4AXG - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF EIF4E-CUP COMPLEX

Authors :   K. Kinkelin, K. Veith, M. Gruenwald, F. Bono

Date :   12 Jun 12 (Deposition) - 29 Aug 12 (Release) - 29 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   4E-Bp, Mrna Localization, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kinkelin, K. Veith, M. Gruenwald, F. Bono
Crystal Structure Of A Minimal Eif4E-Cup Complex Revelas A General Mechanism Of Eif4E Regulation In Translational Repression
Rna V. 18 1624 2012
PubMed-ID: 22832024 | Reference-DOI: 10.1261/RNA.033639.112

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETMCN HIS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Expression System Vector Type	:	PLASMID
	Fragment	:	EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	EIF-4E, EIF4E, EIF-4F 25 KDA SUBUNIT, MRNA CAP-BINDING PROTEIN

Molecule 2 - PROTEIN CUP
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUE 296-425
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227
	Synonym	:	OSKAR RIBONUCLEOPROTEIN COMPLEX 147 KDA SUBUNIT

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4AXG)

(no "Site" information available for 4AXG)

(no "SS Bond" information available for 4AXG)

(no "Cis Peptide Bond" information available for 4AXG)

(no "SAP(SNP)/Variant" information available for 4AXG)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IF4E	PS00813	Eukaryotic initiation factor 4E signature.	IF4E_DROME	134-157	2	A:123-146 B:123-146

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IF4E	PS00813	Eukaryotic initiation factor 4E signature.	IF4E_DROME	134-157	1	A:123-146 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IF4E	PS00813	Eukaryotic initiation factor 4E signature.	IF4E_DROME	134-157	1	- B:123-146

(no "Exon" information available for 4AXG)

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 IF4E_DROME | P48598 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:183
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256   
           IF4E_DROME    77 HLYKHPLMNVWTLWYLENDRSKSWEDMQNEITSFDTVEDFWSLYNHIKPPSEIKLGSDYSLFKKNIRPMWEDAANKQGGRWVITLNKSSKTDLDNLWLDVLLCLIGEAFDHSDQICGAVINIRGKSNKISIWTADGNNEEAALEIGHKLRDALRLGRNNSLQYQLHKDTMVKQGSNVKSIYTL 259
               SCOP domains d4axga_ A: automated matches                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee...........eeeeeeeeehhhhhhhhh...........eeeeeee...............eeeeeeee..hhhhhhhhhhhhhhhhhh....hhh.eeeeeeee...eeeeeeee....hhhhhhhhhhhhhhhh.......eeeee.hhhh...--.....ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------IF4E  PDB: A:123-146    ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4axg A  66 HLYKHPLMNVWTLWYLENDRSKSWEDMQNEITSFDTVEDFWSLYNHIKPPSEIKLGSDYSLFKKNIRPMWEDAANKQGGRWVITLNKSSKTDLDNLWLDVLLCLIGEAFDHSDQICGAVINIRGKSNKISIWTADGNNEEAALEIGHKLRDALRLGRNNSLQYQLHKDTMVKQ--NVKSIYTL 248
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  |  | 245   
                                                                                                                                                                                                      238  |       
                                                                                                                                                                                                         241

Chain B from PDB  Type:PROTEIN  Length:167
 aligned with IF4E_DROME | P48598 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:180
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259
           IF4E_DROME    80 KHPLMNVWTLWYLENDRSKSWEDMQNEITSFDTVEDFWSLYNHIKPPSEIKLGSDYSLFKKNIRPMWEDAANKQGGRWVITLNKSSKTDLDNLWLDVLLCLIGEAFDHSDQICGAVINIRGKSNKISIWTADGNNEEAALEIGHKLRDALRLGRNNSLQYQLHKDTMVKQGSNVKSIYTL 259
               SCOP domains d4axgb_ B: auto        mated matches                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeee..--------.eeeeeeeeehhhhhhhhhhh.........eeeeeee...............eeeeeeee..hhhhhhhhhhhhhhhhhh....hhh.eeeeeeee...eeeeeeee....hhhhhhhhhhhhhhhhh......eeeeehhhhh-----.....eee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------IF4E  PDB: B:123-146    ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4axg B  69 KHPLMNVWTLWYLEN--------MQNEITSFDTVEDFWSLYNHIKPPSEIKLGSDYSLFKKNIRPMWEDAANKQGGRWVITLNKSSKTDLDNLWLDVLLCLIGEAFDHSDQICGAVINIRGKSNKISIWTADGNNEEAALEIGHKLRDALRLGRNNSLQYQLHKDTM-----NVKSIYTL 248
                                    78    |    -   |    98       108       118       128       138       148       158       168       178       188       198       208       218       228      |  -  |    248
                                         83       92                                                                                                                                            235   241

Chain C from PDB  Type:PROTEIN  Length:37
 aligned with CUP_DROME | Q9VMA3 from UniProtKB/Swiss-Prot  Length:1117

    Alignment length:59
                                   327       337       347       357       367         
            CUP_DROME   318 VVSSKPVKSYTRSRLMDIRNGMFNALMHRSKESFVMPRIATCDDIELEGRLRRMNIWRT 376
               SCOP domains ----------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhh.----------------------.hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 4axg C 318 VVSSKPVKSYTRSRLMDIRNGM----------------------IELEGRLRRMNIWRT 376
                                   327       337 |       -         -    |  367         
                                               339                    362

Chain D from PDB  Type:PROTEIN  Length:15
 aligned with CUP_DROME | Q9VMA3 from UniProtKB/Swiss-Prot  Length:1117

    Alignment length:15
                                   334     
            CUP_DROME   325 KSYTRSRLMDIRNGM 339
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 4axg D 325 KSYTRSRLMDIRNGM 339
                                   334

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: eIF4e-like (28)

Superfamily: eIF4e-like (28)

Family: automated matches (10)

Protein domain: automated matches (10)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (1)

1a	d4axga_	A:
1b	d4axgb_	B:

(no "CATH Domain" information available for 4AXG)

(no "Pfam Domain" information available for 4AXG)

Asymmetric Unit(hide GO term definitions)

Chain A,B (IF4E_DROME | P48598)

molecular function
	GO:0000340	RNA 7-methylguanosine cap binding	Interacting selectively and non-covalently with the 7-methylguanosine group added cotranscriptionally to the 5' end of RNA molecules transcribed by polymerase II.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000339	RNA cap binding	Interacting selectively and non-covalently with a 7-methylguanosine (m7G) group or derivative located at the 5' end of an RNA molecule.
	GO:0031370	eukaryotic initiation factor 4G binding	Interacting selectively and non-covalently with eukaryotic initiation factor 4G, a polypeptide factor involved in the initiation of ribosome-mediated translation.
	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:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
	GO:0016070	RNA metabolic process	The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0048102	autophagic cell death	A form of programmed cell death that is accompanied by the formation of autophagosomes. Autophagic cell death is characterized by lack of chromatin condensation and massive vacuolization of the cytoplasm, with little or no uptake by phagocytic cells.
	GO:0002191	cap-dependent translational initiation	The process where the "Cap structure" (composed of a 7- methylguanosine (m7G) group and associated cap-binding proteins) located at the 5' end of an mRNA molecule, which serves as a "molecular tag" that marks the spot where the 40S ribosomal subunit is recruited and will then scan in a 5' to 3' direction until an AUG codon is encountered in an appropriate sequence context to initiate mRNA translation.
	GO:0006325	chromatin organization	Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
	GO:0016321	female meiosis chromosome segregation	The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female.
	GO:0048136	male germ-line cyst formation	Formation of a group of interconnected cells derived from a single male gonial founder cell.
	GO:0007060	male meiosis chromosome segregation	The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a male.
	GO:0007112	male meiosis cytokinesis	A cell cycle process that occurs as part of the male meiotic cell cycle and results in the division of the cytoplasm of a cell to produce two daughter cells.
	GO:0010032	meiotic chromosome condensation	Compaction of chromatin structure prior to meiosis in eukaryotic cells.
	GO:0007076	mitotic chromosome condensation	The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells.
	GO:0000022	mitotic spindle elongation	The cell cycle process in which the distance is lengthened between poles of the mitotic spindle. Mitotic spindle elongation begins during mitotic prophase and ends during mitotic anaphase B.
	GO:0007052	mitotic spindle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
	GO:0022008	neurogenesis	Generation of cells within the nervous system.
	GO:0030307	positive regulation of cell growth	Any process that activates or increases the frequency, rate, extent or direction of cell growth.
	GO:0001558	regulation of cell growth	Any process that modulates the frequency, rate, extent or direction of cell growth.
	GO:0045995	regulation of embryonic development	Any process that modulates the frequency, rate or extent of embryonic development.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0035071	salivary gland cell autophagic cell death	The stage-specific programmed cell death of salivary gland cells during salivary gland histolysis.
	GO:0048515	spermatid differentiation	The process whose specific outcome is the progression of a spermatid over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
	GO:0048137	spermatocyte division	The meiotic divisions undergone by the primary and secondary spermatocytes to produce haploid spermatids.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
	GO:0006413	translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	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:0016281	eukaryotic translation initiation factor 4F complex	The eukaryotic translation initiation factor 4F complex is composed of eIF4E, eIF4A and eIF4G; it is involved in the recognition of the mRNA cap, ATP-dependent unwinding of the 5'-terminal secondary structure and recruitment of the mRNA to the ribosome.
	GO:0005845	mRNA cap binding complex	Any protein complex that binds to an mRNA cap at any time in the lifetime of the mRNA.
	GO:0005875	microtubule associated complex	Any multimeric complex connected to a microtubule.
	GO:0097482	muscle cell postsynaptic density	A postsynaptic specialization that is part of a neuromuscular junction.
	GO:0031594	neuromuscular junction	The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.

Chain C,D (CUP_DROME | Q9VMA3)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0045182	translation regulator activity	Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome.
biological process
	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:0051276	chromosome organization	A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
	GO:0009953	dorsal/ventral pattern formation	The regionalization process in which the areas along the dorsal/ventral axis are established that will lead to differences in cell differentiation. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
	GO:0007143	female meiotic nuclear division	A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline.
	GO:0008298	intracellular mRNA localization	Any process in which mRNA is transported to, or maintained in, a specific location within the cell.
	GO:0045132	meiotic chromosome segregation	The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0007319	negative regulation of oskar mRNA translation	Any process that stops, prevents or reduces the rate that oskar mRNAs are effectively translated into protein.
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0048477	oogenesis	The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
	GO:0007297	ovarian follicle cell migration	The directed movement of an ovarian follicle cell that takes place during oogenesis. During egg chamber formation, follicle cells migrate to envelop the germ-line cysts and move in between cysts. At stage 10B, follicle cells migrate centripetally between the nurse cells and the oocyte, enclosing the anterior of the egg. An example of this is found in Drosophila melanogaster.
	GO:0007317	regulation of pole plasm oskar mRNA localization	Any process that modulates the frequency, rate or extent of the process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	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:0005875	microtubule associated complex	Any multimeric complex connected to a microtubule.
	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.

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	4axg
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	IF4E_DROME \| P48598
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	IF4E_DROME \| P48598	:	4ue8 4ue9 4uea 4ueb 4uec 5abu 5abv 5t47 5t48

(no "Related Entries Specified in the PDB File" available for 4AXG)

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