3LRP - JenaLib

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Title :   CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM ADP-RIBOSYLATION FACTOR 1

Authors :   W. J. Cook, D. Chattopadhyay

Date :   11 Feb 10 (Deposition) - 10 Nov 10 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Adp-Ribosylation Factor, Protein Trafficking, Er-Golgi Transport, Golgi Apparatus, Gtp-Binding, Lipoprotein, Myristate, Nucleotide- Binding, Protein Transport, Transport, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. J. Cook, C. D. Smith, O. Senkovich, A. A. Holder, D. Chattopadhyay
Structure Of Plasmodium Falciparum Adp-Ribosylation Factor 1.
Acta Crystallogr. , Sect. F V. 66 1426 2010
PubMed-ID: 21045287 | Reference-DOI: 10.1107/S1744309110036997

Molecule 1 - ADP-RIBOSYLATION FACTOR 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-3X
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ARF1, ARF, PLARF
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	5833

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:26 , ALA A:27 , ALA A:28 , GLY A:29 , LYS A:30 , THR A:31 , THR A:32 , ASN A:52 , ASP A:67 , ASN A:126 , LYS A:127 , ASP A:129 , LEU A:130 , CYS A:159 , ALA A:160 , THR A:161 , MG A:183 , HOH A:215 , HOH A:257 , HOH A:282 , HOH A:290	BINDING SITE FOR RESIDUE GDP A 182
2	AC2	SOFTWARE	THR A:31 , GDP A:182 , HOH A:282 , HOH A:289 , HOH A:290	BINDING SITE FOR RESIDUE MG A 183
3	AC3	SOFTWARE	GLN A:128 , LEU A:130 , PRO A:131 , ALA A:133 , HOH A:246	BINDING SITE FOR RESIDUE SO4 A 184

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

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARF	PS51417	small GTPase Arf family profile.	ARF1_PLAF7	11-177	1	A:11-177
1	ARF	PS51417	small GTPase Arf family profile.	ARF1_PLAFA	11-177	1	A:11-177

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARF	PS51417	small GTPase Arf family profile.	ARF1_PLAF7	11-177	1	A:11-177
1	ARF	PS51417	small GTPase Arf family profile.	ARF1_PLAFA	11-177	1	A:11-177

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARF	PS51417	small GTPase Arf family profile.	ARF1_PLAF7	11-177	2	A:11-177
1	ARF	PS51417	small GTPase Arf family profile.	ARF1_PLAFA	11-177	2	A:11-177

(no "Exon" information available for 3LRP)

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:181
 aligned with ARF1_PLAF7 | Q7KQL3 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
           ARF1_PLAF7     1 MGLYVSRLFNRLFQKKDVRILMVGLDAAGKTTILYKVKLGEVVTTIPTIGFNVETVEFRNISFTVWDVGGQDKIRPLWRHYYSNTDGLIFVVDSNDRERIDDAREELHRMINEEELKDAIILVFANKQDLPNAMSAAEVTEKLHLNTIRERNWFIQSTCATRGDGLYEGFDWLTTHLNNAK 181
               SCOP domains d3lrpa_ A: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Arf-3lrpA01 A:5-177                                                                                                                                                          ---- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....eeeeeee....hhhhhhhhhh....eee.......eeeeee..eeeeeee......hhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------ARF  PDB: A:11-177 UniProt: 11-177                                                                                                                                     ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lrp A   1 MGLYVSRLFNRLFQKKDVRILMVGLDAAGKTTILYKVKLGEVVTTIPTIGFNVETVEFRNISFTVWDVGGQDKIRPLWRHYYSNTDGLIFVVDSNDRERIDDAREELHRMINEEELKDAIILVFANKQDLPNAMSAAEVTEKLHLNTIRERNWFIQSTCATRGDGLYEGFDWLTTHLNNAK 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain A from PDB  Type:PROTEIN  Length:181
 aligned with ARF1_PLAFA | Q94650 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
           ARF1_PLAFA     1 MGLYVSRLFNRLFQKKDVRILMVGLDAAGKTTILYKVKLGEVVTTIPTIGFNVETVEFRNISFTVWDVGGQDKIRPLWRHYYSNTDGLIFVVDSNDRERIDDAREELHRMINEEELKDAIILVFANKQDLPNAMSAAEVTEKLHLNTIRERNWFIQSTCATRGDGLYEGFDWLTTHLNNAK 181
               SCOP domains d3lrpa_ A: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Arf-3lrpA01 A:5-177                                                                                                                                                          ---- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....eeeeeee....hhhhhhhhhh....eee.......eeeeee..eeeeeee......hhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------ARF  PDB: A:11-177 UniProt: 11-177                                                                                                                                     ---- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lrp A   1 MGLYVSRLFNRLFQKKDVRILMVGLDAAGKTTILYKVKLGEVVTTIPTIGFNVETVEFRNISFTVWDVGGQDKIRPLWRHYYSNTDGLIFVVDSNDRERIDDAREELHRMINEEELKDAIILVFANKQDLPNAMSAAEVTEKLHLNTIRERNWFIQSTCATRGDGLYEGFDWLTTHLNNAK 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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: automated matches (173)

Malaria parasite (Plasmodium falciparum) [TaxId: 5833] (1)

d3lrpa_

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Arf (26)

Plasmodium falciparum (1)

Arf-3lrpA01

A:5-177

Asymmetric Unit(hide GO term definitions)

Chain A (ARF1_PLAFA | Q94650)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	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.
biological process
	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.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	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.

Chain A (ARF1_PLAF7 | Q7KQL3)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	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.
biological process
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0006471	protein ADP-ribosylation	The transfer, from NAD, of ADP-ribose to protein amino acids.
	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.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0020020	food vacuole	Vacuole within a parasite used for digestion of the host cell cytoplasm. An example of this component is found in the Apicomplexa.
	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.

Asymmetric Unit
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	3lrp
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(no "Entries Sharing at Least One Protein Chain" available for 3LRP)

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