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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF HUMAN RAB5A A30P MUTANT COMPLEX WITH GDP AND ALUMINUM FLUORIDE

Authors :   G. Zhu, J. Liu, S. Terzyan, P. Zhai, G. Li, X. C. Zhang

Date :   11 Nov 02 (Deposition) - 27 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym./Biol. Unit : A

Keywords :   Rab, Gtpase, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Zhu, J. Liu, S. Terzyan, P. Zhai, G. Li, X. C. Zhang
High Resolution Crystal Structures Of Human Rab5A And Five Mutants With Substitutions In The Catalytically Important Phosphate-Binding Loop
J. Biol. Chem. V. 278 2452 2003
PubMed-ID: 12433916 | Reference-DOI: 10.1074/JBC.M211042200
(for further references see the PDB file header)

Molecule 1 - RAS-RELATED PROTEIN RAB-5A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	GTPASE DOMAIN
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RAB5A

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 4)

No.	Name	Count	Type	Full Name
1	AF3	1	Ligand/Ion	ALUMINUM FLUORIDE
2	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
4	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:34 , THR A:52 , GDP A:200 , AF3 A:202 , HOH A:301 , HOH A:302	BINDING SITE FOR RESIDUE MG A 201
2	AC2	SOFTWARE	SER A:29 , PRO A:30 , VAL A:31 , GLY A:32 , LYS A:33 , SER A:34 , SER A:35 , PHE A:45 , HIS A:46 , GLU A:47 , GLN A:49 , ASN A:133 , LYS A:134 , ASP A:136 , LEU A:137 , SER A:163 , ALA A:164 , LYS A:165 , LYS A:180 , MG A:201 , AF3 A:202 , HOH A:301 , HOH A:302 , HOH A:304 , HOH A:333 , HOH A:341 , HOH A:400	BINDING SITE FOR RESIDUE GDP A 200
3	AC3	SOFTWARE	SER A:29 , LYS A:33 , SER A:51 , THR A:52 , ALA A:77 , GLY A:78 , GDP A:200 , MG A:201 , HOH A:301 , HOH A:302 , HOH A:303 , HOH A:304	BINDING SITE FOR RESIDUE AF3 A 202
4	AC4	SOFTWARE	GLY A:15 , ALA A:55 , CYS A:63 , ASP A:65 , ASP A:66 , THR A:67 , THR A:68	BINDING SITE FOR RESIDUE BME A 210

(no "SS Bond" information available for 1N6K)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:29	-	Pro A:30

(no "SAP(SNP)/Variant" information available for 1N6K)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAB	PS51419	small GTPase Rab1 family profile.	RAB5A_HUMAN	15-215	1	A:15-181

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000273047	1a	ENSE00001769725	chr3:19988571-19989013	443	RAB5A_HUMAN	-	0	0	-	-
1.2b	ENST00000273047	2b	ENSE00001162720	chr3:19992298-19992553	256	RAB5A_HUMAN	1-55	55	1	A:15-55	41
1.4c	ENST00000273047	4c	ENSE00001691424	chr3:20017093-20017244	152	RAB5A_HUMAN	55-105	51	1	A:55-105	51
1.5b	ENST00000273047	5b	ENSE00001783762	chr3:20017539-20017661	123	RAB5A_HUMAN	106-146	41	1	A:106-146	41
1.6a	ENST00000273047	6a	ENSE00001688303	chr3:20019802-20019895	94	RAB5A_HUMAN	147-178	32	1	A:147-178	32
1.7e	ENST00000273047	7e	ENSE00001368096	chr3:20025200-20026667	1468	RAB5A_HUMAN	178-215	38	1	A:178-181	4

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:167
 aligned with RAB5A_HUMAN | P20339 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:167
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       
          RAB5A_HUMAN    15 GNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL 181
               SCOP domains d1n6ka_ A: Rab5a                                                                                                                                                        SCOP domains
               CATH domains 1n6kA00 A:15-181 P-loop containing nucleotide triphosphate hydrolases                                                                                                   CATH domains
               Pfam domains -------Ras-1n6kA01 A:22-181                                                                                                                                             Pfam domains
         Sec.struct. author ..eeeeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAB  PDB: A:15-181 UniProt: 15-215                                                                                                                                      PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:15-55 UniProt: 1-55    --------------------------------------------------Exon 1.5b  PDB: A:106-146                Exon 1.6a  PDB: A:147-178       --- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.4c  PDB: A:55-105 UniProt: 55-105           ------------------------------------------------------------------------1.7e Transcript 1 (2)
                 1n6k A  15 GNKICQFKLVLLGESPVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKL 181
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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: Rab5a (12)

Human (Homo sapiens) [TaxId: 9606] (12)

d1n6ka_

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

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

Human (Homo sapiens) (413)

1n6kA00

A:15-181

Asymmetric/Biological Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Ras (176)

Homo sapiens (Human) (141)

Ras-1n6kA01

A:22-181

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RAB5A_HUMAN | P20339)

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:0019001	guanyl nucleotide binding	Interacting selectively and non-covalently with guanyl nucleotides, any compound consisting of guanosine esterified with (ortho)phosphate.
	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:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	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:0006897	endocytosis	A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
	GO:0006909	phagocytosis	An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
	GO:0045921	positive regulation of exocytosis	Any process that activates or increases the frequency, rate or extent of exocytosis.
	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:2000286	receptor internalization involved in canonical Wnt signaling pathway	A receptor internalization process that contributes to canonical Wnt signaling pathway.
	GO:2000785	regulation of autophagosome assembly	Any process that modulates the frequency, rate or extent of autophagosome assembly.
	GO:0030100	regulation of endocytosis	Any process that modulates the frequency, rate or extent of endocytosis.
	GO:0051036	regulation of endosome size	Any process that modulates the volume of an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis.
	GO:0051489	regulation of filopodium assembly	Any process that modulates the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
	GO:2000300	regulation of synaptic vesicle exocytosis	Any process that modulates the frequency, rate or extent of synaptic vesicle exocytosis.
	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:0036465	synaptic vesicle recycling	The trafficking of synaptic vesicles from the pre-synaptic membrane so the vesicle can dock and prime for another round of exocytosis and neurotransmitter release. Recycling occurs after synaptic vesicle exocytosis, and is necessary to replenish presynaptic vesicle pools, sustain transmitter release and preserve the structural integrity of the presynaptic membrane. Recycling can occur following transient fusion with the presynaptic membrane (kiss and run), or via endocytosis of presynaptic membrane.
	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:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0043679	axon terminus	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 button is a specialized region of it.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0098559	cytoplasmic side of early endosome membrane	The side (leaflet) of the early endosome membrane that faces the cytoplasm.
	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:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0031901	early endosome membrane	The lipid bilayer surrounding an early endosome.
	GO:0030139	endocytic vesicle	A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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: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:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0001726	ruffle	Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
	GO:0036477	somatodendritic compartment	The region of a neuron that includes the cell body (cell soma) and the dendrite, but excludes the axon.
	GO:0008021	synaptic vesicle	A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ser A:29 - Pro A:30	[ RasMol ]

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	1n6k
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	RAB5A_HUMAN \| P20339
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UniProtKB/Swiss-Prot
	RAB5A_HUMAN \| P20339	:	1n6h 1n6i 1n6l 1n6n 1n6o 1n6p 1n6r 1r2q 1tu3 1tu4 3mjh 4q9u

1n6h	RAB5A WILD TYPE
1n6i	RAB5A A30P MUTANT COMPLEX WITH GDP
1n6l	RAB5A A30P MUTANT COMPLEX WITH GTP
1n6n	RAB5A A30R MUTANT COMPLEX WITH GPPNHP
1n6o	RAB5A A30K MUTANT COMPLEX WITH GPPNHP
1n6p	RAB5A A30E MUTANT COMPLEX WITH GPPNHP
1n6r	RAB5A A30L MUTANT COMPLEX WITH GPPNHP

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (5, 5)

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SCOP Domains (1, 1)

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Gene Ontology (47, 47)

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