2YQM - JenaLib

NMR Structure - manually

NMR Structure - model 1

NMR Structure - model 1, sites

NMR Structure - all models

collapse

expand

NMR Structure - manually (Jmol Viewer)

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Description

Title :   SOLUTION STRUCTURE OF THE FYVE DOMAIN IN ZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 12

Authors :   F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   30 Mar 07 (Deposition) - 02 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Nmr, Fyve Domain, Zinc Finger Fyve Domain-Containing Protein 12, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of The Fyve Domain In Zinc Finger Fyve Domain-Containing Protein 12
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - RUN AND FYVE DOMAIN-CONTAINING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P060327-08
	Expression System Vector Type	:	PLASMID
	Fragment	:	FYVE DOMAIN, UNP RESIDUES 627-708
	Gene	:	RUFY1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	FYVE-FINGER PROTEIN EIP1, ZINC FINGER FYVE DOMAIN- CONTAINING PROTEIN 12, LA-BINDING PROTEIN 1, RAB4- INTERACTING PROTEIN

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 2)

NMR Structure (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Sites (2, 2)

NMR Structure (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:29 , CYS A:32 , CYS A:53 , CYS A:56	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	CYS A:45 , CYS A:48 , CYS A:73 , CYS A:76	BINDING SITE FOR RESIDUE ZN A 401

SS Bonds (0, 0)

(no "SS Bond" information available for 2YQM)

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_FYVE	PS50178	Zinc finger FYVE/FYVE-related type profile.	RUFY1_HUMAN	642-700	1	A:23-81

Exons (4, 4)

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000319449	1a	ENSE00001372451	chr5:178977559-178977880	322	RUFY1_HUMAN	1-104	104	0	-	-
1.3d	ENST00000319449	3d	ENSE00001770679	chr5:178987026-178987199	174	RUFY1_HUMAN	104-162	59	0	-	-
1.4a	ENST00000319449	4a	ENSE00001240095	chr5:178989548-178989665	118	RUFY1_HUMAN	162-201	40	0	-	-
1.5a	ENST00000319449	5a	ENSE00001240088	chr5:178994462-178994563	102	RUFY1_HUMAN	201-235	35	0	-	-
1.6b	ENST00000319449	6b	ENSE00001240082	chr5:178996303-178996426	124	RUFY1_HUMAN	235-276	42	0	-	-
1.7a	ENST00000319449	7a	ENSE00001240078	chr5:179004076-179004137	62	RUFY1_HUMAN	277-297	21	0	-	-
1.8	ENST00000319449	8	ENSE00001240074	chr5:179007948-179008013	66	RUFY1_HUMAN	297-319	23	0	-	-
1.9	ENST00000319449	9	ENSE00001240067	chr5:179012797-179012866	70	RUFY1_HUMAN	319-342	24	0	-	-
1.11b	ENST00000319449	11b	ENSE00001795047	chr5:179016547-179016648	102	RUFY1_HUMAN	343-376	34	0	-	-
1.13	ENST00000319449	13	ENSE00001649014	chr5:179018626-179018742	117	RUFY1_HUMAN	377-415	39	0	-	-
1.14b	ENST00000319449	14b	ENSE00001689103	chr5:179020479-179020646	168	RUFY1_HUMAN	416-471	56	0	-	-
1.15b	ENST00000319449	15b	ENSE00001689109	chr5:179021867-179021964	98	RUFY1_HUMAN	472-504	33	0	-	-
1.16c	ENST00000319449	16c	ENSE00001644060	chr5:179023563-179023682	120	RUFY1_HUMAN	504-544	41	0	-	-
1.17	ENST00000319449	17	ENSE00001742098	chr5:179025693-179025822	130	RUFY1_HUMAN	544-587	44	0	-	-
1.18a	ENST00000319449	18a	ENSE00001666679	chr5:179028893-179028987	95	RUFY1_HUMAN	588-619	32	1	A:1-4 (gaps)	6
1.19a	ENST00000319449	19a	ENSE00001750822	chr5:179032877-179032925	49	RUFY1_HUMAN	619-635	17	1	A:4-16 (gaps)	17
1.20d	ENST00000319449	20d	ENSE00001696739	chr5:179034583-179034660	78	RUFY1_HUMAN	636-661	26	1	A:17-42	26
1.22g	ENST00000319449	22g	ENSE00001515319	chr5:179036377-179037027	651	RUFY1_HUMAN	662-708	47	1	A:43-89	47

Sequences/Alignments

NMR Structure

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:89
 aligned with RUFY1_HUMAN | Q96T51 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:95
                                   623       633       643       653       663       673       683       693       703     
          RUFY1_HUMAN   614 GLHLSQSKLKMEDIKEVNQALKGHAWLKDDEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNELALPSYPKPVRVCDSCHTLLLQRCSSTAS 708
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------FYVE-2yqmA01 A:18-82                                             ------- Pfam domains
         Sec.struct. author ..--...----....................................eee......eeehhh..eee........eee.hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------ZF_FYVE  PDB: A:23-81 UniProt: 642-700                     -------- PROSITE
           Transcript 1 (1) 1.18a ----------------Exon 1.20d  PDB: A:17-42  Exon 1.22g  PDB: A:43-89 UniProt: 662-708       Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.19a       ------------------------------------------------------------------------- Transcript 1 (2)
                 2yqm A   1 GS--SGS----SGIKEVNQALKGHAWLKDDEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNELALPSYPKPVRVCDSCHTLLLQRCSSTAS  89
                             |  | |  - |      14        24        34        44        54        64        74        84     
                             2  3 5    6

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 (0, 0)

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

CATH Domains (0, 0)

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

Pfam Domains (1, 1)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: zf-FYVE-PHD (57)

Family: FYVE (5)

Homo sapiens (Human) (4)

FYVE-2yqmA01

A:18-82

Gene Ontology (15, 15)

NMR Structure(hide GO term definitions)

Chain A (RUFY1_HUMAN | Q96T51)

molecular function
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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:0008565	protein transporter activity	Enables the directed movement of proteins into, out of or within a cell, or between cells.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0030100	regulation of endocytosis	Any process that modulates the frequency, rate or extent of endocytosis.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Visualization

Interactive Views

NMR Structure
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2yqm)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - model 1, sites PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2yqm
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RUFY1_HUMAN \| Q96T51
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RUFY1_HUMAN \| Q96T51
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	RUFY1_HUMAN \| Q96T51	:	2yw8

Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YQM)