1JHJ - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE APC10/DOC1 SUBUNIT OF THE HUMAN ANAPHASE-PROMOTING COMPLEX

Authors :   K. S. Wendt, H. C. Vodermaier, U. Jacob, C. Gieffers, M. Gmachl, J. -M. Pe R. Huber, P. Sondermann

Date :   28 Jun 01 (Deposition) - 24 Oct 01 (Release) - 29 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Beta Sandwich, Jellyroll, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. S. Wendt, H. C. Vodermaier, U. Jacob, C. Gieffers, M. Gmachl, J. M. Peters, R. Huber, P. Sondermann
Crystal Structure Of The Apc10/Doc1 Subunit Of The Human Anaphase-Promoting Complex.
Nat. Struct. Biol. V. 8 784 2001
PubMed-ID: 11524682 | Reference-DOI: 10.1038/NSB0901-784

Molecule 1 - APC10
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11D
	Expression System Strain	:	B834(DE3)PUBS250
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NI	1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:2 , GLU A:87 , HOH A:404 , HOH A:427 , HOH A:464	BINDING SITE FOR RESIDUE NI A 320

(no "SS Bond" information available for 1JHJ)

Asymmetric/Biological Unit

No.	Residues
1	Gln A:60	-	Pro A:61

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_025200	R	46	Q	APC10_HUMAN	Polymorphism	35257136	A	R	46	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1JHJ)

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000309439	2b	ENSE00001385530	chr4:146019365-146019283	83	APC10_HUMAN	-	0	0	-	-
1.5	ENST00000309439	5	ENSE00002201146	chr4:146017263-146017137	127	APC10_HUMAN	1-39	39	1	A:2-39	38
1.6a	ENST00000309439	6a	ENSE00002167820	chr4:146002902-146002812	91	APC10_HUMAN	39-69	31	1	A:39-69	31
1.7	ENST00000309439	7	ENSE00002201140	chr4:145985844-145985724	121	APC10_HUMAN	69-109	41	1	A:69-109	41
1.12e	ENST00000309439	12e	ENSE00002083761	chr4:145916755-145916310	446	APC10_HUMAN	110-185	76	1	A:110-162	53

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:161
 aligned with APC10_HUMAN | Q9UM13 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
          APC10_HUMAN     2 TTPNKTPPGADPKQLERTGTVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQPHLVNIQFRRKTTVKTLCIYADYKSDESYTPSKISVRVGNNFHNLQEIRQLELVEPSGWIHVPLTDNHKKPTRTFMIQIAVLANHQNGRDTHMRQIKIYTPV 162
               SCOP domains d1jhja_ A: APC10/DOC1 subunit of the anaphase-promoting complex                                                                                                   SCOP domains
               CATH domains 1jhjA00 A:2-162 Galactose-binding domain-like                                                                                                                     CATH domains
               Pfam domains -APC10-1jhjA01 A:3-162                                                                                                                                            Pfam domains
         Sec.struct. author ..........hhhhhhhh..eee.hhhheeee........hhhhhh......ee......eeeeeeeeeeeee.eeeeeeehhhhh...eeeeeeeee......eeeeeee....eeeeeee........eeeeeeeeeeeee.hhh...ee.eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------Q-------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:2-39 UniProt: 1-39   -----------------------------Exon 1.7  PDB: A:69-109 UniProt: 69-109  Exon 1.12e  PDB: A:110-162 UniProt: 110-185           Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.6a  PDB: A:39-69        --------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1jhj A   2 ATPNKTPPGADPKQLERTGTVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQPHLVNIQFRRKTTVKTLCIYADYKSDESYTPSKISVRVGNNFHNLQEIRQLELVEPSGWIHVPLTDNHKKPTRTFMIQIAVLANHQNGRDTHMRQIKIYTPV 162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Galactose-binding domain-like (314)

Superfamily: Galactose-binding domain-like (314)

Family: APC10-like (4)

Protein domain: APC10/DOC1 subunit of the anaphase-promoting complex (2)

Human (Homo sapiens) [TaxId: 9606] (1)

d1jhja_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Galactose-binding domain-like (195)

Human (Homo sapiens) (39)

1jhjA00

A:2-162

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GBD (153)

Family: APC10 (1)

Homo sapiens (Human) (1)

APC10-1jhjA01

A:3-162

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (APC10_HUMAN | Q9UM13)

biological process
	GO:0031145	anaphase-promoting complex-dependent 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 ubiquitin, with ubiquitin-protein ligation catalyzed by the anaphase-promoting complex, and mediated by the proteasome.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0051436	negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	Any process that stops, prevents, or reduces the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.
	GO:0051437	positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition	Any process that activates, maintains or increases the rate of ubiquitin ligase activity that contributes to the regulation of the mitotic cell cycle phase transition.
	GO:0043161	proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
	GO:0070979	protein K11-linked ubiquitination	A protein ubiquitination process in which ubiquitin monomers are attached to a protein, and then ubiquitin polymers are formed by linkages between lysine residues at position 11 of the ubiquitin monomers. K11-linked polyubiquitination targets the substrate protein for degradation. The anaphase-promoting complex promotes the degradation of mitotic regulators by assembling K11-linked polyubiquitin chains.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0042787	protein ubiquitination involved in ubiquitin-dependent protein catabolic process	The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
	GO:0030071	regulation of mitotic metaphase/anaphase transition	Any process that modulates the frequency, rate or extent of the cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin.
	GO:0051439	regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle	A cell cycle process that modulates the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.
cellular component
	GO:0005680	anaphase-promoting complex	A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Asymmetric/Biological Unit
	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
		NI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gln A:60 - Pro A:61	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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)

Access by PDB/NDB ID
	1jhj
		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
	APC10_HUMAN \| Q9UM13
		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

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
	APC10_HUMAN \| Q9UM13
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	APC10_HUMAN \| Q9UM13	:	4ui9 5a31 5g04 5g05 5khr 5khu 5l9t 5l9u 5lcw

(no "Related Entries Specified in the PDB File" available for 1JHJ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (0, 0)

Exons (4, 4)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (15, 15)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File