2Q3F - JenaLib

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Title :   X-RAY CRYSTAL STRUCTURE OF PUTATIVE HUMAN RAS-RELATED GTP BINDING D IN COMPLEX WITH GMPPNP

Authors :   A. M. Mulichak, W. M. Rabeh, W. Tempel, L. Nedyalkova, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, L. J. Keefe, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)

Date :   30 May 07 (Deposition) - 12 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Structural Genomics, Gtp-Binding, Rragd, Structural Genomics Consortium, Sgc, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Mulichak, W. M. Rabeh, W. Tempel, L. Nedyalkova, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, L. J. Keefe, A. Bochkarev, H. Park
Crystal Structure Of Human Ras-Related Gtp-Binding D.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - RAS-RELATED GTP-BINDING PROTEIN D
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	P28A-LIC
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RRAGD
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RAG D

		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 (3, 12)

No.	Name	Count	Type	Full Name
1	GNP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:57 , THR A:78 , GNP A:401 , HOH A:406 , HOH A:408	BINDING SITE FOR RESIDUE MG A 301
2	AC2	SOFTWARE	SER B:57 , THR B:78 , GNP B:402 , HOH B:415 , HOH B:425	BINDING SITE FOR RESIDUE MG B 302
3	AC3	SOFTWARE	ARG A:52 , ARG A:53 , SER A:54 , GLY A:55 , LYS A:56 , SER A:57 , SER A:58 , THR A:72 , LEU A:73 , THR A:78 , GLY A:101 , GLN A:129 , HIS A:160 , LYS A:161 , ASP A:163 , SER A:201 , ILE A:202 , MG A:301 , HOH A:406 , HOH A:408 , HOH A:422 , HOH A:430	BINDING SITE FOR RESIDUE GNP A 401
4	AC4	SOFTWARE	LEU B:51 , ARG B:52 , ARG B:53 , SER B:54 , GLY B:55 , LYS B:56 , SER B:57 , SER B:58 , THR B:72 , LEU B:73 , THR B:78 , GLY B:101 , HIS B:160 , LYS B:161 , ASP B:163 , SER B:201 , ILE B:202 , TYR B:203 , MG B:302 , HOH B:410 , HOH B:415 , HOH B:417 , HOH B:425 , HOH B:440	BINDING SITE FOR RESIDUE GNP B 402

(no "SS Bond" information available for 2Q3F)

(no "Cis Peptide Bond" information available for 2Q3F)

(no "SAP(SNP)/Variant" information available for 2Q3F)

(no "PROSITE Motif" information available for 2Q3F)

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000369415	1a	ENSE00001449989	chr6:90121989-90121565	425	RRAGD_HUMAN	1-50	50	0	-	-
1.3	ENST00000369415	3	ENSE00002197569	chr6:90097309-90097014	296	RRAGD_HUMAN	50-148	99	2	A:42-129 B:42-129	88 88
1.4a	ENST00000369415	4a	ENSE00002195650	chr6:90090086-90089887	200	RRAGD_HUMAN	149-215	67	2	A:130-196 B:130-196	67 67
1.5	ENST00000369415	5	ENSE00002151390	chr6:90089057-90088943	115	RRAGD_HUMAN	215-253	39	2	A:196-220 B:196-219	25 24
1.6b	ENST00000369415	6b	ENSE00001888083	chr6:90087532-90087390	143	RRAGD_HUMAN	254-301	48	0	-	-
1.7	ENST00000369415	7	ENSE00000760434	chr6:90082304-90082156	149	RRAGD_HUMAN	301-351	51	0	-	-
1.8b	ENST00000369415	8b	ENSE00001449984	chr6:90077926-90074355	3572	RRAGD_HUMAN	351-400	50	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:179
 aligned with RRAGD_HUMAN | Q9NQL2 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:179
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
          RRAGD_HUMAN    61 VKPRILLMGLRRSGKSSIQKVVFHKMSPNETLFLESTNKICREDVSNSSFVNFQIWDFPGQIDFFDPTFDYEMIFRGTGALIFVIDSQDDYMEALARLHLTVTRAYKVNTDINFEVFIHKVDGLSDDHKIETQRDIHQRANDDLADAGLEKIHLSFYLTSIYDHSIFEAFSKVVQKLIP 239
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhh.hhhhhhhh......eeeee.......eeeee............hhhhhhhheeeeeeeee....hhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh..hhhhhhhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:42-129 UniProt: 50-148 [INCOMPLETE]                                    Exon 1.4a  PDB: A:130-196 UniProt: 149-215                         ------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: A:196-220  Transcript 1 (2)
                 2q3f A  42 VKPRILLmGLRRSGKSSIQKVVFHKmSPNETLFLESTNKICREDVSNSSFVNFQIWDFPGQIDFFDPTFDYEmIFRGTGALIFVIDSQDDYmEALARLHLTVTRAYKVNTDINFEVFIHKVDGLSDDHKIETQRDIHQRANDDLADAGLEKIHLSFYLTSIYDHSIFEAFSKVVQKLIP 220
                                   |51        61     |  71        81        91       101       111  |    121       131 |     141       151       161       171       181       191       201       211         
                                  49-MSE            67-MSE                                        114-MSE            133-MSE

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with RRAGD_HUMAN | Q9NQL2 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:178
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
          RRAGD_HUMAN    61 VKPRILLMGLRRSGKSSIQKVVFHKMSPNETLFLESTNKICREDVSNSSFVNFQIWDFPGQIDFFDPTFDYEMIFRGTGALIFVIDSQDDYMEALARLHLTVTRAYKVNTDINFEVFIHKVDGLSDDHKIETQRDIHQRANDDLADAGLEKIHLSFYLTSIYDHSIFEAFSKVVQKLI 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Gtr1_RagA-2q3fB01 B:45-219                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) ---Gtr1_RagA-2q3fB02 B:45-219                                                                                                                                                      Pfam domains (2)
         Sec.struct. author ...eeeee.....hhhhhhhhhhh..hhhhhhhh......eeeee.......eeeee............hhhhhhhheeeeeeeee....hhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:42-129 UniProt: 50-148 [INCOMPLETE]                                    Exon 1.4a  PDB: B:130-196 UniProt: 149-215                         ----------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5  PDB: B:196-219 Transcript 1 (2)
                 2q3f B  42 VKPRILLmGLRRSGKSSIQKVVFHKmSPNETLFLESTNKICREDVSNSSFVNFQIWDFPGQIDFFDPTFDYEmIFRGTGALIFVIDSQDDYmEALARLHLTVTRAYKVNTDINFEVFIHKVDGLSDDHKIETQRDIHQRANDDLADAGLEKIHLSFYLTSIYDHSIFEAFSKVVQKLI 219
                                   |51        61     |  71        81        91       101       111  |    121       131 |     141       151       161       171       181       191       201       211        
                                  49-MSE            67-MSE                                        114-MSE            133-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 '\|'

(no "SCOP Domain" information available for 2Q3F)

(no "CATH Domain" information available for 2Q3F)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Gtr1_RagA (2)

Homo sapiens (Human) (2)

1a	Gtr1_RagA-2q3fB01	B:45-219
1b	Gtr1_RagA-2q3fB02	B:45-219

Asymmetric Unit(hide GO term definitions)

Chain A,B (RRAGD_HUMAN | Q9NQL2)

molecular function
	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).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0007050	cell cycle arrest	A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
	GO:0034613	cellular protein localization	Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
	GO:0071230	cellular response to amino acid stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
	GO:0009267	cellular response to starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
	GO:0016236	macroautophagy	The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
	GO:0032008	positive regulation of TOR signaling	Any process that activates or increases the frequency, rate or extent of TOR signaling.
	GO:0010506	regulation of autophagy	Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
cellular component
	GO:0034448	EGO complex	A vacuolar membrane-associated protein complex that is required for activation of microautophagy during exit from rapamycin-induced growth arrest. In budding yeast, S. cerevisiae, this complex includes Gtr1p, Gtr2p, Meh1p, and Slm4p.
	GO:1990131	Gtr1-Gtr2 GTPase complex	A heterodimer GTPase complex. In S. cerevisiae, this complex contains Gtr1p and Gtr2p proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (4, 4)

SS Bonds (0, 0)

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Exons (3, 6)

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