1OM9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF THE GGA1-APPENDAGE IN COMPLEX WITH THE P56 BINDING PEPTIDE

Authors :   B. M. Collins, G. J. K. Praefcke, M. S. Robinson, D. J. Owen

Date :   25 Feb 03 (Deposition) - 29 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,P,Q
Biol. Unit 1: A,P  (1x)
Biol. Unit 2: B,Q  (1x)
Biol. Unit 3: A,B,P,Q  (1x)

Keywords :   Beta Sandwich, Beta Augmentation, Gga, Adaptin, Clathrin Adaptor, Protein Transport, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. M. Collins, G. J. K. Praefcke, M. S. Robinson, D. J. Owen
Structural Basis For Binding Of Accessory Proteins By The Appendage Domain Of Ggas
Nat. Struct. Biol. V. 10 607 2003
PubMed-ID: 12858163 | Reference-DOI: 10.1038/NSB955
(for further references see the PDB file header)

Molecule 1 - ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMWH6172
	Expression System Strain	:	BL21(DE3)/PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	IPTG INDUCIBLE T7 RNA POLYMERASE PROMOTER
	Fragment	:	APPENDAGE DOMAIN, RESIDUES 494-639 OF SWS Q9UJY5
	Gene	:	GGA1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GGA1-APPENDAGE DOMAIN

Molecule 2 - 15-MER PEPTIDE FRAGMENT OF P56
	Chains	:	P, Q
	Engineered	:	YES
	Other Details	:	SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	P	Q
Biological Unit 1 (1x)	:	A		P
Biological Unit 2 (1x)	:		B		Q
Biological Unit 3 (1x)	:	A	B	P	Q

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1OM9)

(no "Site" information available for 1OM9)

(no "SS Bond" information available for 1OM9)

(no "Cis Peptide Bond" information available for 1OM9)

(no "SAP(SNP)/Variant" information available for 1OM9)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GAE	PS50180	Gamma-adaptin ear (GAE) domain profile.	GGA1_HUMAN	510-631	2	A:510-631 B:510-631

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GAE	PS50180	Gamma-adaptin ear (GAE) domain profile.	GGA1_HUMAN	510-631	1	A:510-631 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GAE	PS50180	Gamma-adaptin ear (GAE) domain profile.	GGA1_HUMAN	510-631	1	- B:510-631

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GAE	PS50180	Gamma-adaptin ear (GAE) domain profile.	GGA1_HUMAN	510-631	2	A:510-631 B:510-631

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000343632	1a	ENSE00001813421	chr22:38004482-38004910	429	GGA1_HUMAN	1-15	15	0	-	-
1.7c	ENST00000343632	7c	ENSE00002140158	chr22:38010197-38010281	85	GGA1_HUMAN	15-43	29	0	-	-
1.8a	ENST00000343632	8a	ENSE00001612880	chr22:38012929-38013004	76	GGA1_HUMAN	43-68	26	0	-	-
1.9c	ENST00000343632	9c	ENSE00001683976	chr22:38014455-38014553	99	GGA1_HUMAN	69-101	33	0	-	-
1.10f	ENST00000343632	10f	ENSE00000880168	chr22:38016245-38016368	124	GGA1_HUMAN	102-143	42	0	-	-
1.11b	ENST00000343632	11b	ENSE00000880169	chr22:38016820-38016920	101	GGA1_HUMAN	143-176	34	0	-	-
1.12c	ENST00000343632	12c	ENSE00000653934	chr22:38017623-38017703	81	GGA1_HUMAN	177-203	27	0	-	-
1.13	ENST00000343632	13	ENSE00000880172	chr22:38019334-38019474	141	GGA1_HUMAN	204-250	47	0	-	-
1.14b	ENST00000343632	14b	ENSE00000880174	chr22:38019559-38019640	82	GGA1_HUMAN	251-278	28	0	-	-
1.14e	ENST00000343632	14e	ENSE00001286815	chr22:38020976-38021083	108	GGA1_HUMAN	278-314	37	0	-	-
1.15a	ENST00000343632	15a	ENSE00000653938	chr22:38021804-38021956	153	GGA1_HUMAN	314-365	52	0	-	-
1.16	ENST00000343632	16	ENSE00000653944	chr22:38025469-38025533	65	GGA1_HUMAN	365-386	22	0	-	-
1.17a	ENST00000343632	17a	ENSE00000653945	chr22:38026005-38026177	173	GGA1_HUMAN	387-444	58	0	-	-
1.18b	ENST00000343632	18b	ENSE00000653946	chr22:38026910-38027106	197	GGA1_HUMAN	444-510	67	2	A:498-510 B:498-510	13 13
1.19	ENST00000343632	19	ENSE00000653947	chr22:38028003-38028172	170	GGA1_HUMAN	510-566	57	2	A:510-566 B:510-566	57 57
1.20	ENST00000343632	20	ENSE00000653948	chr22:38028412-38028522	111	GGA1_HUMAN	567-603	37	2	A:567-603 B:567-603	37 37
1.21d	ENST00000343632	21d	ENSE00001823052	chr22:38028608-38029571	964	GGA1_HUMAN	604-639	36	2	A:604-639 B:604-639	36 36

2.1	ENST00000381259	1	ENSE00001319793	chr12:28410133-28410178	46	CCD91_HUMAN	1-10	10	2	P:3-9 Q:4-9	7 6
2.2	ENST00000381259	2	ENSE00001297407	chr12:28412297-28412375	79	CCD91_HUMAN	11-37	27	2	P:10-13 Q:10-13	4 4
2.4	ENST00000381259	4	ENSE00001157215	chr12:28458582-28458739	158	CCD91_HUMAN	37-89	53	0	-	-
2.5	ENST00000381259	5	ENSE00001157204	chr12:28459675-28459878	204	CCD91_HUMAN	90-157	68	0	-	-
2.6	ENST00000381259	6	ENSE00001158522	chr12:28460578-28460682	105	CCD91_HUMAN	158-192	35	0	-	-
2.7	ENST00000381259	7	ENSE00001157193	chr12:28515371-28515448	78	CCD91_HUMAN	193-218	26	0	-	-
2.8	ENST00000381259	8	ENSE00001132871	chr12:28544237-28544344	108	CCD91_HUMAN	219-254	36	0	-	-
2.9	ENST00000381259	9	ENSE00000835968	chr12:28603094-28603186	93	CCD91_HUMAN	255-285	31	0	-	-
2.10	ENST00000381259	10	ENSE00000835969	chr12:28603283-28603351	69	CCD91_HUMAN	286-308	23	0	-	-
2.11	ENST00000381259	11	ENSE00000835970	chr12:28605411-28605587	177	CCD91_HUMAN	309-367	59	0	-	-
2.12	ENST00000381259	12	ENSE00000835971	chr12:28636985-28637098	114	CCD91_HUMAN	368-405	38	0	-	-
2.13	ENST00000381259	13	ENSE00001487987	chr12:28701996-28703098	1103	CCD91_HUMAN	406-441	36	0	-	-

Asymmetric 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:142
 aligned with GGA1_HUMAN | Q9UJY5 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:142
                                   507       517       527       537       547       557       567       577       587       597       607       617       627       637  
           GGA1_HUMAN   498 ASITVPLESIKPSNILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETWGSL 639
               SCOP domains d1om9a_ A: ADP-ribosylation factor binding protein Gga1 domain                                                                                 SCOP domains
               CATH domains 1om9A00 A:498-639  [code=2.60.40.1230, no name defined]                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......eeeeee..eeeeeeeee........eeeeeeeeee.....eeeeeeeee.....eeee..................eeeeeeeee........eeeeeeeee..eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------GAE  PDB: A:510-631 UniProt: 510-631                                                                                      -------- PROSITE
           Transcript 1 (1) Exon 1.18b   --------------------------------------------------------Exon 1.20  PDB: A:567-603            Exon 1.21d  PDB: A:604-639           Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.19  PDB: A:510-566 UniProt: 510-566               ------------------------------------------------------------------------- Transcript 1 (2)
                 1om9 A 498 ASITVPLESIKPSNILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETWGSL 639
                                   507       517       527       537       547       557       567       577       587       597       607       617       627       637

Chain B from PDB  Type:PROTEIN  Length:142
 aligned with GGA1_HUMAN | Q9UJY5 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:142
                                   507       517       527       537       547       557       567       577       587       597       607       617       627       637  
           GGA1_HUMAN   498 ASITVPLESIKPSNILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETWGSL 639
               SCOP domains d1om9b_ B: ADP-ribosylation factor binding protein Gga1 domain                                                                                 SCOP domains
               CATH domains 1om9B00 B:498-639  [code=2.60.40.1230, no name defined]                                                                                        CATH domains
           Pfam domains (1) ---------------Alpha_adaptinC2-1om9B01 B:513-631                                                                                      -------- Pfam domains (1)
           Pfam domains (2) ---------------Alpha_adaptinC2-1om9B02 B:513-631                                                                                      -------- Pfam domains (2)
         Sec.struct. author .....hhhhh.......eeeeee..eeeeeeeee........eeeeeeeeee.....eeeeeeeee.....eeeeeee...............eeeeeeeee........eeeeeeeee..eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------GAE  PDB: B:510-631 UniProt: 510-631                                                                                      -------- PROSITE
           Transcript 1 (1) Exon 1.18b   --------------------------------------------------------Exon 1.20  PDB: B:567-603            Exon 1.21d  PDB: B:604-639           Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.19  PDB: B:510-566 UniProt: 510-566               ------------------------------------------------------------------------- Transcript 1 (2)
                 1om9 B 498 ASITVPLESIKPSNILPVTVYDQHGFRILFHFARDPLPGRSDVLVVVVSMLSTAPQPIRNIVFQSAVPKVMKVKLQPPSGTELPAFNPIVHPSAITQVLLLANPQKEKVRLRYKLTFTMGDQTYNEMGDVDQFPPPETWGSL 639
                                   507       517       527       537       547       557       567       577       587       597       607       617       627       637

Chain P from PDB  Type:PROTEIN  Length:11
 aligned with CCD91_HUMAN | Q7Z6B0 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:11
                                    13 
          CCD91_HUMAN     4 DDFGGFEAAET  14
               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 2 2.1    2.2  Transcript 2
                 1om9 P   3 DDFGGFEAAET  13
                                    12

Chain Q from PDB  Type:PROTEIN  Length:10
 aligned with CCD91_HUMAN | Q7Z6B0 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:10
                                    14
          CCD91_HUMAN     5 DFGGFEAAET  14
               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 2 2.1   2.2  Transcript 2
                 1om9 Q   4 DFGGFEAAET  13
                                    13

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Clathrin adaptor appendage domain (28)

Family: gamma-adaptin C-terminal appendage domain-like (10)

Protein domain: ADP-ribosylation factor binding protein Gga1 domain (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d1om9a_	A:
1b	d1om9b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.1230, no name defined] (9)

Human (Homo sapiens) (5)

1a	1om9A00	A:498-639
1b	1om9B00	B:498-639

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: E-set (290)

Family: Alpha_adaptinC2 (13)

Homo sapiens (Human) (3)

1a	Alpha_adaptinC2-1om9B01	B:513-631
1b	Alpha_adaptinC2-1om9B02	B:513-631

Asymmetric Unit(hide GO term definitions)

Chain A,B (GGA1_HUMAN | Q9UJY5)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	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:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0045732	positive regulation of protein catabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	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:1901998	toxin transport	The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0030131	clathrin adaptor complex	A membrane coat adaptor complex that links clathrin to a membrane.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Chain P,Q (CCD91_HUMAN | Q7Z6B0)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
biological process
	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: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:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

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1gyu	STRUCTURE OF THE UNLIGANDED GAMMA-APPENDAGE DOMAIN
1iu1	STRUCTURE OF THE UNLIGANDED GAMMA-APPENDAGE DOMAIN
1na8	STRUCTURE OF THE UNLIGANDED GGA1-APPENDAGE DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (6, 12)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (18, 23)

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