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Title :   AN OPEN CONFORMATION OF SWITCH I REVEALED BY SAR1-GDP CRYSTAL STRUCTURE AT LOW MG(2+)

Authors :   Y. Rao, C. Bian, C. Yuan, Y. Li, M. Huang

Date :   10 Jan 06 (Deposition) - 05 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.82

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

Keywords :   Sar1, Crystal Structure, Cop Ii Assembly, Dimerization, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Rao, C. Bian, C. Yuan, Y. Li, L. Chen, X. Ye, Z. Huang, M. Huang
An Open Conformation Of Switch I Revealed By Sar1-Gdp Crystal Structure At Low Mg(2+)
Biochem. Biophys. Res. Commun. V. 348 908 2006
PubMed-ID: 16899220 | Reference-DOI: 10.1016/J.BBRC.2006.07.148
(for further references see the PDB file header)

Molecule 1 - GTP-BINDING PROTEIN SAR1B
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11D
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 10-198
	Organism Common	:	CHINESE HAMSTER
	Organism Scientific	:	CRICETULUS GRISEUS
	Organism Taxid	:	10029
	Synonym	:	SAR1, GTBPB

		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, 5)

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

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, 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

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:18 , GLY A:185 , TYR A:186 , GLY A:187 , GLU A:188 , ARG A:191 , HOH A:4781 , HOH A:4856	BINDING SITE FOR RESIDUE SO4 A 4770
2	AC2	SOFTWARE	PHE B:18 , GLY B:185 , TYR B:186 , GLY B:187 , GLU B:188 , ARG B:191 , HOH B:4795	BINDING SITE FOR RESIDUE SO4 B 4771
3	AC3	SOFTWARE	THR B:39 , GDP B:2568 , HOH B:4773 , HOH B:4794 , HOH B:4826	BINDING SITE FOR RESIDUE MG B 504
4	AC4	SOFTWARE	ASP A:34 , ASN A:35 , ALA A:36 , GLY A:37 , LYS A:38 , THR A:39 , THR A:40 , ASN A:134 , LYS A:135 , ASP A:137 , SER A:179 , VAL A:180 , LEU A:181 , HOH A:4808 , HOH A:4830 , HOH A:4845 , HOH A:4857	BINDING SITE FOR RESIDUE GDP A 2567
5	AC5	SOFTWARE	LEU B:33 , ASN B:35 , ALA B:36 , GLY B:37 , LYS B:38 , THR B:39 , THR B:40 , ASN B:134 , LYS B:135 , ASP B:137 , ARG B:138 , SER B:179 , VAL B:180 , LEU B:181 , MG B:504 , HOH B:4794 , HOH B:4826 , HOH B:4863	BINDING SITE FOR RESIDUE GDP B 2568

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAR1	PS51422	small GTPase SAR1 family profile.	SAR1B_CRIGR	19-197	2	A:19-197 B:19-197

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAR1	PS51422	small GTPase SAR1 family profile.	SAR1B_CRIGR	19-197	1	A:19-197 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAR1	PS51422	small GTPase SAR1 family profile.	SAR1B_CRIGR	19-197	1	- B:19-197

(no "Exon" information available for 2FMX)

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:180
 aligned with SAR1B_CRIGR | Q9QVY3 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:186
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192      
          SAR1B_CRIGR    13 SSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHIQARRVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYID 198
               SCOP domains d2fmxa_ A: automated matches                                                                                                                                                               SCOP domains
               CATH domains 2fmxA00 A:13-198 P-loop containing nucleotide triphosphate hydrol      ases                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh......eeeeeeee...hhhhhhhhhhh..............eeeee..eeeeeeee.------hhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhh.....................eeeee.......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------SAR1  PDB: A:19-197 UniProt: 19-197                                                                                                                                                - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fmx A  13 SSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLG------RVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYID 198
                                    22        32        42        52        62        72    |    - |      92       102       112       122       132       142       152       162       172       182       192      
                                                                                           77     84

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with SAR1B_CRIGR | Q9QVY3 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:186
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192      
          SAR1B_CRIGR    13 SSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMTFTTFDLGGHIQARRVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYID 198
               SCOP domains d2fmxb_ B: automated matches                                                                                                                                                               SCOP domains
               CATH domains 2fmxB00 B:13-198 P-loop containing        nucleotide triphosphate        hydrolases                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhh......eeeeee.....hhhhhhhhh..-------......eeeeee..eeeee....-------hhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhh.....................eeeee.......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------SAR1  PDB: B:19-197 UniProt: 19-197                                                                                                                                                - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fmx B  13 SSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKD-------PTLHPTSEELTIAGMTFTTFDLG-------VWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRPEAISEERLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYID 198
                                    22        32        42    |    -  |     62        72    |    -  |     92       102       112       122       132       142       152       162       172       182       192      
                                                             47      55                    77      85

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	-	→ 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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

Chinese hamster (Cricetulus griseus) [TaxId: 10029] (2)

1a	d2fmxa_	A:
1b	d2fmxb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Chinese hamster (Cricetulus griseus) (5)

1a	2fmxA00	A:13-198
1b	2fmxB00	B:13-198

(no "Pfam Domain" information available for 2FMX)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SAR1B_CRIGR | Q9QVY3)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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: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: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:0032580	Golgi cisterna membrane	The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	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.

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