1186	BINDING SITE FOR RESIDUE PG4 A2367
3	AC3	SOFTWARE	GLU A:1081 , TYR A:1082 , ARG A:1083	BINDING SITE FOR RESIDUE EDO A2368
4	AC4	SOFTWARE	GLY A:974 , SER A:976 , VAL A:1012	BINDING SITE FOR RESIDUE EDO A2369
5	AC5	SOFTWARE	MET A:1130 , THR A:1198	BINDING SITE FOR RESIDUE EDO A2370
6	AC6	SOFTWARE	TYR A:1040 , GLN A:1041 , LEU A:1084 , TYR A:1085 , HOH A:2052	BINDING SITE FOR RESIDUE EDO A2371

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

Asymmetric/Biological Unit

No.	Residues
1	Pro A:1051	-	Pro A:1052
2	Tyr A:1085	-	Pro A:1086

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

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

Asymmetric/Biological Unit (12, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000371591	2b	ENSE00001455603	chr1:52682052-52682146	95	ZFYV9_HUMAN	-	0	0	-	-
1.3	ENST00000371591	3	ENSE00001233936	chr1:52698843-52698948	106	ZFYV9_HUMAN	1-24	24	0	-	-
1.4	ENST00000371591	4	ENSE00001140996	chr1:52703160-52705267	2108	ZFYV9_HUMAN	24-726	703	0	-	-
1.5a	ENST00000371591	5a	ENSE00001140989	chr1:52729445-52729544	100	ZFYV9_HUMAN	727-760	34	0	-	-
1.6	ENST00000371591	6	ENSE00001030124	chr1:52732327-52732503	177	ZFYV9_HUMAN	760-819	60	0	-	-
1.7	ENST00000371591	7	ENSE00001030120	chr1:52734135-52734304	170	ZFYV9_HUMAN	819-875	57	0	-	-
1.8	ENST00000371591	8	ENSE00001030105	chr1:52740136-52740256	121	ZFYV9_HUMAN	876-916	41	1	A:895-911	17
1.9	ENST00000371591	9	ENSE00001030109	chr1:52744164-52744286	123	ZFYV9_HUMAN	916-957	42	1	A:917-957 (gaps)	41
1.10	ENST00000371591	10	ENSE00001030112	chr1:52747333-52747488	156	ZFYV9_HUMAN	957-1009	53	1	A:957-1009	53
1.11	ENST00000371591	11	ENSE00001064551	chr1:52759125-52759349	225	ZFYV9_HUMAN	1009-1084	76	1	A:1009-1084	76
1.12	ENST00000371591	12	ENSE00001064557	chr1:52761567-52761649	83	ZFYV9_HUMAN	1084-1111	28	1	A:1084-1111	28
1.13	ENST00000371591	13	ENSE00001157067	chr1:52769493-52769597	105	ZFYV9_HUMAN	1112-1146	35	1	A:1112-1146	35
1.14	ENST00000371591	14	ENSE00001064556	chr1:52798440-52798590	151	ZFYV9_HUMAN	1147-1197	51	1	A:1147-1197	51
1.15a	ENST00000371591	15a	ENSE00001064560	chr1:52800360-52800440	81	ZFYV9_HUMAN	1197-1224	28	1	A:1197-1224 (gaps)	28
1.16	ENST00000371591	16	ENSE00001191836	chr1:52803444-52803606	163	ZFYV9_HUMAN	1224-1278	55	1	A:1224-1278 (gaps)	55
1.17	ENST00000371591	17	ENSE00001191763	chr1:52805798-52805903	106	ZFYV9_HUMAN	1278-1313	36	1	A:1278-1313 (gaps)	36
1.18	ENST00000371591	18	ENSE00001352195	chr1:52810440-52810616	177	ZFYV9_HUMAN	1314-1372	59	1	A:1314-1372 (gaps)	59
1.19c	ENST00000371591	19c	ENSE00001455602	chr1:52811732-52812358	627	ZFYV9_HUMAN	1373-1425	53	1	A:1373-1424 (gaps)	52

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:479
 aligned with ZFYV9_HUMAN | O95405 from UniProtKB/Swiss-Prot  Length:1425

    Alignment length:530
                                   904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384      1394      1404      1414      1424
         ZFYV9_HUMAN    895 AMNLIPEDGLPPILISTGVKGDYAVEEKPSQISVMQQLEDGGPDPLVFVLNANLLSMVKIVNYVNRKCWCFTTKGMHAVGQSEIVILLQCLPDEKCLPKDIFNHFVQLYRDALAGNVVSNLGHSFFSQSFLGSKEHGGFLYVTSTYQSLQDLVLPTPPYLFGILIQKWETPWAKVFPIRLMLRLGAEYRLYPCPLFSVRFRKPLFGETGHTIMNLLADFRNYQYTLPVVQGLVVDMEVRKTSIKIPSNRYNEMMKAMNKSNEHVLAGGACFNEKADSHLVCVQNDDGNYQTQAISIHNQPRKVTGASFFVFSGALKSSSGYLAKSSIVEDGVMVQITAENMDSLRQALREMKDFTITCGKADAEEPQEHIHIQWVDDDKNVSKGVVSPIDGKSMETITNVKIFHGSEYKANGKVIRWTEVFFLENDDQHNCLSDPADHSRLTEHVAKAFCLALCPHLKLLKEDGMTKLGLRVTLDSDQVGYQAGSNGQPLPSQYMNDLDSALVPVIHGGACQLSEGPVVMELIFYILENI 1424
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..-----.eee...hhhhhhhhhh.--...eeeeee..eeeeeeeeee..eeeeeeeee.hhhhh..eeeeeee.........hhhhhhhhhhhhhhhh........eee..........eeeeeee................eeeeeeee..hhhhhhhhhhhhhhhhhhhhh......ee.............hhhhhh................eeeee..eeeeeee..hhhhhhhhhhh....eeeee........eeeeeee.....eeeeeee........ee..eeeee...-------.eeeee..eeeee.hhhhhhhhhhhhhh...eee-----------.eeeeeee......................eeee...--.eee..eeeeeeeeee..--------------hhhhhhhhhhhhhhhh.hhhhhhhh...eeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhh----------.eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8 [INCOMPLETE] ----------------------------------------Exon 1.10  PDB: A:957-1009 UniProt: 957-1009         --------------------------------------------------------------------------Exon 1.12  PDB: A:1084-1111 Exon 1.13  PDB: A:1112-1146        Exon 1.14  PDB: A:1147-1197 UniProt: 1147-1197     --------------------------Exon 1.16  PDB: A:1224-1278 (gaps) UniProt: 1224-1278  -----------------------------------Exon 1.18  PDB: A:1314-1372 (gaps) UniProt: 1314-1372      Exon 1.19c  PDB: A:1373-1424 (gaps) [INCOMPLETE]     Transcript 1 (1)
           Transcript 1 (2) ---------------------Exon 1.9  PDB: A:917-957 (gaps)           ---------------------------------------------------Exon 1.11  PDB: A:1009-1084 UniProt: 1009-1084                              ----------------------------------------------------------------------------------------------------------------Exon 1.15a                  -----------------------------------------------------Exon 1.17  PDB: A:1278-1313 (gaps)  --------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                4bkw A  895 AMNLIPEDGLPPILIST-----YAVEEKPSQISVMQQLED--PDPLVFVLNANLLSMVKIVNYVNRKCWCFTTKGMHAVGQSEIVILLQCLPDEKCLPKDIFNHFVQLYRDALAGNVVSNLGHSFFSQSFLGSKEHGGFLYVTSTYQSLQDLVLPTPPYLFGILIQKWETPWAKVFPIRLMLRLGAEYRLYPCPLFSVRFRKPLFGETGHTIMNLLADFRNYQYTLPVVQGLVVDMEVRKTSIKIPSNRYNEMMKAMNKSNEHVLAGGACFNEKADSHLVCVQNDDGNYQTQAISIHNQPRKVTGASFFVFSGAL-------AKSSIVEDGVMVQITAENMDSLRQALREMKDFTI-----------EHIHIQWVDDDKNVSKGVVSPIDGKSMETITNVKIFH--EYKANGKVIRWTEVFFLE--------------SRLTEHVAKAFCLALCPHLKLLKEDGMTKLGLRVTLDSDQVGYQAGSNGQPLPSQYMNDLDSALVPVIH----------VVMELIFYILENI 1424
                                   904      |  -  |    924       934  |    944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204    |    -  |   1224      1234      1244     |   -      1264      1274      1284      1294   |  1304      1314   |     -      1334      1344      1354      1364      1374      1384      1394      |  -      1414      1424
                                          911   917              934  |                                                                                                                                                                                                                                                                            1209    1217                             1250        1262                                1298  |             1318           1333                                                                1401       1412            
                                                                    937                                                                                                                                                                                                                                                                                                                                                                        1301

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 4BKW)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ZFYV9_HUMAN | O95405)

molecular function
	GO:0005545	1-phosphatidylinositol binding	Interacting selectively and non-covalently with phosphatidylinositol, any glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0007183	SMAD protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex that contains SMAD proteins.
	GO:0007184	SMAD protein import into nucleus	The directed movement of a SMAD proteins from the cytoplasm into the nucleus. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
	GO:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0007179	transforming growth factor beta receptor signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0031901	early endosome membrane	The lipid bilayer surrounding an early endosome.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Pro A:1051 - Pro A:1052	[ RasMol ]
		Tyr A:1085 - Pro A:1086	[ RasMol ]

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	4bkw
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(no "Related Entries Specified in the PDB File" available for 4BKW)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (12, 12)

Sequences/Alignments

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Gene Ontology (14, 14)

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