3Q72 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RAD G-DOMAIN-GTP ANALOG COMPLEX

Authors :   Y. Sasson, L. Navon-Perry, J. A. Hirsch

Date :   04 Jan 11 (Deposition) - 21 Sep 11 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.66

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

Keywords :   G-Domain, G-Protein, Cav2 Beta, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Sasson, L. Navon-Perry, D. Huppert, J. A. Hirsch
Rgk Family G-Domain:Gtp Analog Complex Structures And Nucleotide-Binding Properties.
J. Mol. Biol. V. 413 372 2011
PubMed-ID: 21903096 | Reference-DOI: 10.1016/J.JMB.2011.08.017

Molecule 1 - GTP-BINDING PROTEIN RAD
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21D
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	G-DOMAIN, RESIDUES 90-255
	Gene	:	RRAD, RAD
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RAD1, RAS ASSOCIATED WITH DIABETES

		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	CA	2	Ligand/Ion	CALCIUM ION
2	GNP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GNP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:6 , HOH A:63 , PRO A:100 , GLY A:101 , VAL A:102 , GLY A:103 , LYS A:104 , SER A:105 , ALA A:106 , ASN A:203 , LYS A:204 , ASP A:206 , LEU A:207 , SER A:233 , ALA A:234 , ALA A:235 , MG A:257 , HOH A:266 , HOH A:273 , HOH B:75 , ARG B:188 , HOH B:258	BINDING SITE FOR RESIDUE GNP A 256
2	AC2	SOFTWARE	HOH A:6 , HOH A:17 , HOH A:84 , SER A:105 , ASP A:144 , GNP A:256	BINDING SITE FOR RESIDUE MG A 257
3	AC3	SOFTWARE	HOH A:74 , GLU A:212 , ARG A:252 , ARG A:255 , HOH A:263 , HOH A:269	BINDING SITE FOR RESIDUE CA A 1
4	AC4	SOFTWARE	HOH B:14 , HOH B:21 , HOH B:38 , HOH B:49 , PRO B:100 , GLY B:101 , VAL B:102 , GLY B:103 , LYS B:104 , SER B:105 , ALA B:106 , GLU B:147 , ASN B:203 , LYS B:204 , ASP B:206 , LEU B:207 , SER B:233 , ALA B:234 , ALA B:235 , MG B:257 , HOH B:263 , HOH B:268	BINDING SITE FOR RESIDUE GNP B 256
5	AC5	SOFTWARE	HOH B:14 , HOH B:21 , SER B:105 , GLU B:147 , GNP B:256	BINDING SITE FOR RESIDUE MG B 257
6	AC6	SOFTWARE	ASP B:173 , GLU B:212 , ARG B:252 , ARG B:255 , HOH B:266	BINDING SITE FOR RESIDUE CA B 1

(no "SS Bond" information available for 3Q72)

Asymmetric Unit

No.	Residues
1	Gly A:112	-	Gly A:113
2	Gly A:113	-	Val A:114
3	Val A:133	-	Asp A:134
4	Gly B:113	-	Val B:114
5	Gly B:124	-	His B:125
6	Val B:133	-	Asp B:134

(no "SAP(SNP)/Variant" information available for 3Q72)

(no "PROSITE Motif" information available for 3Q72)

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000299759	1a	ENSE00001943321	chr16:66959547-66959312	236	RAD_HUMAN	-	0	0	-	-
1.2b	ENST00000299759	2b	ENSE00001104552	chr16:66959097-66958713	385	RAD_HUMAN	1-124	124	2	A:90-114 B:90-124 (gaps)	25 35
1.3	ENST00000299759	3	ENSE00001104559	chr16:66957822-66957749	74	RAD_HUMAN	124-148	25	2	A:125-146 B:124-147	22 24
1.4	ENST00000299759	4	ENSE00001104564	chr16:66957623-66957419	205	RAD_HUMAN	149-217	69	2	A:162-217 (gaps) B:160-217 (gaps)	56 58
1.5a	ENST00000299759	5a	ENSE00001931509	chr16:66956256-66955588	669	RAD_HUMAN	217-308	92	2	A:217-255 B:217-255	39 39

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
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Chain A from PDB  Type:PROTEIN  Length:138
 aligned with RAD_HUMAN | P55042 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:166
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249      
            RAD_HUMAN    90 SVYKVLLLGAPGVGKSALARIFGGVEDGPEAEAAGHTYDRSIVVDGEEASLMVYDIWEQDGGRWLPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLRR 255
               SCOP domains d3q72a_ A: automated matc          hes                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhh..----------.eeeeeeee..eeeeeeeee..---------------..eeeeeee..hhhhhhhhhhhhhhhhhh.---...eeeeee..........hhhhhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:90-114           ------------------------Exon 1.4  PDB: A:162-217 (gaps) UniProt: 149-217 [INCOMPLETE]        -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: A:125-146 --------------------------------------------------------------------Exon 1.5a  PDB: A:217-255 [INCOMPLETE]  Transcript 1 (2)
                 3q72 A  90 SVYKVLLLGAPGVGKSALARIFGGV----------HTYDRSIVVDGEEASLMVYDIW---------------GDAYVIVYSVTDKGSFEKASELRVQLRRAR---DVPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLRR 255
                                    99       109    |    -     | 129       139      |  -         -  |    169       179       189 |   | 199       209       219       229       239       249      
                                                  114        125                  146             162                          191 195

Chain B from PDB  Type:PROTEIN  Length:145
 aligned with RAD_HUMAN | P55042 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:166
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249      
            RAD_HUMAN    90 SVYKVLLLGAPGVGKSALARIFGGVEDGPEAEAAGHTYDRSIVVDGEEASLMVYDIWEQDGGRWLPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLRR 255
               SCOP domains d3q72b_ B: automated matc        hes                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhh.--------...ee..eee....eeeeeee....------------....eeeeeee..hhhhhhhhhhhhhhhhh...-....eeeeee..........hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: B:90-124 (gaps)    ------------------------Exon 1.4  PDB: B:160-217 (gaps) UniProt: 149-217 [INCOMPLETE]        -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: B:124-147 --------------------------------------------------------------------Exon 1.5a  PDB: B:217-255 [INCOMPLETE]  Transcript 1 (2)
                 3q72 B  90 SVYKVLLLGAPGVGKSALARIFGGV--------AGHTYDRSIVVDGEEASLMVYDIWE------------AMGDAYVIVYSVTDKGSFEKASELRVQLRRARQ-DDVPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLRR 255
                                    99       109    |    -   |   129       139       | -         -|      169       179       189  | |  199       209       219       229       239       249      
                                                  114      123                     147          160                             192 |                                                             
                                                                                                                                  194

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)

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

1a	d3q72a_	A:
1b	d3q72b_	B:

(no "CATH Domain" information available for 3Q72)

(no "Pfam Domain" information available for 3Q72)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RAD_HUMAN | P55042)

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:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	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:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	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: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.
	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.

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	Cis Peptide Bonds
		Gly A:112 - Gly A:113	[ RasMol ]
		Gly A:113 - Val A:114	[ RasMol ]
		Gly B:113 - Val B:114	[ RasMol ]
		Gly B:124 - His B:125	[ RasMol ]
		Val A:133 - Asp A:134	[ RasMol ]
		Val B:133 - Asp B:134	[ RasMol ]

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	3q72
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	RAD_HUMAN \| P55042	:	2dpx 2gjs 3q7p 3q7q

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (4, 8)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

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Gene Ontology (11, 11)

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