1KL9 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE N-TERMINAL SEGMENT OF HUMAN EUKARYOTIC INITIATION FACTOR 2ALPHA

Authors :   M. C. Nonato, J. Widom, J. Clardy

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

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: A  (2x)

Keywords :   Ob Fold, Helical Domain, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Nonato, J. Widom, J. Clardy
Crystal Structure Of The N-Terminal Segment Of Human Eukaryotic Translation Initiation Factor 2Alpha
J. Biol. Chem. V. 277 17057 2002
PubMed-ID: 11859078 | Reference-DOI: 10.1074/JBC.M111804200

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 1-182
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	EUKARYOTIC TRANSLATION INITIATION FACTOR 2 ALPHA SUBUNIT

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A
Biological Unit 3 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:42 , HIS A:154 , ASP A:158 , HOH A:592	BINDING SITE FOR RESIDUE ZN A 501
2	AC2	SOFTWARE	HIS A:10 , HOH A:587 , HOH A:596	BINDING SITE FOR RESIDUE ZN A 502
3	AC3	SOFTWARE	HIS A:10 , LYS A:11 , PHE A:12 , LYS A:77 , LYS A:142	BINDING SITE FOR RESIDUE ZN A 503
4	AC4	SOFTWARE	HIS A:113 , GLU A:119 , HOH A:584	BINDING SITE FOR RESIDUE ZN A 504

Asymmetric Unit

No.	Residues
1	A:69	-	A:97

(no "Cis Peptide Bond" information available for 1KL9)

(no "SAP(SNP)/Variant" information available for 1KL9)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S1	PS50126	S1 domain profile.	IF2A_HUMAN	17-88	1	A:16-87

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S1	PS50126	S1 domain profile.	IF2A_HUMAN	17-88	1	A:16-87

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S1	PS50126	S1 domain profile.	IF2A_HUMAN	17-88	2	A:16-87

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S1	PS50126	S1 domain profile.	IF2A_HUMAN	17-88	2	A:16-87

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000256383	1a	ENSE00001931166	chr14:67826745-67827173	429	IF2A_HUMAN	-	0	0	-	-
1.2b	ENST00000256383	2b	ENSE00002024286	chr14:67831484-67831725	242	IF2A_HUMAN	1-81	81	1	A:3-80 (gaps)	78
1.3b	ENST00000256383	3b	ENSE00000911628	chr14:67841185-67841264	80	IF2A_HUMAN	81-107	27	1	A:80-106	27
1.4	ENST00000256383	4	ENSE00000911630	chr14:67843156-67843307	152	IF2A_HUMAN	108-158	51	1	A:107-157	51
1.5	ENST00000256383	5	ENSE00000911632	chr14:67847376-67847482	107	IF2A_HUMAN	158-194	37	1	A:157-182	26
1.6	ENST00000256383	6	ENSE00000911634	chr14:67848310-67848407	98	IF2A_HUMAN	194-226	33	0	-	-
1.7	ENST00000256383	7	ENSE00000911635	chr14:67849164-67849307	144	IF2A_HUMAN	227-274	48	0	-	-
1.8b	ENST00000256383	8b	ENSE00001168441	chr14:67850032-67853233	3202	IF2A_HUMAN	275-315	41	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:168
 aligned with IF2A_HUMAN | P05198 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:180
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
           IF2A_HUMAN     4 LSCRFYQHKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRR 183
               SCOP domains d1kl9a2 A:3-88 Eukaryotic initiation factor 2alp            ha, eIF2alpha, N-terminal d1kl9a1 A:89-182 Eukaryotic initiation factor 2alpha, eIF2alpha, domain 2                      SCOP domains
               CATH domains 1kl9A01 A:3-89 Nucleic acid-binding proteins                                           1kl9A02 A:90-181 Translation initiation factor 2; subunit 1; domain 2                       - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eeeeeeeee...eeeeee......eeeee.hhh------------....eeeeeeeeee....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------S1  PDB: A:16-87 UniProt: 17-88                                         ----------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:3-80 (gaps) UniProt: 1-81 [INCOMPLETE]                      --------------------------Exon 1.4  PDB: A:107-157 UniProt: 108-158          ------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------Exon 1.3b  PDB: A:80-106   --------------------------------------------------Exon 1.5  PDB: A:157-182   Transcript 1 (2)
                 1kl9 A   3 LSCRFYQHKFPEVEDVVmVNVRSIAEmGAYVSLLEYNNIEGmILLSEL------------RIGRNECVVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQLESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRR 182
                                    12       |22      | 32        42 |     | -         -|       72        82        92       102       112       122       132       142       152       162       172       182
                                            20-MSE   29-MSE         44-MSE50           63

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: Translation initiation factor 2; subunit 1; domain 2 (5)

Human (Homo sapiens) (2)

1kl9A02

A:90-181

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: Nucleic acid-binding proteins (483)

Human (Homo sapiens) (27)

1kl9A01

A:3-89

(no "Pfam Domain" information available for 1KL9)

Asymmetric Unit(hide GO term definitions)

Chain A (IF2A_HUMAN | P05198)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
	GO:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
	GO:0036499	PERK-mediated unfolded protein response	A series of molecular signals mediated by the endoplasmic reticulum membrane stress sensor PERK (PKR-like ER kinase). Begins with activation of PERK in response to endoplasmic reticulum (ER) stress and ends with regulation of a downstream cellular process, e.g. transcription. The main substrate of PERK is the translation initiation factor eIF2alpha. Serine-phosphorylation of eIF2alpha by PERK inactivates eIF2alpha and inhibits general protein translation. In addition, eIF2alpha phosphorylation preferentially increases the translation of selective mRNAs such as ATF4 (activating transcription factor 4), which up regulates a subset of UPR genes required to restore folding capacity.
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0034644	cellular response to UV	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 an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
	GO:0034198	cellular response to amino acid starvation	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 deprivation of amino acids.
	GO:0034605	cellular response to heat	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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0032057	negative regulation of translational initiation in response to stress	Any process that stops, prevents or reduces the rate of translation initiation as a result of a stimulus indicating the organism is under stress.
	GO:0002230	positive regulation of defense response to virus by host	Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
	GO:0098779	positive regulation of macromitophagy in response to mitochondrial depolarization	The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
	GO:1901216	positive regulation of neuron death	Any process that activates or increases the frequency, rate or extent of neuron death.
	GO:2000676	positive regulation of type B pancreatic cell apoptotic process	Any process that activates or increases the frequency, rate or extent of type B pancreatic cell apoptotic process.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	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:0043558	regulation of translational initiation in response to stress	Any process that modulates the frequency, rate or extent of translation initiation, as a result of a stimulus indicating the organism is under stress.
	GO:0034976	response to endoplasmic reticulum stress	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 stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
	GO:1990737	response to manganese-induced endoplasmic reticulum stress	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 endoplasmic reticulum stress caused by a manganese stimulus.
	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.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0098792	xenophagy	The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	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:0033290	eukaryotic 48S preinitiation complex	A protein complex composed of the small ribosomal subunit, eIF3, eIF1A, methionyl-initiatior methionine and a capped mRNA. The complex is initially positioned at the 5'-end of the capped mRNA.
	GO:0005850	eukaryotic translation initiation factor 2 complex	Complex of three heterogeneous polypeptide chains, that form a ternary complex with initiator methionyl-tRNA and GTP. This ternary complex binds to free 40S subunit, which subsequently binds the 5' end of mRNA.
	GO:0005851	eukaryotic translation initiation factor 2B complex	A multisubunit guanine nucleotide exchange factor which catalyzes the exchange of GDP bound to initiation factor eIF2 for GTP, generating active eIF2-GTP. In humans, it is composed of five subunits, alpha, beta, delta, gamma and epsilon.
	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:0097451	glial limiting end-foot	Terminal process of astrocyte that extends to the surface of the central nervous system. Together, glial limiting end-feet form the glial limiting membrane or glia limitans.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043614	multi-eIF complex	A multifactor complex composed of multiple translation initiation factors and the initiatior tRNAiMet, which is ready to bind to the small (40S) ribosome to form the 43S preinitiation complex. In S. cerevisiae, this complex is composed of eIF1, eIF2, eIF3, and eIF5.
	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:0005844	polysome	A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
	GO:0044207	translation initiation ternary complex	A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).

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(no "Related Entries Specified in the PDB File" available for 1KL9)

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