1VG8 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   GPPNHP-BOUND RAB7

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

Date :   23 Apr 04 (Deposition) - 20 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Gtp-Binding Protein, Protein Transport (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 - RAS-RELATED PROTEIN RAB-7
	Chains	:	A, B, C, D
	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	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	GNP	4	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:1022 , THR A:1040 , GNP A:1400 , HOH A:5002 , HOH A:5314	BINDING SITE FOR RESIDUE MG A 1401
2	AC2	SOFTWARE	THR B:2022 , THR B:2040 , GNP B:2400 , HOH B:5006 , HOH B:5315	BINDING SITE FOR RESIDUE MG B 2401
3	AC3	SOFTWARE	THR C:3022 , THR C:3040 , GNP C:3400 , HOH C:5001 , HOH C:5009	BINDING SITE FOR RESIDUE MG C 3401
4	AC4	SOFTWARE	THR D:4022 , THR D:4040 , GNP D:4400 , HOH D:5003 , HOH D:5316	BINDING SITE FOR RESIDUE MG D 4401
5	AC5	SOFTWARE	SER A:1017 , GLY A:1018 , VAL A:1019 , GLY A:1020 , LYS A:1021 , THR A:1022 , SER A:1023 , PHE A:1033 , SER A:1034 , ASN A:1035 , TYR A:1037 , THR A:1040 , GLY A:1066 , ASN A:1125 , LYS A:1126 , ASP A:1128 , LEU A:1129 , SER A:1155 , ALA A:1156 , LYS A:1157 , MG A:1401 , HOH A:5002 , HOH A:5017 , HOH A:5033 , HOH A:5079 , HOH A:5314 , HOH A:5456	BINDING SITE FOR RESIDUE GNP A 1400
6	AC6	SOFTWARE	SER B:2017 , GLY B:2018 , VAL B:2019 , GLY B:2020 , LYS B:2021 , THR B:2022 , SER B:2023 , PHE B:2033 , SER B:2034 , ASN B:2035 , TYR B:2037 , THR B:2040 , GLY B:2066 , ASN B:2125 , LYS B:2126 , ASP B:2128 , LEU B:2129 , SER B:2155 , ALA B:2156 , LYS B:2157 , MG B:2401 , HOH B:5006 , HOH B:5020 , HOH B:5028 , HOH B:5156 , HOH B:5315	BINDING SITE FOR RESIDUE GNP B 2400
7	AC7	SOFTWARE	SER C:3017 , GLY C:3018 , VAL C:3019 , GLY C:3020 , LYS C:3021 , THR C:3022 , SER C:3023 , PHE C:3033 , SER C:3034 , ASN C:3035 , TYR C:3037 , THR C:3040 , GLY C:3066 , ASN C:3125 , LYS C:3126 , ASP C:3128 , LEU C:3129 , SER C:3155 , ALA C:3156 , LYS C:3157 , MG C:3401 , HOH C:5001 , HOH C:5009 , HOH C:5013 , HOH C:5032 , HOH C:5219	BINDING SITE FOR RESIDUE GNP C 3400
8	AC8	SOFTWARE	SER D:4017 , GLY D:4018 , VAL D:4019 , GLY D:4020 , LYS D:4021 , THR D:4022 , SER D:4023 , PHE D:4033 , SER D:4034 , ASN D:4035 , TYR D:4037 , THR D:4040 , GLY D:4066 , ASN D:4125 , LYS D:4126 , ASP D:4128 , LEU D:4129 , SER D:4155 , ALA D:4156 , LYS D:4157 , MG D:4401 , HOH D:5003 , HOH D:5024 , HOH D:5027 , HOH D:5069 , HOH D:5177 , HOH D:5316 , HOH D:5425	BINDING SITE FOR RESIDUE GNP D 4400

(no "SS Bond" information available for 1VG8)

(no "Cis Peptide Bond" information available for 1VG8)

(no "SAP(SNP)/Variant" information available for 1VG8)

(no "PROSITE Motif" information available for 1VG8)

Asymmetric Unit (5, 20)

	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	4	A:1007-1018 B:2006-2018 C:3007-3018 D:4007-4018	12 13 12 12
1.2	ENSRNOT00000016432	2	ENSRNOE00000116592	chr4:122217534-122217408	127	RAB7A_RAT	18-60	43	4	A:1018-1060 B:2018-2060 C:3018-3060 D:4018-4060	43 43 43 43
1.3	ENSRNOT00000016432	3	ENSRNOE00000116782	chr4:122208992-122208774	219	RAB7A_RAT	61-133	73	4	A:1061-1133 B:2061-2133 C:3061-3133 D:4061-4133	73 73 73 73
1.4	ENSRNOT00000016432	4	ENSRNOE00000116963	chr4:122208105-122207977	129	RAB7A_RAT	134-176	43	4	A:1134-1176 B:2134-2176 C:3134-3176 D:4134-4176	43 43 43 43
1.5	ENSRNOT00000016432	5	ENSRNOE00000117137	chr4:122204075-122202697	1379	RAB7A_RAT	177-207	31	4	A:1177-1190 B:2177-2184 C:3177-3184 D:4177-4190	14 8 8 14

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:184
 aligned with RAB7A_RAT | P09527 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:184
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
           RAB7A_RAT      7 VLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYNEFPEPI  190
               SCOP domains d1vg8a_ A: Rab7                                                                                                                                                                          SCOP domains
               CATH domains 1vg8A00 A:1007-1190 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh...........eeeeeeeee....eeeeeeeee..hhhhh...hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.........hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1    ------------------------------------------Exon 1.3  PDB: A:1061-1133 UniProt: 61-133                               Exon 1.4  PDB: A:1134-1176 UniProt: 134-176Exon 1.5       Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.2  PDB: A:1018-1060 UniProt: 18-60  ---------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1vg8 A 1007 VLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYNEFPEPI 1190
                                  1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with RAB7A_RAT | P09527 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:179
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175         
           RAB7A_RAT      6 KVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYN  184
               SCOP domains d1vg8b_ B: Rab7                                                                                                                                                                     SCOP domains
               CATH domains 1vg8B00 B:2006-2184 P-loop containing nucleotide triphosphate hydrolases                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhh............eeeeeeee....eeeeeeee...hhhhh...hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.........hhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1     ------------------------------------------Exon 1.3  PDB: B:2061-2133 UniProt: 61-133                               Exon 1.4  PDB: B:2134-2176 UniProt: 134-176Exon 1.5 Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.2  PDB: B:2018-2060 UniProt: 18-60  ---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1vg8 B 2006 KVLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYN 2184
                                  2015      2025      2035      2045      2055      2065      2075      2085      2095      2105      2115      2125      2135      2145      2155      2165      2175

Chain C from PDB  Type:PROTEIN  Length:178
 aligned with RAB7A_RAT | P09527 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:178
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176        
           RAB7A_RAT      7 VLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYN  184
               SCOP domains d1vg8c_ C: Rab7                                                                                                                                                                    SCOP domains
               CATH domains 1vg8C00 C:3007-3184 P-loop containing nucleotide triphosphate hydrolases                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh............eeeeeeeee..eeeeeeeee...hhhhh...hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.........hhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1    ------------------------------------------Exon 1.3  PDB: C:3061-3133 UniProt: 61-133                               Exon 1.4  PDB: C:3134-3176 UniProt: 134-176Exon 1.5 Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.2  PDB: C:3018-3060 UniProt: 18-60  ---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1vg8 C 3007 VLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYN 3184
                                  3016      3026      3036      3046      3056      3066      3076      3086      3096      3106      3116      3126      3136      3146      3156      3166      3176

Chain D from PDB  Type:PROTEIN  Length:184
 aligned with RAB7A_RAT | P09527 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:184
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186    
           RAB7A_RAT      7 VLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYNEFPEPI  190
               SCOP domains d1vg8d_ D: Rab7                                                                                                                                                                          SCOP domains
               CATH domains 1vg8D00 D:4007-4190 P-loop containing nucleotide triphosphate hydrolases                                                                                                                 CATH domains
           Pfam domains (1) ---Ras-1vg8D01 D:4010-4175                                                                                                                                               --------------- Pfam domains (1)
           Pfam domains (2) ---Ras-1vg8D02 D:4010-4175                                                                                                                                               --------------- Pfam domains (2)
           Pfam domains (3) ---Ras-1vg8D03 D:4010-4175                                                                                                                                               --------------- Pfam domains (3)
           Pfam domains (4) ---Ras-1vg8D04 D:4010-4175                                                                                                                                               --------------- Pfam domains (4)
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh...........eeeeeeeee....eeeeeeeee..hhhhh...hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeee.........hhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1    ------------------------------------------Exon 1.3  PDB: D:4061-4133 UniProt: 61-133                               Exon 1.4  PDB: D:4134-4176 UniProt: 134-176Exon 1.5       Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.2  PDB: D:4018-4060 UniProt: 18-60  ---------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1vg8 D 4007 VLLKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVMVDDRLVTMQIWDTAGQERFQSLGVAFYRGADCCVLVFDVTAPNTFKTLDSWRDEFLIQASPRDPENFPFVVLGNKIDLENRQVATKRAQAWCYSKNNIPYFETSAKEAINVEQAFQTIARNALKQETEVELYNEFPEPI 4190
                                  4016      4026      4036      4046      4056      4066      4076      4086      4096      4106      4116      4126      4136      4146      4156      4166      4176      4186

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: G proteins (693)

Protein domain: Rab7 (6)

Norway rat (Rattus norvegicus) [TaxId: 10116] (4)

1a	d1vg8a_	A:
1b	d1vg8b_	B:
1c	d1vg8c_	C:
1d	d1vg8d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Norway rat (Rattus norvegicus) (38)

1a	1vg8A00	A:1007-1190
1b	1vg8D00	D:4007-4190
1c	1vg8B00	B:2006-2184
1d	1vg8C00	C:3007-3184

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Ras (176)

Rattus norvegicus (Rat) (6)

1a	Ras-1vg8D01	D:4010-4175
1b	Ras-1vg8D02	D:4010-4175
1c	Ras-1vg8D03	D:4010-4175
1d	Ras-1vg8D04	D:4010-4175

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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.

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	1vg8
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	RAB7A_RAT \| P09527
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	RAB7A_RAT \| P09527
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UniProtKB/Swiss-Prot
	RAB7A_RAT \| P09527	:	1vg0 1vg1 1vg9

1vg0	THE REP-1 PROTEIN IN COMPLEX WITH MONOPRENYLATED RAB7 PROTEIN
1vg1	GDP-BOUND RAB7
1vg9	THE REP-1 PROTEIN IN COMPLEX WITH C-TERMINALLY TRUNCATED RAB7 PROTEIN

Description

Compounds

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Ligands, Modified Residues, Ions (2, 8)

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Exons (5, 20)

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Entries Sharing at Least One Protein Chain (UniProt ID)

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