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Title :   CRYSTAL STRUCTURE OF HUMAN RAB18 IN COMPLEX WITH GPPNHP

Authors :   M. Kukimoto-Niino, K. Murayama, L. Chen, Z. J. Liu, B. C. Wang, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   10 May 05 (Deposition) - 10 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.32

Chains :   Asym./Biol. Unit : A

Keywords :   Gtpase, Rab, Gnp, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kukimoto-Niino, K. Murayama, L. Chen, Z. J. Liu, B. C. Wang, M. Shirouzu, S. Yokoyama
Crystal Structure Of Human Rab18 In Complex With Gppnhp
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - RAS-RELATED PROTEIN RAB-18
	Chains	:	A
	Engineered	:	YES
	Fragment	:	GTPASE DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS SYSTEM
	Synonym	:	GTP-BINDING PROTEIN RAB18

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:22 , THR A:40 , GNP A:300 , HOH A:301 , HOH A:303	BINDING SITE FOR RESIDUE MG A 200
2	AC2	SOFTWARE	SER A:17 , GLY A:18 , VAL A:19 , GLY A:20 , LYS A:21 , SER A:22 , SER A:23 , PHE A:33 , ASP A:34 , PRO A:35 , ALA A:39 , THR A:40 , GLY A:66 , ASN A:122 , LYS A:123 , ASP A:125 , LYS A:126 , SER A:151 , ALA A:152 , LYS A:153 , MG A:200 , HOH A:301 , HOH A:303 , HOH A:309 , HOH A:319 , HOH A:330 , HOH A:357 , HOH A:360 , HOH A:361	BINDING SITE FOR RESIDUE GNP A 300

(no "SS Bond" information available for 1X3S)

(no "Cis Peptide Bond" information available for 1X3S)

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_066495	L	24	Q	RAB18_HUMAN	Disease (WARBM3)	387906832	A	L	24	Q
2	UniProt	VAR_051713	N	113	S	RAB18_HUMAN	Polymorphism	12268932	A	N	113	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RAB	PS51419	small GTPase Rab1 family profile.	RAB18_HUMAN	2-199	1	A:2-178

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000356940	1a	ENSE00001907702	chr10:27793197-27793366	170	RAB18_HUMAN	1-23	23	1	A:2-23	22
1.4a	ENST00000356940	4a	ENSE00001700205	chr10:27798804-27798859	56	RAB18_HUMAN	23-42	20	1	A:23-42	20
1.6	ENST00000356940	6	ENSE00000985386	chr10:27815757-27815818	62	RAB18_HUMAN	42-62	21	1	A:42-62	21
1.8	ENST00000356940	8	ENSE00000985387	chr10:27821436-27821508	73	RAB18_HUMAN	63-87	25	1	A:63-87	25
1.9	ENST00000356940	9	ENSE00000985388	chr10:27822664-27822782	119	RAB18_HUMAN	87-126	40	1	A:87-126	40
1.10	ENST00000356940	10	ENSE00000985389	chr10:27822857-27822923	67	RAB18_HUMAN	127-149	23	1	A:127-149	23
1.11e	ENST00000356940	11e	ENSE00001415399	chr10:27826805-27829092	2288	RAB18_HUMAN	149-206	58	1	A:149-178	30

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:177
 aligned with RAB18_HUMAN | Q9NP72 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       
          RAB18_HUMAN     2 DEDVLTTLKILIIGESGVGKSSLLLRFTDDTFDPELAATIGVDFKVKTISVDGNKAKLAIWDTAGQERFRTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNMLVGNKIDKENREVDRNEGLKFARKHSMLFIEASAKTCDGVQCAFEELVEKIIQTPGLWES 178
               SCOP domains d1x3sa1 A:2-178 Rab18                                                                                                                                                             SCOP domains
               CATH domains 1x3sA00 A:2-178 P-loop containing nucleotide triphosphate hydrolases                                                                                                              CATH domains
               Pfam domains --------Ras-1x3sA01 A:10-171                                                                                                                                              ------- Pfam domains
         Sec.struct. author ...eeeeeeeeee.....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhh.hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhh........eeeeeee.........hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------Q----------------------------------------------------------------------------------------S----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RAB  PDB: A:2-178 UniProt: 2-199                                                                                                                                                  PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:2-23------------------Exon 1.6  PDB: A:42-6Exon 1.8  PDB: A:63-87   ---------------------------------------Exon 1.10              ----------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------Exon 1.4a           --------------------------------------------Exon 1.9  PDB: A:87-126 UniProt: 87-126 ----------------------Exon 1.11e  PDB: A:149-178     Transcript 1 (2)
                 1x3s A   2 DEDVLTTLKILIIGESGVGKSSLLLRFTDDTFDPELAATIGVDFKVKTISVDGNKAKLAIWDTAGQERFRTLTPSYYRGAQGVILVYDVTRRDTFVKLDNWLNELETYCTRNDIVNmLVGNKIDKENREVDRNEGLKFARKHSmLFIEASAKTCDGVQCAFEELVEKIIQTPGLWES 178
                                    11        21        31        41        51        61        71        81        91       101       111      |121       131       141   |   151       161       171       
                                                                                                                                              118-MSE                    145-MSE

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(

)

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: Rab18 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d1x3sa1

A:2-178

Asymmetric/Biological 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)

Human (Homo sapiens) (413)

1x3sA00

A:2-178

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Ras (176)

Homo sapiens (Human) (141)

Ras-1x3sA01

A:10-171

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RAB18_HUMAN | Q9NP72)

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: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:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0071786	endoplasmic reticulum tubular network organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum (ER) tubular network. The ER tubular network is the ER part that that has membranes with high curvature in cross-section.
	GO:0001654	eye development	The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
	GO:0034389	lipid particle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lipid particle.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	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: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.
cellular component
	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:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0071782	endoplasmic reticulum tubular network	A subcompartment of the endoplasmic reticulum consisting of tubules having membranes with high curvature in cross-section.
	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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Asymmetric/Biological Unit
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