1JYR - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   XRAY STRUCTURE OF GRB2 SH2 DOMAIN COMPLEXED WITH A PHOSPHORYLATED PEPTIDE

Authors :   P. Nioche, W. -Q. Liu, I. Broutin, F. Charbonnier, M. -T. Latreille, M. V B. Roques, C. Garbay, A. Ducruix

Date :   13 Sep 01 (Deposition) - 13 Mar 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Receptor Binding, Regulatory, Inhibitor, Signaling Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Nioche, W. Q. Liu, I. Broutin, F. Charbonnier, M. T. Latreille, M. Vidal, B. Roques, C. Garbay, A. Ducruix
Crystal Structures Of The Sh2 Domain Of Grb2: Highlight On The Binding Of A New High-Affinity Inhibitor.
J. Mol. Biol. V. 315 1167 2002
PubMed-ID: 11827484 | Reference-DOI: 10.1006/JMBI.2001.5299

Molecule 1 - GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	SH2 DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GRB2 ADAPTER PROTEIN

Molecule 2
	Chains	:	L
	Engineered	:	YES
	Other Details	:	THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED.
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:67 , SER A:75 , ARG A:86 , SER A:88 , SER A:90 , SER A:96 , LYS A:100 , ASN A:103 , HIS A:107 , PHE A:108 , LYS A:109 , LEU A:111 , LEU A:120 , TRP A:121 , TYR A:134 , SER A:137 , THR A:138 , ARG A:149 , HOH A:2036 , HOH A:2071 , HOH A:2081 , HOH A:2089 , HOH L:2017 , HOH L:2044 , HOH L:2046 , HOH L:2077	BINDING SITE FOR CHAIN L OF PEPTIDE: PSPYVNVQN

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

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	GRB2_HUMAN	60-152	1	A:60-151

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	GRB2_HUMAN	60-152	1	A:60-151

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	GRB2_HUMAN	60-152	2	A:60-151

Asymmetric Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3a	ENST00000392564	3a	ENSE00001512384	chr17:73389945-73389632	314	GRB2_HUMAN	1-26	26	0	-	-
1.4	ENST00000392564	4	ENSE00000387085	chr17:73328878-73328781	98	GRB2_HUMAN	27-59	33	1	A:57-59	3
1.6	ENST00000392564	6	ENSE00000855724	chr17:73322101-73321979	123	GRB2_HUMAN	59-100	42	1	A:59-100	42
1.7	ENST00000392564	7	ENSE00000744359	chr17:73317908-73317740	169	GRB2_HUMAN	100-156	57	1	A:100-151	52
1.8b	ENST00000392564	8b	ENSE00001512383	chr17:73316634-73314157	2478	GRB2_HUMAN	157-217	61	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:96
 aligned with GRB2_HUMAN | P62993 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:130
                                    31        41        51        61        71        81        91       101       111       121       131       141       151
          GRB2_HUMAN     22 GDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDI  151
               SCOP domains d                                  1jyra_ A: Growth factor receptor-bound protein 2 (GRB2)                                         SCOP domains
               CATH domains 1                                  jyrA00 A:56-151 SHC Adaptor Protein                                                             CATH domains
               Pfam domains --------------------------------------SH2-1jyrA01 A:60-135                                                        ---------------- Pfam domains
         Sec.struct. author .----------------------------------.........hhhhhhhhhhh......eeeee.......eeeeeee..eeeeee.ee.....ee....ee.hhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------SH2  PDB: A:60-151 UniProt: 60-152                                                           PROSITE
           Transcript 1 (1) 1.3a Exon 1.4  PDB: A:57-59           ----------------------------------------Exon 1.7  PDB: A:100-151 UniProt: 100-156            Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.6  PDB: A:59-100 UniProt: 59-100   --------------------------------------------------- Transcript 1 (2)
                1jyr A   56 G----------------------------------SMAWFFGKIPRAKAEEMLSKQRHDGAFLIRESESAPGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDI  151
                            |        -         -         -     |  61        71        81        91       101       111       121       131       141       151
                            |                                 57                                                                                              
                           56

Chain L from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                1jyr L 1000 APSyVNVQN 1008
                               |     
                            1003-PTR

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) (23004)

Fold: SH2-like (260)

Superfamily: SH2 domain (260)

Family: SH2 domain (225)

Protein domain: Growth factor receptor-bound protein 2 (GRB2) (34)

Human (Homo sapiens) [TaxId: 9606] (34)

d1jyra_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: SHC Adaptor Protein (206)

Homologous Superfamily: SHC Adaptor Protein (206)

Human (Homo sapiens) (147)

1jyrA00

A:56-151

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SH2] (119)

Family: SH2 (119)

Homo sapiens (Human) (79)

SH2-1jyrA01

A:60-135

Asymmetric Unit(hide GO term definitions)

Chain A (GRB2_HUMAN | P62993)

molecular function
	GO:0016303	1-phosphatidylinositol-3-kinase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ADP + 2 H(+).
	GO:0005088	Ras guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0017124	SH3 domain binding	Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
	GO:0005070	SH3/SH2 adaptor activity	Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
	GO:0046875	ephrin receptor binding	Interacting selectively and non-covalently with an ephrin receptor.
	GO:0005154	epidermal growth factor receptor binding	Interacting selectively and non-covalently with the epidermal growth factor receptor.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0043560	insulin receptor substrate binding	Interacting selectively and non-covalently with any of the insulin receptor substrate (IRS) proteins, adaptor proteins that bind to the transphosphorylated insulin and insulin-like growth factor receptors, are themselves phosphorylated and in turn recruit SH2 domain-containing signaling molecules to form a productive signaling complex.
	GO:0005168	neurotrophin TRKA receptor binding	Interacting selectively and non-covalently with the neurotrophin TRKA receptor.
	GO:0046934	phosphatidylinositol-4,5-bisphosphate 3-kinase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+).
	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:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0019903	protein phosphatase binding	Interacting selectively and non-covalently with any protein phosphatase.
biological process
	GO:0038128	ERBB2 signaling pathway	A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.
	GO:0038095	Fc-epsilon receptor signaling pathway	A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
	GO:0038096	Fc-gamma receptor signaling pathway involved in phagocytosis	An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0007265	Ras protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	GO:0048646	anatomical structure formation involved in morphogenesis	The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
	GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0060670	branching involved in labyrinthine layer morphogenesis	The process in which the branches of the fetal placental villi are generated and organized. The villous part of the placenta is called the labyrinth layer.
	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:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0071479	cellular response to ionizing radiation	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 a ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
	GO:0007173	epidermal growth factor receptor signaling pathway	A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0008543	fibroblast growth factor receptor signaling pathway	The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
	GO:0008286	insulin receptor signaling pathway	The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0042059	negative regulation of epidermal growth factor receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
	GO:0046854	phosphatidylinositol phosphorylation	The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
	GO:0036092	phosphatidylinositol-3-phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of phosphatidylinositol-3-phosphate, a phosphatidylinositol monophosphate carrying the phosphate group at the 3-position.
	GO:0048015	phosphatidylinositol-mediated signaling	A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0030838	positive regulation of actin filament polymerization	Any process that activates or increases the frequency, rate or extent of actin polymerization.
	GO:2000379	positive regulation of reactive oxygen species metabolic process	Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process.
	GO:0009967	positive regulation of signal transduction	Any process that activates or increases the frequency, rate or extent of signal transduction.
	GO:0031623	receptor internalization	A receptor-mediated endocytosis process that results in the movement of receptors from the plasma membrane to the inside of the cell. The process begins when cell surface receptors are monoubiquitinated following ligand-induced activation. Receptors are subsequently taken up into endocytic vesicles from where they are either targeted to the lysosome or vacuole for degradation or recycled back to the plasma membrane.
	GO:0043408	regulation of MAPK cascade	Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade.
	GO:0014066	regulation of phosphatidylinositol 3-kinase signaling	Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0042770	signal transduction in response to DNA damage	A cascade of processes induced by the detection of DNA damage within a cell.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0008180	COP9 signalosome	A protein complex that catalyzes the deneddylation of proteins, including the cullin component of SCF ubiquitin E3 ligase; deneddylation increases the activity of cullin family ubiquitin ligases. The signalosome is involved in many regulatory process, including some which control development, in many species; also regulates photomorphogenesis in plants; in many species its subunits are highly similar to those of the proteasome.
	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:0070436	Grb2-EGFR complex	A protein complex that contains the epidermal growth factor receptor (EGFR) and Grb2, and is involved in linking EGFR activation to the p21-Ras pathway.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	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:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.
	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.
	GO:0012506	vesicle membrane	The lipid bilayer surrounding any membrane-bounded vesicle in the cell.

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1jyq	XRAY STRUCTURE OF GRB2 SH2 DOMAIN COMPLEXED WITH A DOUBLY PHOSPHORYLATED PSEUDOPEPTIDE
1jyu	XRAY STRUCTURE OF GRB2 SH2 DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (3, 3)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (57, 57)

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