2O52 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN RAB4B IN COMPLEX WITH GDP

Authors :   H. Zhu, W. Tempel, J. Wang, Y. Shen, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)

Date :   05 Dec 06 (Deposition) - 19 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   G-Protein, Rab, Gdp, Structural Genomics, Structural Genomics Consortium, Sgc, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Zhu, W. Tempel, J. Wang, Y. Shen, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of Human Rab4B In Complex With Gdp
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - RAS-RELATED PROTEIN RAB-4B
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P28A-THROMBIN-LIC
	Expression System Strain	:	BL21-CODONPLUS (DE-3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RAB4B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	UNX	1	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	UNX	1	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	UNX	-1	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:22 , GDP A:601 , HOH A:1004 , HOH A:1005 , HOH A:1006 , HOH A:1007	BINDING SITE FOR RESIDUE MG A 602
2	AC2	SOFTWARE	SER B:22 , GDP B:601 , HOH B:604 , HOH B:605 , HOH B:606 , HOH B:607	BINDING SITE FOR RESIDUE MG B 602
3	AC3	SOFTWARE	SER A:16 , GLY A:18 , THR A:19 , GLY A:20 , LYS A:21 , SER A:22 , CYS A:23 , ASN A:121 , LYS A:122 , ASP A:124 , LEU A:125 , SER A:151 , ALA A:152 , LEU A:153 , MG A:602 , HOH A:1005 , HOH A:1006 , HOH A:1007	BINDING SITE FOR RESIDUE GDP A 601
4	AC4	SOFTWARE	CYS A:23 , LEU A:153	BINDING SITE FOR RESIDUE BME A 603
5	AC5	SOFTWARE	GLY A:53 , GLY A:54 , LYS A:55 , SER B:16 , GLY B:18 , THR B:19 , GLY B:20 , LYS B:21 , SER B:22 , CYS B:23 , ARG B:69 , ASN B:121 , LYS B:122 , ASP B:124 , LEU B:125 , SER B:151 , ALA B:152 , LEU B:153 , MG B:602 , BME B:603 , HOH B:604 , HOH B:606	BINDING SITE FOR RESIDUE GDP B 601
6	AC6	SOFTWARE	CYS B:23 , GDP B:601	BINDING SITE FOR RESIDUE BME B 603
7	AC7	SOFTWARE	HOH A:1023 , ASN B:157	BINDING SITE FOR RESIDUE UNX A 1003

(no "SS Bond" information available for 2O52)

(no "Cis Peptide Bond" information available for 2O52)

(no "SAP(SNP)/Variant" information available for 2O52)

(no "PROSITE Motif" information available for 2O52)

Asymmetric Unit (7, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000357052	1a	ENSE00001414417	chr19:41284171-41284296	126	RAB4B_HUMAN	1-6	6	2	A:5-6 B:5-6	2 2
1.2b	ENST00000357052	2b	ENSE00001675527	chr19:41285924-41286004	81	RAB4B_HUMAN	6-33	28	2	A:6-30 B:6-30	25 25
1.3	ENST00000357052	3	ENSE00001137689	chr19:41286290-41286404	115	RAB4B_HUMAN	33-71	39	2	A:43-71 B:43-71	29 29
1.4	ENST00000357052	4	ENSE00001767433	chr19:41289683-41289745	63	RAB4B_HUMAN	71-92	22	2	A:71-92 B:71-92	22 22
1.5	ENST00000357052	5	ENSE00001114548	chr19:41289826-41289980	155	RAB4B_HUMAN	92-144	53	2	A:92-144 B:92-144	53 53
1.6	ENST00000357052	6	ENSE00001754869	chr19:41292570-41292665	96	RAB4B_HUMAN	144-176	33	2	A:144-176 B:144-174	33 31
1.7	ENST00000357052	7	ENSE00001636714	chr19:41292753-41292883	131	RAB4B_HUMAN	176-213	38	1	A:176-183 -	8 -
1.8b	ENST00000357052	8b	ENSE00001477004	chr19:41302475-41302847	373	RAB4B_HUMAN	-	0	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:167
 aligned with RAB4B_HUMAN | P61018 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:179
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174         
          RAB4B_HUMAN     5 YDFLFKFLVIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKTVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRETYNSLAAWLTDARTLASPNIVVILCGNKKDLDPEREVTFLEASRFAQENELMFLETSALTGENVEEAFLKCARTILNKIDSGELDPERM 183
               SCOP domains d2o52a_ A: automated match            es                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee....hhhhhhhhhhh------------..eeeeeeee..eeeeeeee...hhhhhh..hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhh..hhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.--------------------------Exon 1.3  PDB: A:43-71 UniProt: 33-71  --------------------Exon 1.5  PDB: A:92-144 UniProt: 92-144              -------------------------------Exon 1.7 Transcript 1 (1)
           Transcript 1 (2) -Exon 1.2b  PDB: A:6-30      -------------------------------------Exon 1.4  PDB: A:71-92---------------------------------------------------Exon 1.6  PDB: A:144-176         ------- Transcript 1 (2)
                 2o52 A   5 SDFLFKFLVIGSAGTGKSCLLHQFIE------------VEFGSRVVNVGGKTVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRETYNSLAAWLTDARTLASPNIVVILCGNKKDLDPEREVTFLEASRFAQENELMFLETSALTGENVEEAFLKCARTILNKIDSGELDPERM 183
                                    14        24     |   -        44        54        64        74        84        94       104       114       124       134       144       154       164       174         
                                                    30           43

Chain B from PDB  Type:PROTEIN  Length:158
 aligned with RAB4B_HUMAN | P61018 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:170
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174
          RAB4B_HUMAN     5 YDFLFKFLVIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKTVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRETYNSLAAWLTDARTLASPNIVVILCGNKKDLDPEREVTFLEASRFAQENELMFLETSALTGENVEEAFLKCARTILNKID 174
               SCOP domains d2o52b_ B: automated match            es                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Ras-2o52B01 B:10-171                                                                                                                                              --- Pfam domains (1)
           Pfam domains (2) -----Ras-2o52B02 B:10-171                                                                                                                                              --- Pfam domains (2)
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhh------------..eeeeeeee..eeeeeeee...hhhhh...hhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.--------------------------Exon 1.3  PDB: B:43-71 UniProt: 33-71  --------------------Exon 1.5  PDB: B:92-144 UniProt: 92-144              ------------------------------ Transcript 1 (1)
           Transcript 1 (2) -Exon 1.2b  PDB: B:6-30      -------------------------------------Exon 1.4  PDB: B:71-92---------------------------------------------------Exon 1.6  PDB: B:144-174        Transcript 1 (2)
                 2o52 B   5 SDFLFKFLVIGSAGTGKSCLLHQFIE------------VEFGSRVVNVGGKTVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRETYNSLAAWLTDARTLASPNIVVILCGNKKDLDPEREVTFLEASRFAQENELMFLETSALTGENVEEAFLKCARTILNKID 174
                                    14        24     |   -        44        54        64        74        84        94       104       114       124       134       144       154       164       174
                                                    30           43

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	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: automated matches (173)

Human (Homo sapiens) [TaxId: 9606] (112)

1a	d2o52a_	A:
1b	d2o52b_	B:

(no "CATH Domain" information available for 2O52)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Ras (176)

Homo sapiens (Human) (141)

1a	Ras-2o52B01	B:10-171
1b	Ras-2o52B02	B:10-171

Asymmetric Unit(hide GO term definitions)

Chain A,B (RAB4B_HUMAN | P61018)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	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:0046323	glucose import	The directed movement of the hexose monosaccharide glucose into a cell or organelle.
	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:0030100	regulation of endocytosis	Any process that modulates the frequency, rate or extent of endocytosis.
	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:0032593	insulin-responsive compartment	A small membrane-bounded vesicle that releases its contents by exocytosis in response to insulin stimulation; the contents are enriched in GLUT4, IRAP and VAMP2.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	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: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.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (7, 13)

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