3E1R - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   MIDBODY TARGETING OF THE ESCRT MACHINERY BY A NON-CANONICAL COILED-COIL IN CEP55

Authors :   H. H. Lee, N. Elia, R. Ghirlando, J. Lippincott-Schwartz, J. H. Hurley

Date :   04 Aug 08 (Deposition) - 04 Nov 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Cep55, Alix, Cytokinesis, Escrt, Alternative Splicing, Cell Cycle, Cell Division, Coiled Coil, Mitosis, Phosphoprotein, Polymorphism, Acetylation, Apoptosis, Cytoplasm, Host-Virus Interaction, Protein Transport, Transport, Cell Cycle/Transport Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. H. Lee, N. Elia, R. Ghirlando, J. Lippincott-Schwartz, J. H. Hurley
Midbody Targeting Of The Escrt Machinery By A Noncanonical Coiled Coil In Cep55.
Science V. 322 576 2008
PubMed-ID: 18948538 | Reference-DOI: 10.1126/SCIENCE.1162042
(for further references see the PDB file header)

Molecule 1 - CENTROSOMAL PROTEIN OF 55 KDA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PARALLEL GST2
	Expression System Strain	:	BL21 CODONPLUS(DE3)-RIL
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 160-217
	Gene	:	CEP55, C10ORF3, URCC6
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CEP55, UP-REGULATED IN COLON CANCER 6

Molecule 2 - PROGRAMMED CELL DEATH 6-INTERACTING PROTEIN
	Chains	:	C
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 797-809
	Other Details	:	SYNTHETIC PEPTIDE
	Synonym	:	PDCD6-INTERACTING PROTEIN, ALG-2-INTERACTING PROTEIN 1, HP95
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3E1R)

(no "Site" information available for 3E1R)

(no "SS Bond" information available for 3E1R)

(no "Cis Peptide Bond" information available for 3E1R)

(no "SAP(SNP)/Variant" information available for 3E1R)

(no "PROSITE Motif" information available for 3E1R)

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000307296	1b	ENSE00001884181	chr3:33839844-33840429	586	PDC6I_HUMAN	1-70	70	0	-	-
1.4	ENST00000307296	4	ENSE00001770534	chr3:33853564-33853618	55	PDC6I_HUMAN	70-88	19	0	-	-
1.5b	ENST00000307296	5b	ENSE00001632925	chr3:33855051-33855120	70	PDC6I_HUMAN	89-112	24	0	-	-
1.6c	ENST00000307296	6c	ENSE00001802994	chr3:33863447-33863574	128	PDC6I_HUMAN	112-154	43	0	-	-
1.7d	ENST00000307296	7d	ENSE00001141015	chr3:33866679-33866832	154	PDC6I_HUMAN	155-206	52	0	-	-
1.8b	ENST00000307296	8b	ENSE00001141009	chr3:33867972-33868072	101	PDC6I_HUMAN	206-239	34	0	-	-
1.10c	ENST00000307296	10c	ENSE00001141002	chr3:33870345-33870461	117	PDC6I_HUMAN	240-278	39	0	-	-
1.12b	ENST00000307296	12b	ENSE00001608471	chr3:33877536-33877758	223	PDC6I_HUMAN	279-353	75	0	-	-
1.13b	ENST00000307296	13b	ENSE00001630102	chr3:33879696-33879819	124	PDC6I_HUMAN	353-394	42	0	-	-
1.14	ENST00000307296	14	ENSE00001140976	chr3:33883389-33883566	178	PDC6I_HUMAN	394-453	60	0	-	-
1.15b	ENST00000307296	15b	ENSE00001785905	chr3:33885604-33885715	112	PDC6I_HUMAN	454-491	38	0	-	-
1.16	ENST00000307296	16	ENSE00001732288	chr3:33886911-33887080	170	PDC6I_HUMAN	491-547	57	0	-	-
1.18a	ENST00000307296	18a	ENSE00001783635	chr3:33893980-33894228	249	PDC6I_HUMAN	548-630	83	0	-	-
1.19b	ENST00000307296	19b	ENSE00001596979	chr3:33895371-33895505	135	PDC6I_HUMAN	631-675	45	0	-	-
1.20b	ENST00000307296	20b	ENSE00001097440	chr3:33896658-33896752	95	PDC6I_HUMAN	676-707	32	0	-	-
1.21c	ENST00000307296	21c	ENSE00001140939	chr3:33905498-33905621	124	PDC6I_HUMAN	707-748	42	0	-	-
1.22b	ENST00000307296	22b	ENSE00001140934	chr3:33906735-33906922	188	PDC6I_HUMAN	749-811	63	1	C:797-809	13
1.23b	ENST00000307296	23b	ENSE00001218677	chr3:33907843-33911194	3352	PDC6I_HUMAN	811-868	58	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:46
 aligned with CEP55_HUMAN | Q53EZ4 from UniProtKB/Swiss-Prot  Length:464

    Alignment length:46
                                   174       184       194       204      
          CEP55_HUMAN   165 NNIHEMEIQLKDALEKNQQWLVYDQQREVYVKGLLAKIFELEKKTE 210
               SCOP domains ---------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 3e1r A 165 NNIHEMEIQLKDALEKNQQWLVYDQQREVYVKGLLAKIFELEKKTE 210
                                   174       184       194       204

Chain B from PDB  Type:PROTEIN  Length:42
 aligned with CEP55_HUMAN | Q53EZ4 from UniProtKB/Swiss-Prot  Length:464

    Alignment length:42
                                   176       186       196       206  
          CEP55_HUMAN   167 IHEMEIQLKDALEKNQQWLVYDQQREVYVKGLLAKIFELEKK 208
               SCOP domains ------------------------------------------ SCOP domains
               CATH domains ------------------------------------------ CATH domains
               Pfam domains ------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------ PROSITE
                 Transcript ------------------------------------------ Transcript
                 3e1r B 167 IHEMEIQLKDALEKNQQWLVYDQQREVYVKGLLAKIFELEKK 208
                                   176       186       196       206

Chain C from PDB  Type:PROTEIN  Length:13
 aligned with PDC6I_HUMAN | Q8WUM4 from UniProtKB/Swiss-Prot  Length:868

    Alignment length:13
                                   806   
          PDC6I_HUMAN   797 QAQGPPYPTYPGY 809
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
               Transcript 1 Exon 1.22b    Transcript 1
                 3e1r C 797 QAQGPPYPTYPGY 809
                                   806

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 3E1R)

(no "CATH Domain" information available for 3E1R)

(no "Pfam Domain" information available for 3E1R)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CEP55_HUMAN | Q53EZ4)

molecular function
	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: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:0000920	cell separation after cytokinesis	The process of physically separating progeny cells after cytokinesis; this may involve enzymatic digestion of septum or cell wall components.
	GO:0045184	establishment of protein localization	The directed movement of a protein to a specific location.
	GO:0000281	mitotic cytokinesis	A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.
	GO:0007080	mitotic metaphase plate congression	The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis.
	GO:0006997	nucleus organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
cellular component
	GO:0005814	centriole	A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0032154	cleavage furrow	The cleavage furrow is a plasma membrane invagination at the cell division site. The cleavage furrow begins as a shallow groove and eventually deepens to divide the cytoplasm.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0045171	intercellular bridge	A direct connection between the cytoplasm of two cells that is formed following the completion of cleavage furrow ingression during cell division. They are usually present only briefly prior to completion of cytokinesis. However, in some cases, such as the bridges between germ cells during their development, they become stabilised.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	GO:0030496	midbody	A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.

Chain C (PDC6I_HUMAN | Q8WUM4)

molecular function
	GO:0048306	calcium-dependent 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), in the presence of calcium.
	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:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0031871	proteinase activated receptor binding	Interacting selectively and non-covalently with a proteinase activated receptor.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	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:0000920	cell separation after cytokinesis	The process of physically separating progeny cells after cytokinesis; this may involve enzymatic digestion of septum or cell wall components.
	GO:0007080	mitotic metaphase plate congression	The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis.
	GO:0036258	multivesicular body assembly	The aggregation, arrangement and bonding together of a set of components to form a multivesicular body, a type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
	GO:0006997	nucleus organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
	GO:1903543	positive regulation of exosomal secretion	Any process that activates or increases the frequency, rate or extent of exosomal secretion.
	GO:1903553	positive regulation of extracellular exosome assembly	Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly.
	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:0010824	regulation of centrosome duplication	Any process that modulates the frequency, rate or extent of centrosome duplication. Centrosome duplication is the replication of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized.
	GO:1903551	regulation of extracellular exosome assembly	Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly.
	GO:1901673	regulation of mitotic spindle assembly	Any process that modulates the frequency, rate or extent of mitotic spindle assembly.
	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.
	GO:0090611	ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway	The chemical reactions and pathways resulting in the breakdown of a protein or peptide, via the multivesicular body (MVB) sorting pathway; proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation. This process is independent of ubiquitination.
	GO:0039702	viral budding via host ESCRT complex	Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
	GO:0019058	viral life cycle	A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0070971	endoplasmic reticulum exit site	An endoplasmic reticulum part at which COPII-coated vesicles are produced.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.
	GO:1903561	extracellular vesicle	Any vesicle that is part of the extracellular region.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0001772	immunological synapse	An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
	GO:0042470	melanosome	A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.

Asymmetric/Biological Unit
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