1ZCA - JenaLib

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Title :   CRYSTAL STRUCTURE OF G ALPHA 12 IN COMPLEX WITH GDP, MG2+ AND ALF4-

Authors :   M. R. Nance, J. J. G. Tesmer

Date :   11 Apr 05 (Deposition) - 15 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Gtp-Binding, Lipoprotein, Membrane, Palmitate, Transducer, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Kreutz, D. M. Yau, M. R. Nance, S. Tanabe, J. J. Tesmer, T. Kozasa
A New Approach To Producing Functional G Alpha Subunits Yields The Activated And Deactivated Structures Of G Alpha(12/13) Proteins.
Biochemistry V. 45 167 2006
PubMed-ID: 16388592 | Reference-DOI: 10.1021/BI051729T
(for further references see the PDB file header)

Molecule 1 - G ALPHA I/12
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Plasmid	:	PFASTBACHTA
	Expression System Strain	:	SF9
	Expression System Taxid	:	7108
	Expression System Vector Type	:	VIRUS
	Fragment	:	N-TERMINAL RESIDUES 1-28 OF G ALPHA I FOLLOWED BY RESIDUES 49-379 OF G ALPHA 12
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		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, 6)

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

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:69 , THR A:206 , GDP A:382 , ALF A:384 , HOH A:386 , HOH A:387	BINDING SITE FOR RESIDUE MG A 383
2	AC2	SOFTWARE	GLY A:64 , GLU A:65 , LYS A:68 , ARG A:203 , ALA A:205 , THR A:206 , VAL A:226 , GLY A:228 , GLN A:229 , GDP A:382 , MG A:383 , HOH A:385 , HOH A:386 , HOH A:387	BINDING SITE FOR RESIDUE ALF A 384
3	AC3	SOFTWARE	SER B:69 , THR B:206 , GDP B:1382 , ALF B:1384 , HOH B:1386 , HOH B:1387	BINDING SITE FOR RESIDUE MG B 1383
4	AC4	SOFTWARE	GLY B:64 , GLU B:65 , LYS B:68 , ARG B:203 , ALA B:205 , THR B:206 , VAL B:226 , GLY B:227 , GLY B:228 , GLN B:229 , GDP B:1382 , MG B:1383 , HOH B:1385 , HOH B:1386 , HOH B:1387	BINDING SITE FOR RESIDUE ALF B 1384
5	AC5	SOFTWARE	GLU A:65 , SER A:66 , GLY A:67 , LYS A:68 , SER A:69 , THR A:70 , SER A:176 , LEU A:200 , LEU A:201 , ALA A:202 , ARG A:203 , ASN A:294 , LYS A:295 , ASP A:297 , LEU A:298 , THR A:350 , ALA A:351 , ILE A:352 , MG A:383 , ALF A:384 , HOH A:386 , HOH A:387	BINDING SITE FOR RESIDUE GDP A 382
6	AC6	SOFTWARE	GLU B:65 , SER B:66 , GLY B:67 , LYS B:68 , SER B:69 , THR B:70 , SER B:176 , LEU B:200 , LEU B:201 , ARG B:203 , ASN B:294 , LYS B:295 , ASP B:297 , LEU B:298 , THR B:350 , ALA B:351 , ILE B:352 , MG B:1383 , ALF B:1384 , HOH B:1386 , HOH B:1387	BINDING SITE FOR RESIDUE GDP B 1382

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

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

(no "SAP(SNP)/Variant" information available for 1ZCA)

(no "PROSITE Motif" information available for 1ZCA)

(no "Exon" information available for 1ZCA)

Asymmetric Unit

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	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:318
 aligned with GNA12_MOUSE | P27600 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:318
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363        
          GNA12_MOUSE    54 RLVKILLLGAGESGKSTFLKQMRIIHGREFDQKALLEFRDTIFDNILKGSRVLVDARDKLGIPWQHSENEKHGMFLMAFENKAGLPVEPATFQLYVPALSALWRDSGIREAFSRRSEFQLGESVKYFLDNLDRIGQLNYFPSKQDILLARKATKGIVEHDFVIKKIPFKMVDVGGQRSQRQKWFQCFDGITSILFMVSSSEYDQVLMEDRRTNRLVESMNIFETIVNNKLFFNVSIILFLNKMDLLVEKVKSVSIKKHFPDFKGDPHRLEDVQRYLVQCFDRKRRNRSKPLFHHFTTAIDTENIRFVFHAVKDTILQE 371
               SCOP domains d1zcaa2 A:54-82,A:205-371    d1zcaa1 A:83-204 Transducin (alpha subunit), insertion domain                                                             d1zcaa2 A:54-82,A:205-371 Transducin (alpha subunit)                                                                                                                    SCOP domains
               CATH domains 1zcaA01 A:54-83,A:206-371     1zcaA02 A:84-205 GI Alpha 1, domain 2-like                                                                                1zcaA01 A:54-83,A:206-371 P-loop containing nucleotide triphosphate hydrolases                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhh......eeeeeeee..eeeeeeee..hhhhhhhhhhh.....eeeeeee..............hhhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..............hhhhhhhhhhhhhhhh.........eee....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zca A  54 RLVKILLLGAGESGKSTFLKQMRIIHGREFDQKALLEFRDTIFDNILKGSRVLVDARDKLGIPWQHSENEKHGMFLMAFENKAGLPVEPATFQLYVPALSALWRDSGIREAFSRRSEFQLGESVKYFLDNLDRIGQLNYFPSKQDILLARKATKGIVEHDFVIKKIPFKMVDVGGQRSQRQKWFQCFDGITSILFMVSSSEYDQVLMEDRRTNRLVESMNIFETIVNNKLFFNVSIILFLNKMDLLVEKVKSVSIKKHFPDFKGDPHRLEDVQRYLVQCFDRKRRNRSKPLFHHFTTAIDTENIRFVFHAVKDTILQE 371
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363

Chain B from PDB  Type:PROTEIN  Length:317
 aligned with GNA12_MOUSE | P27600 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:317
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       
          GNA12_MOUSE    54 RLVKILLLGAGESGKSTFLKQMRIIHGREFDQKALLEFRDTIFDNILKGSRVLVDARDKLGIPWQHSENEKHGMFLMAFENKAGLPVEPATFQLYVPALSALWRDSGIREAFSRRSEFQLGESVKYFLDNLDRIGQLNYFPSKQDILLARKATKGIVEHDFVIKKIPFKMVDVGGQRSQRQKWFQCFDGITSILFMVSSSEYDQVLMEDRRTNRLVESMNIFETIVNNKLFFNVSIILFLNKMDLLVEKVKSVSIKKHFPDFKGDPHRLEDVQRYLVQCFDRKRRNRSKPLFHHFTTAIDTENIRFVFHAVKDTILQ 370
               SCOP domains d1zcab2 B:54-82,B:205-370    d1zcab1 B:83-204 Transducin (alpha subunit), insertion domain                                                             d1zcab2 B:54-82,B:205-370 Transducin (alpha subunit)                                                                                                                   SCOP domains
               CATH domains 1zcaB01 B:54-83,B:206-370     1zcaB02 B:84-205 GI Alpha 1, domain 2-like                                                                                1zcaB01 B:54-83,B:206-370 P-loop containing nucleotide triphosphate hydrolases                                                                                        CATH domains
           Pfam domains (1) G-alpha-1zcaB01 B:54-370                                                                                                                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) G-alpha-1zcaB02 B:54-370                                                                                                                                                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhh......eeeeeeee..eeeeeeee..hhhhhhhhhhh.....eeeeeee..............hhhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhh..............hhhhhhhhhhhhhhhh.........eee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zca B  54 RLVKILLLGAGESGKSTFLKQMRIIHGREFDQKALLEFRDTIFDNILKGSRVLVDARDKLGIPWQHSENEKHGMFLMAFENKAGLPVEPATFQLYVPALSALWRDSGIREAFSRRSEFQLGESVKYFLDNLDRIGQLNYFPSKQDILLARKATKGIVEHDFVIKKIPFKMVDVGGQRSQRQKWFQCFDGITSILFMVSSSEYDQVLMEDRRTNRLVESMNIFETIVNNKLFFNVSIILFLNKMDLLVEKVKSVSIKKHFPDFKGDPHRLEDVQRYLVQCFDRKRRNRSKPLFHHFTTAIDTENIRFVFHAVKDTILQ 370
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

)

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)

House mouse (Mus musculus) (47)

1a	1zcaA01	A:54-83,A:206-371
1b	1zcaB01	B:54-83,B:206-370

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: GI Alpha 1, domain 2-like (67)

Homologous Superfamily: GI Alpha 1, domain 2-like (66)

House mouse (Mus musculus) (4)

2a	1zcaA02	A:84-205
2b	1zcaB02	B:84-205

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: G-alpha (24)

Mus musculus (Mouse) (5)

1a	G-alpha-1zcaB01	B:54-370
1b	G-alpha-1zcaB02	B:54-370

Asymmetric Unit(hide GO term definitions)

Chain A,B (GNA12_MOUSE | P27600)

molecular function
	GO:0031752	D5 dopamine receptor binding	Interacting selectively and non-covalently with a D5 dopamine receptor.
	GO:0031683	G-protein beta/gamma-subunit complex binding	Interacting selectively and non-covalently with a complex of G-protein beta/gamma subunits.
	GO:0001664	G-protein coupled receptor binding	Interacting selectively and non-covalently with a G-protein coupled receptor.
	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:0019001	guanyl nucleotide binding	Interacting selectively and non-covalently with guanyl nucleotides, any compound consisting of guanosine esterified with (ortho)phosphate.
	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:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0007266	Rho protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
	GO:0007188	adenylate cyclase-modulating G-protein coupled receptor signaling pathway	The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds through activation or inhibition of adenylyl cyclase activity and a subsequent change in the concentration of cyclic AMP (cAMP).
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0042733	embryonic digit morphogenesis	The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe.
	GO:0001701	in utero embryonic development	The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0032006	regulation of TOR signaling	Any process that modulates the frequency, rate or extent of TOR signaling.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0010762	regulation of fibroblast migration	Any process that modulates the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium.
	GO:0032434	regulation of proteasomal ubiquitin-dependent protein catabolic process	Any process that modulates the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	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.
cellular component
	GO:0031526	brush border membrane	The portion of the plasma membrane surrounding the brush border.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0005834	heterotrimeric G-protein complex	Any of a family of heterotrimeric GTP-binding and hydrolyzing proteins; they belong to a superfamily of GTPases that includes monomeric proteins such as EF-Tu and RAS. Heterotrimeric G-proteins consist of three subunits; the alpha subunit contains the guanine nucleotide binding site and possesses GTPase activity; the beta and gamma subunits are tightly associated and function as a beta-gamma heterodimer; extrinsic plasma membrane proteins (cytoplasmic face) that function as a complex to transduce signals from G-protein coupled receptors to an effector protein.
	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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1zcb	CRYSTAL STRUCTURE OF G ALPHA 13 IN COMPLEX WITH GDP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 4)

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