3MJH - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN RAB5A IN COMPLEX WITH THE C2H2 ZINC FINGER OF EEA1

Authors :   A. K. Mishra, S. Eathiraj, D. G. Lambright

Date :   12 Apr 10 (Deposition) - 05 May 10 (Release) - 14 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

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

Keywords :   Protein-Zinc Finger Complex, Beta Beta Alpha Fold, Beta Hairpin, Rab5A Gtpase, Eea1, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Mishra, S. Eathiraj, S. Corvera, D. G. Lambright
Structural Basis For Rab Gtpase Recognition And Endosome Tethering By The C2H2 Zinc Finger Of Early Endosomal Autoantigen 1 (Eea1).
Proc. Natl. Acad. Sci. Usa V. 107 10866 2010
PubMed-ID: 20534488 | Reference-DOI: 10.1073/PNAS.1000843107

Molecule 1 - RAS-RELATED PROTEIN RAB-5A
	Chains	:	A, C
	EC Number	:	3.6.5.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MODIFIED PET15B, MODIFIED PET28A,PGEX
	Expression System Strain	:	K12, BL21 (DE3)CODON PLUS RIL CELLS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 16-183
	Gene	:	RAB5, RAB5A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - EARLY ENDOSOME ANTIGEN 1
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MODIFIED PET15B
	Expression System Strain	:	K12, BL21(DE3)CODON PLUS RIL CELLS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C2H2-TYPE, RESIDUES 36-69
	Gene	:	EARLY ENDOSOMAL ANTIGEN1(EEA1), EEA1, ZFYVE2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ENDOSOME-ASSOCIATED PROTEIN P162, ZINC FINGER FYVE DOMAIN- CONTAINING PROTEIN 2

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	GTP	2	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:6 , SER A:29 , ALA 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 , SER A:51 , THR A:52 , GLY A:78 , ASN A:133 , LYS A:134 , ASP A:136 , SER A:163 , ALA A:164 , LYS A:165 , HOH A:196 , MG A:201 , HOH A:259 , HOH A:302 , HOH A:306	BINDING SITE FOR RESIDUE GTP A 200
2	AC2	SOFTWARE	SER A:34 , THR A:52 , GTP A:200 , HOH A:302 , HOH A:306	BINDING SITE FOR RESIDUE MG A 201
3	AC3	SOFTWARE	CYS B:43 , CYS B:46 , HIS B:59 , HIS B:64	BINDING SITE FOR RESIDUE ZN B 70
4	AC4	SOFTWARE	HOH C:12 , SER C:29 , ALA C:30 , VAL C:31 , GLY C:32 , LYS C:33 , SER C:34 , SER C:35 , PHE C:45 , HIS C:46 , GLU C:47 , GLN C:49 , THR C:52 , GLY C:78 , ASN C:133 , LYS C:134 , ASP C:136 , LEU C:137 , SER C:163 , ALA C:164 , LYS C:165 , HOH C:193 , MG C:201 , HOH C:272 , HOH C:274 , HOH C:306	BINDING SITE FOR RESIDUE GTP C 200
5	AC5	SOFTWARE	SER C:34 , THR C:52 , GTP C:200 , HOH C:272 , HOH C:274	BINDING SITE FOR RESIDUE MG C 201
6	AC6	SOFTWARE	CYS D:43 , CYS D:46 , HIS D:59 , HIS D:64	BINDING SITE FOR RESIDUE ZN D 70

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_FINGER_C2H2_1	PS00028	Zinc finger C2H2 type domain signature.	EEA1_HUMAN	43-64	2	B:43-64 D:43-64

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_FINGER_C2H2_1	PS00028	Zinc finger C2H2 type domain signature.	EEA1_HUMAN	43-64	1	B:43-64 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_FINGER_C2H2_1	PS00028	Zinc finger C2H2 type domain signature.	EEA1_HUMAN	43-64	1	- D:43-64

Asymmetric Unit (7, 14)

	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	2	A:16-55 C:17-55	40 39
1.4c	ENST00000273047	4c	ENSE00001691424	chr3:20017093-20017244	152	RAB5A_HUMAN	55-105	51	2	A:55-105 C:55-105	51 51
1.5b	ENST00000273047	5b	ENSE00001783762	chr3:20017539-20017661	123	RAB5A_HUMAN	106-146	41	2	A:106-146 C:106-146	41 41
1.6a	ENST00000273047	6a	ENSE00001688303	chr3:20019802-20019895	94	RAB5A_HUMAN	147-178	32	2	A:147-178 C:147-178	32 32
1.7e	ENST00000273047	7e	ENSE00001368096	chr3:20025200-20026667	1468	RAB5A_HUMAN	178-215	38	2	A:178-183 C:178-183	6 6

2.1	ENST00000322349	1	ENSE00001477661	chr12:93323107-93322819	289	EEA1_HUMAN	1-8	8	0	-	-
2.3	ENST00000322349	3	ENSE00001282982	chr12:93285497-93285405	93	EEA1_HUMAN	9-39	31	2	B:36-39 D:37-39	4 3
2.4	ENST00000322349	4	ENSE00000676847	chr12:93258763-93258636	128	EEA1_HUMAN	40-82	43	2	B:40-69 D:40-69	30 30
2.5	ENST00000322349	5	ENSE00000676849	chr12:93251261-93251207	55	EEA1_HUMAN	82-100	19	0	-	-
2.6	ENST00000322349	6	ENSE00000676865	chr12:93251116-93251051	66	EEA1_HUMAN	101-122	22	0	-	-
2.7	ENST00000322349	7	ENSE00000676885	chr12:93247730-93247691	40	EEA1_HUMAN	123-136	14	0	-	-
2.8	ENST00000322349	8	ENSE00000676904	chr12:93246801-93246688	114	EEA1_HUMAN	136-174	39	0	-	-
2.9	ENST00000322349	9	ENSE00000676922	chr12:93246072-93245951	122	EEA1_HUMAN	174-214	41	0	-	-
2.10	ENST00000322349	10	ENSE00000676940	chr12:93245042-93244887	156	EEA1_HUMAN	215-266	52	0	-	-
2.11	ENST00000322349	11	ENSE00000676942	chr12:93236357-93236241	117	EEA1_HUMAN	267-305	39	0	-	-
2.12	ENST00000322349	12	ENSE00000921615	chr12:93226626-93226288	339	EEA1_HUMAN	306-418	113	0	-	-
2.13	ENST00000322349	13	ENSE00000676944	chr12:93221837-93221688	150	EEA1_HUMAN	419-468	50	0	-	-
2.14	ENST00000322349	14	ENSE00000676945	chr12:93220061-93219942	120	EEA1_HUMAN	469-508	40	0	-	-
2.15	ENST00000322349	15	ENSE00000921614	chr12:93213287-93213084	204	EEA1_HUMAN	509-576	68	0	-	-
2.16	ENST00000322349	16	ENSE00000921613	chr12:93210176-93209976	201	EEA1_HUMAN	577-643	67	0	-	-
2.17	ENST00000322349	17	ENSE00000921612	chr12:93206869-93206756	114	EEA1_HUMAN	644-681	38	0	-	-
2.18	ENST00000322349	18	ENSE00000921611	chr12:93205210-93205055	156	EEA1_HUMAN	682-733	52	0	-	-
2.19	ENST00000322349	19	ENSE00000921610	chr12:93202932-93202793	140	EEA1_HUMAN	734-780	47	0	-	-
2.20	ENST00000322349	20	ENSE00000921609	chr12:93196510-93196180	331	EEA1_HUMAN	780-890	111	0	-	-
2.21	ENST00000322349	21	ENSE00000921608	chr12:93195477-93195376	102	EEA1_HUMAN	891-924	34	0	-	-
2.22	ENST00000322349	22	ENSE00000921607	chr12:93192862-93192668	195	EEA1_HUMAN	925-989	65	0	-	-
2.23	ENST00000322349	23	ENSE00000921606	chr12:93181825-93181643	183	EEA1_HUMAN	990-1050	61	0	-	-
2.24	ENST00000322349	24	ENSE00000921605	chr12:93175911-93175726	186	EEA1_HUMAN	1051-1112	62	0	-	-
2.25	ENST00000322349	25	ENSE00000921604	chr12:93174187-93174056	132	EEA1_HUMAN	1113-1156	44	0	-	-
2.26	ENST00000322349	26	ENSE00000921603	chr12:93173076-93172891	186	EEA1_HUMAN	1157-1218	62	0	-	-
2.27	ENST00000322349	27	ENSE00000921602	chr12:93171955-93171717	239	EEA1_HUMAN	1219-1298	80	0	-	-
2.28	ENST00000322349	28	ENSE00000921601	chr12:93171439-93171319	121	EEA1_HUMAN	1298-1338	41	0	-	-
2.29	ENST00000322349	29	ENSE00000921600	chr12:93170718-93170620	99	EEA1_HUMAN	1339-1371	33	0	-	-
2.30b	ENST00000322349	30b	ENSE00001198267	chr12:93169909-93166286	3624	EEA1_HUMAN	1372-1411	40	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:168
 aligned with RAB5A_HUMAN | P20339 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:168
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175        
          RAB5A_HUMAN    16 NKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPK 183
               SCOP domains d3mjha_ A: Rab5a                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhh..hhhhhhhhhhh...eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:16-55 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)
                 3mjh A  16 NKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGLERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPK 183
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175

Chain B from PDB  Type:PROTEIN  Length:34
 aligned with EEA1_HUMAN | Q15075 from UniProtKB/Swiss-Prot  Length:1411

    Alignment length:34
                                    45        55        65    
           EEA1_HUMAN    36 SSSEGFICPQCMKSLGSADELFKHYEAVHDAGND  69
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author ...eeee......ee.hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE -------ZINC_FINGER_C2H2_1    ----- PROSITE
               Transcript 2 2.3 Exon 2.4  PDB: B:40-69         Transcript 2
                 3mjh B  36 SSSEGFICPQCMKSLGSADELFKHYEAVHDAGND  69
                                    45        55        65

Chain C from PDB  Type:PROTEIN  Length:167
 aligned with RAB5A_HUMAN | P20339 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:167
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       
          RAB5A_HUMAN    17 KICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPK 183
               SCOP domains d3mjhc_ C: Rab5a                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Ras-3mjhC01 C:22-183                                                                                                                                               Pfam domains (1)
           Pfam domains (2) -----Ras-3mjhC02 C:22-183                                                                                                                                               Pfam domains (2)
         Sec.struct. author .eeeeeeeee.....hhhhhhhhhhhh...........eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: C:17-55 UniProt: 1-55  --------------------------------------------------Exon 1.5b  PDB: C:106-146                Exon 1.6a  PDB: C:147-178       ----- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.4c  PDB: C:55-105 UniProt: 55-105           ------------------------------------------------------------------------1.7e   Transcript 1 (2)
                 3mjh C  17 KICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGLERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPK 183
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

Chain D from PDB  Type:PROTEIN  Length:33
 aligned with EEA1_HUMAN | Q15075 from UniProtKB/Swiss-Prot  Length:1411

    Alignment length:33
                                    46        56        66   
           EEA1_HUMAN    37 SSEGFICPQCMKSLGSADELFKHYEAVHDAGND  69
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ..eeee......ee.hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE ------ZINC_FINGER_C2H2_1    ----- PROSITE
               Transcript 2 2.3Exon 2.4  PDB: D:40-69         Transcript 2
                 3mjh D  37 SSEGFICPQCMKSLGSADELFKHYEAVHDAGND  69
                                    46        56        66

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: Rab5a (12)

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

1a	d3mjha_	A:
1b	d3mjhc_	C:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Ras (176)

Homo sapiens (Human) (141)

1a	Ras-3mjhC01	C:22-183
1b	Ras-3mjhC02	C:22-183

Asymmetric Unit(hide GO term definitions)

Chain A,C (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.

Chain B,D (EEA1_HUMAN | Q15075)

molecular function
	GO:0005545	1-phosphatidylinositol binding	Interacting selectively and non-covalently with phosphatidylinositol, any glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
	GO:0030742	GTP-dependent protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) using energy from the hydrolysis of GTP.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0016189	synaptic vesicle to endosome fusion	Fusion of a synaptic vesicle with an endosome.
	GO:0006906	vesicle fusion	Fusion of the membrane of a transport vesicle with its target membrane.
cellular component
	GO:0044308	axonal spine	A spine that originates from the axon, usually from the initial segment.
	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: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: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:0019897	extrinsic component of plasma membrane	The component of a plasma 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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0055037	recycling endosome	An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.
	GO:0005969	serine-pyruvate aminotransferase complex	An enzyme complex that catalyzes the formation of hydroxypyruvate and alanine from serine and pyruvate.

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	3mjh
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	EEA1_HUMAN \| Q15075
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	RAB5A_HUMAN \| P20339
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	3.6.5.2
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(no "Related Entries Specified in the PDB File" available for 3MJH)

Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

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Exons (7, 14)

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