1VG0 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   THE CRYSTAL STRUCTURES OF THE REP-1 PROTEIN IN COMPLEX WITH MONOPRENYLATED RAB7 PROTEIN

Authors :   A. Rak, O. Pylypenko, A. Niculae, K. Pyatkov, R. S. Goody, K. Alexandrov

Date :   22 Apr 04 (Deposition) - 20 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Rab Prenylation, Post-Translational Modification, Protein Binding/Protein Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Rak, O. Pylypenko, A. Niculae, K. Pyatkov, R. S. Goody, K. Alexandrov
Structure Of The Rab7:Rep-1 Complex: Insights Into The Mechanism Of Rab Prenylation And Choroideremia Disease
Cell(Cambridge, Mass. ) V. 117 749 2004
PubMed-ID: 15186776 | Reference-DOI: 10.1016/J.CELL.2004.05.017
(for further references see the PDB file header)

Molecule 1 - RAB PROTEINS GERANYLGERANYLTRANSFERASE COMPONENT A 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF21
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector	:	PBLUEBAC
	Expression System Vector Type	:	BACULOVIRUS
	Mutation	:	YES
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	RAB ESCORT PROTEIN 1, REP-1

Molecule 2 - RAS-RELATED PROTEIN RAB-7
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET19
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	RAS-RELATED PROTEIN P23, RAS-RELATED PROTEIN BRL- RAS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 5)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	GER	1	Ligand/Ion	GERAN-8-YL GERAN
4	MG	1	Ligand/Ion	MAGNESIUM ION
5	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR B:22 , GDP B:1557 , HOH B:5583 , HOH B:5584 , HOH B:5585 , HOH B:5586	BINDING SITE FOR RESIDUE MG B 3000
2	AC2	SOFTWARE	TYR A:234 , ASN A:581 , HOH A:3012 , HOH A:3026	BINDING SITE FOR RESIDUE CL A 3001
3	AC3	SOFTWARE	PRO A:272 , SER A:274 , ARG A:275 , LEU A:292 , MET A:293 , VAL A:300 , PHE A:333 , LEU A:362	BINDING SITE FOR RESIDUE GER A 952
4	AC4	SOFTWARE	ASP B:16 , SER B:17 , GLY B:18 , VAL B:19 , GLY B:20 , LYS B:21 , THR B:22 , SER B:23 , PHE B:33 , ASN B:125 , LYS B:126 , ASP B:128 , LEU B:129 , SER B:155 , ALA B:156 , LYS B:157 , MG B:3000 , HOH B:5527 , HOH B:5547 , HOH B:5570 , HOH B:5583 , HOH B:5585 , HOH B:5586	BINDING SITE FOR RESIDUE GDP B 1557
5	AC5	SOFTWARE	GLN B:71 , SER B:101 , TRP B:102 , GLU B:105	BINDING SITE FOR RESIDUE PG4 B 5502

(no "SS Bond" information available for 1VG0)

(no "Cis Peptide Bond" information available for 1VG0)

(no "SAP(SNP)/Variant" information available for 1VG0)

(no "PROSITE Motif" information available for 1VG0)

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000016432	1	ENSRNOE00000116420	chr4:122220655-122220588	68	RAB7A_RAT	1-18	18	1	B:6-18	13
1.2	ENSRNOT00000016432	2	ENSRNOE00000116592	chr4:122217534-122217408	127	RAB7A_RAT	18-60	43	1	B:18-60 (gaps)	43
1.3	ENSRNOT00000016432	3	ENSRNOE00000116782	chr4:122208992-122208774	219	RAB7A_RAT	61-133	73	1	B:61-133	73
1.4	ENSRNOT00000016432	4	ENSRNOE00000116963	chr4:122208105-122207977	129	RAB7A_RAT	134-176	43	1	B:134-176	43
1.5	ENSRNOT00000016432	5	ENSRNOE00000117137	chr4:122204075-122202697	1379	RAB7A_RAT	177-207	31	1	B:177-192	16

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:481
 aligned with RAE1_RAT | P37727 from UniProtKB/Swiss-Prot  Length:650

    Alignment length:604
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602    
             RAE1_RAT     3 DNLPSDFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQENNDVVTENSMWQEQILENEEAIPLSSKDKTIQHVEVFCYASQDLHKDVEEAGALQKNHASVTSAQSAEAAEAAETSCLPTAVEPLSMGSCEIPAEQSQCPGPESSPEVNDAEATGKKENSDAKSSTEEPSENVPKVQDNTETPKKNRITYSQIIKEGRRFNIDLVSQLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGTVEQVPCSRADVFNSKQLTMVEKRMLMKFLTFCVEYEEHPDEYRAYEGTTFSEYLKTQKLTPNLQYFVLHSIAMTSETTSCTVDGLKATKKFLQCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCKAVIDQFGQRIISKHFIIEDSYLSENTCSRVQYRQISRAVLITDGSVLKTDADQQVSILAVPAEEPGSFGVRVIELCSSTMTCMKGTYLVHLTCMSSKTAREDLERVVQKLFTPYTEIEAENEQVEKPRLLWALYFNMRDSSDISRDCYNDLPSNVYVCSGPDSGLGNDNAVKQAETLFQQICPNEDFCPAPP 606
               SCOP domains d1vg0a1 A:3-444,A:558-606 Rab escort protein 1                                                                                                                                                                                                                                                                                                                                                                                                            d1vg0a2 A:445-557 Rab escort protein 1                                                                           d1vg0a1 A:3-444,A:558-606 Rab escort protein 1    SCOP domains
               CATH domains 1vg0A01 A:3-92,A:370-446,A:554-601  [code=3.50.50.60, no name           defined]          1vg0A02 A:93-2                                                                                                        70,A:447-553                                                1vg0A03 A:271-369 Guanine Nucleotide Dissociation Inhibitor, domain 1                              1vg0A01 A:3-92,A:370-446,A:554-601  [code=3.50.50.60, no name defined]       1vg0A02 A:93-270,A:447-553 Guanine Nucleotide Dissociation Inhibitor, domain 2                             1vg0A01 A:3-92,A:370-446,A:554-601              ----- CATH domains
           Pfam domains (1) -------------------------------------------------------------          ---------------------------------                                                                                                        GDI-1vg0A01 A:211-542                                                                                                                                                                                                                                                                                                                       ---------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------          ---------------------------------                                                                                                        GDI-1vg0A02 A:211-542                                                                                                                                                                                                                                                                                                                       ---------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ........eeee..hhhhhhhhhhhhhh...eeee......hhhh.eehhhhhhhhhhhhh----------hhhhhh...eeeee.......eeeeeeee....--------------------------------------------------------------------------------------------------------..hhhhhhhhhhhh.ee.....ee..hhhhhhhhhhhhhhhh.eee..eeeee....eee...hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhhhh..--....hhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhh..eee....eeeeeee.....eeeeee....eee..eeeee.hhh..........eeeeeeeeee.............eeeee.........eeeeeehhhhh......eeeeeeee...hhhhhhhhhhhhhh......-------....eeeeeeeeeee....hhhhh......eeee........hhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vg0 A   3 DNLPSDFDVIVIGTGLPESIIAAACSRSGQRVLHVDSRSYYGGNWASFSFSGLLSWLKEYQ----------MWQEQILENEEAIPLSSKDKTIQHVEVFCYASQ--------------------------------------------------------------------------------------------------------RITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGTVEQVPCSRADVFNSKQLTMVEKRMLMKFLTFCVEYEEHPDEYRAYEGTTFSEYLKTQKLTPNLQYFVLHSIAM--ETTSCTVDGLKATKKFLQCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCKAVIDQFGQRIISKHFIIEDSYLSENTCSRVQYRQISRAVLITDGSVLRTDADQQVSILTVPAEEPGSFAVRVIELCSSTMTCMKGTYLVHLTCMSSKTAREDLERVVQKLFTPYTEI-------EKPRLLWALYFNMRDSSDISRDCYNDLPSNVYVCSGPDSGLGNDNAVKQAETLFQQICPNEDFCPAPP 606
                                    12        22        32        42        52        62|        - |      82        92       102   |     -         -         -         -         -         -         -         -         -         -       212       222       232       242       252       262       272       282       292       302       312       322       332       | -|      352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522        |-      |542       552       562       572       582       592       602    
                                                                                       63         74                             106                                                                                                      211                                                                                                                              340  |                                                                                                                                                                                         531     539                                                                   
                                                                                                                                                                                                                                                                                                                                                                              343

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with RAB7A_RAT | P09527 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:187
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       
            RAB7A_RAT     6 KVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYNEFPEPIKL 192
               SCOP domains d1vg0b_ B: Rab7                                                                                                                                                                             SCOP domains
               CATH domains 1vg0B00 B:6-192 P-loop contain     ing nucleotide triphosphate hydrolases                                                                                                                   CATH domains
               Pfam domains ----Ras-1vg0B01 B:10-175                                                                                                                                                  ----------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhh....-----....eeeeeeee..eeeeeeee...........hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.........hhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1     ------------------------------------------Exon 1.3  PDB: B:61-133 UniProt: 61-133                                  Exon 1.4  PDB: B:134-176 UniProt: 134-176  Exon 1.5         Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.2  PDB: B:18-60 (gaps)              ------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1vg0 B   6 KVLLKVIILGDSGVGKTSLMNQYVNKKFSN-----IGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYNEFPEPIKL 192
                                    15        25        35     |  45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       
                                                        35    41

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: GDI (6)

Rattus norvegicus (Rat) (3)

1a	GDI-1vg0A01	A:211-542
1b	GDI-1vg0A02	A:211-542

Clan: P-loop_NTPase (1112)

Family: Ras (176)

Rattus norvegicus (Rat) (6)

Ras-1vg0B01

B:10-175

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RAE1_RAT | P37727)

molecular function
	GO:0005092	GDP-dissociation inhibitor activity	Prevents the dissociation of GDP from a GTPase, thereby preventing GTP from binding.
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0017137	Rab GTPase binding	Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	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: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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0018344	protein geranylgeranylation	The covalent attachment of a geranylgeranyl group to a protein.
	GO:0006612	protein targeting to membrane	The process of directing proteins towards a membrane, usually using signals contained within the protein.
	GO:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	GO:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
	GO:0005968	Rab-protein geranylgeranyltransferase complex	A heterodimeric enzyme complex, which in mammals is composed of an alpha and a beta subunit, and which associates with an accessory protein Rep (Rab escort protein). Catalyzes of the transfer of a geranyl-geranyl group from geranylgeranyl pyrophosphate to a Rab protein.
	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.

Chain B (RAB7A_RAT | P09527)

molecular function
	GO:0019003	GDP binding	Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0048365	Rac GTPase binding	Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0045453	bone resorption	The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products.
	GO:0045022	early endosome to late endosome transport	The directed movement of substances, in membrane-bounded vesicles, from the early sorting endosomes to the late sorting endosomes; transport occurs along microtubules and can be experimentally blocked with microtubule-depolymerizing drugs.
	GO:0008333	endosome to lysosome transport	The directed movement of substances from endosomes to lysosomes.
	GO:0007174	epidermal growth factor catabolic process	The chemical reactions and pathways resulting in the breakdown of epidermal growth factor (EGF), following internalization of the receptor-bound ligand into the signal-receiving cell. Full breakdown of epidermal growth factor results in a ligand that is unable to bind and activate its receptor.
	GO:0016042	lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0061724	lipophagy	The autophagic process in which lipid droplets are delivered to the vacuole and degraded in response to changing cellular conditions.
	GO:0090383	phagosome acidification	Any process that reduces the pH of the phagosome, measured by the concentration of the hydrogen ion.
	GO:0090385	phagosome-lysosome fusion	The creation of a phagolysosome from a phagosome and a lysosome.
	GO:1903543	positive regulation of exosomal secretion	Any process that activates or increases the frequency, rate or extent of exosomal secretion.
	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:0048524	positive regulation of viral process	Any process that activates or increases the frequency, rate or extent of a multi-organism process in which a virus is a participant.
	GO:0006622	protein targeting to lysosome	The process of directing proteins towards the lysosome using signals contained within the protein.
	GO:0022615	protein to membrane docking	The initial attachment of a protein to a target membrane, mediated by a proteins protruding from the target membrane. Docking requires only that the proteins come close enough to interact and adhere.
	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:2000785	regulation of autophagosome assembly	Any process that modulates the frequency, rate or extent of autophagosome assembly.
	GO:0042147	retrograde transport, endosome to Golgi	The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport.
	GO:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
	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:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell 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:0097208	alveolar lamellar body	A specialized secretory organelle found in type II pneumocytes and involved in the synthesis, secretion, and reutilization of pulmonary surfactant.
	GO:0000421	autophagosome membrane	The lipid bilayer surrounding an autophagosome, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	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:0032419	extrinsic component of lysosome membrane	The component of an lysosome membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	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:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0005811	lipid droplet	An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0033162	melanosome membrane	The lipid bilayer surrounding a melanosome.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045335	phagocytic vesicle	A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
	GO:0030670	phagocytic vesicle membrane	The lipid bilayer surrounding a phagocytic vesicle.
	GO:0034045	pre-autophagosomal structure membrane	A cellular membrane associated with the pre-autophagosomal structure.
	GO:0030904	retromer complex	A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35.
	GO:0043195	terminal bouton	Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.
	GO:0005774	vacuolar membrane	The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vg0)

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	1vg0
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
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	RAB7A_RAT \| P09527
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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	RAE1_RAT \| P37727
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	RAB7A_RAT \| P09527
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	RAE1_RAT \| P37727
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RAB7A_RAT \| P09527	:	1vg1 1vg8 1vg9
	RAE1_RAT \| P37727	:	1ltx 1vg9

1ltx	RABGGTASE:REP1 COMPLEX STRUCTURE
1vg1	GDP-BOUND RAB7
1vg8	GPPNHP-BOUND RAB7
1vg9	THE REP-1 PROTEIN IN COMPLEX WITH C-TERMINALLY TRUNCATED RAB7 PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (5, 5)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (4, 4)

Pfam Domains (2, 3)

Gene Ontology (61, 65)

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