2G9N - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE DEAD DOMAIN OF HUMAN EUKARYOTIC INITIATION FACTOR 4A, EIF4A

Authors :   M. Hogbom, D. Ogg, C. Arrowsmith, H. Berglund, R. Collins, A. Edwards, M S. Flodin, A. Flores, S. Graslund, B. M. Hallberg, M. Hammarstrom, T. K P. Nilsson-Ehle, P. Nordlund, T. Nyman, C. Persson, J. Sagemark, P. St M. Sundstrom, A. G. Thorsell, J. Uppenberg, S. Van Den Berg, J. Weige L. Holmberg-Schiavone, Structural Genomics Consortium (Sgc)

Date :   07 Mar 06 (Deposition) - 14 Mar 06 (Release) - 27 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Dead-Box, Helicase, Ddx2A, Rna, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Schutz, T. Karlberg, S. Van Den Berg, R. Collins, L. Lehtio, M. Hogbom, L. Holmberg-Schiavone, W. Tempel, H. W. Park, M. Hammarstrom, M. Moche, A. G. Thorsell, H. Schuler
Comparative Structural Analysis Of Human Dead-Box Rna Helicases.
Plos One V. 5 12791 2010
PubMed-ID: 20941364 | Reference-DOI: 10.1371/JOURNAL.PONE.0012791

Molecule 1 - EUKARYOTIC INITIATION FACTOR 4A-I
	Chains	:	A, B
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-28-BSA1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DEAD DOMAIN
	Gene	:	EIF4A1, DDX2A, EIF4A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ATP-DEPENDENT RNA HELICASE EIF4A-1, EIF4A-I, EIF-4A-I

		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 (1, 27)

No.	Name	Count	Type	Full Name
1	MLY	27	Mod. Amino Acid	N-DIMETHYL-LYSINE

Biological Unit 1 (1, 14)

No.	Name	Count	Type	Full Name
1	MLY	14	Mod. Amino Acid	N-DIMETHYL-LYSINE

Biological Unit 2 (1, 13)

No.	Name	Count	Type	Full Name
1	MLY	13	Mod. Amino Acid	N-DIMETHYL-LYSINE

(no "Site" information available for 2G9N)

(no "SS Bond" information available for 2G9N)

Asymmetric Unit

No.	Residues
1	Mly A:146	-	Leu A:147

(no "SAP(SNP)/Variant" information available for 2G9N)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	IF4A1_HUMAN	32-60	2	A:32-60 B:32-60
2	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	IF4A1_HUMAN	180-188	2	A:180-188 B:180-188

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	IF4A1_HUMAN	32-60	1	A:32-60 -
2	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	IF4A1_HUMAN	180-188	1	A:180-188 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	IF4A1_HUMAN	32-60	1	- B:32-60
2	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	IF4A1_HUMAN	180-188	1	- B:180-188

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000293831	1a	ENSE00001710114	chr17:7476024-7476182	159	IF4A1_HUMAN	1-8	8	0	-	-
1.2	ENST00000293831	2	ENSE00001631751	chr17:7477578-7477626	49	IF4A1_HUMAN	8-24	17	2	A:21-24 B:23-24	4 2
1.3	ENST00000293831	3	ENSE00001762686	chr17:7477864-7477996	133	IF4A1_HUMAN	25-69	45	2	A:25-69 B:25-69	45 45
1.4a	ENST00000293831	4a	ENSE00001726391	chr17:7478437-7478576	140	IF4A1_HUMAN	69-115	47	2	A:69-115 B:69-115	47 47
1.5	ENST00000293831	5	ENSE00001061690	chr17:7479842-7480010	169	IF4A1_HUMAN	116-172	57	2	A:116-172 (gaps) B:116-172	57 57
1.6	ENST00000293831	6	ENSE00001061689	chr17:7480374-7480483	110	IF4A1_HUMAN	172-208	37	2	A:172-208 B:172-208	37 37
1.7	ENST00000293831	7	ENSE00001061692	chr17:7480662-7480805	144	IF4A1_HUMAN	209-256	48	2	A:209-238 B:209-237	30 29
1.8	ENST00000293831	8	ENSE00001799518	chr17:7480887-7481024	138	IF4A1_HUMAN	257-302	46	0	-	-
1.9	ENST00000293831	9	ENSE00001061685	chr17:7481145-7481234	90	IF4A1_HUMAN	303-332	30	0	-	-
1.10	ENST00000293831	10	ENSE00001061694	chr17:7481483-7481562	80	IF4A1_HUMAN	333-359	27	0	-	-
1.11	ENST00000293831	11	ENSE00001485271	chr17:7481660-7482324	665	IF4A1_HUMAN	359-406	48	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:216
 aligned with IF4A1_HUMAN | P60842 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:218
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
          IF4A1_HUMAN    21 GVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKK 238
               SCOP domains d2g9na1 A:21-238 Initiation factor 4a                                                                                                                                                                                      SCOP domains
               CATH domains 2g9nA00 A:21-236 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                   -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhhh.....eeee..--...............eeeehhhhhhhhhhh.........eeeeehhhhhhhh.hhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------Q_MOTIF  PDB: A:32-60        -----------------------------------------------------------------------------------------------------------------------DEAD_ATP_-------------------------------------------------- PROSITE
           Transcript 1 (1) 1.2 Exon 1.3  PDB: A:25-69 UniProt: 25-69        ----------------------------------------------Exon 1.5  PDB: A:116-172 (gaps) UniProt: 116-172         ------------------------------------Exon 1.7  PDB: A:209-238       Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.4a  PDB: A:69-115 UniProt: 69-115       --------------------------------------------------------Exon 1.6  PDB: A:172-208             ------------------------------ Transcript 1 (2)
                 2g9n A  21 GVIESNWNEIVDSFDDMNLSESLLRGIYAYGFEkPSAIQQRAILPCIkGYDVIAQAQSGTGkTATFAISILQQIELDLkATQALVLAPTRELAQQIQkVVMALGDYMGASCHACIG--NVRAEVQkLQMEAPHIIVGTPGRVFDMLNRRYLSPkYIkMFVLDEADEMLSRGFkDQIYDIFQkLNSNTQVVLLSATMPSDVLEVTkkFMRDPIRILVkk 238
                                    30        40        50   |    60       |70        80 |      90       100       110       120       130     | 140     | 150       160       170   |  |180       190  |    200 |     210       220    || 230      ||
                                                            54-MLY        68-MLY        82-MLY           99-MLY            118-MLY           136  |      |                         174-MLY            193-MLY  202-MLY                225-MLY     237-MLY
                                                                                                                                                139      |                            177-MLY                                          226-MLY     238-MLY
                                                                                                                                                       146-MLY

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with IF4A1_HUMAN | P60842 from UniProtKB/Swiss-Prot  Length:406

    Alignment length:215
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     
          IF4A1_HUMAN    23 IESNWNEIVDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELDLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNRRYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK 237
               SCOP domains d2g9nb_ B: Initiation factor 4a                                                                                                                                                                                         SCOP domains
               CATH domains 2g9nB00 B:23-236 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                 - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhh....eeeehhhhhhhhhhh.........eeeeehhhhhhhh.hhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------Q_MOTIF  PDB: B:32-60        -----------------------------------------------------------------------------------------------------------------------DEAD_ATP_------------------------------------------------- PROSITE
           Transcript 1 (1) 1.Exon 1.3  PDB: B:25-69 UniProt: 25-69        ----------------------------------------------Exon 1.5  PDB: B:116-172 UniProt: 116-172                ------------------------------------Exon 1.7  PDB: B:209-237      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.4a  PDB: B:69-115 UniProt: 69-115       --------------------------------------------------------Exon 1.6  PDB: B:172-208             ----------------------------- Transcript 1 (2)
                 2g9n B  23 IESNWNEIVDSFDDMNLSESLLRGIYAYGFEkPSAIQQRAILPCIkGYDVIAQAQSGTGkTATFAISILQQIELDLkATQALVLAPTRELAQQIQkVVMALGDYMGASCHACIGGTNVRAEVQkLQMEAPHIIVGTPGRVFDMLNRRYLSPkYIkMFVLDEADEMLSRGFkDQIYDIFQkLNSNTQVVLLSATMPSDVLEVTkkFMRDPIRILVk 237
                                    32        42        52 |      62     |  72        82        92      |102       112     | 122       132       142   |   152       162       172 |  |  182       192|      202       212       222  ||   232    |
                                                          54-MLY        68-MLY        82-MLY           99-MLY            118-MLY                     146-MLY                     174-MLY            193-MLY  202-MLY                225-MLY     237-MLY
                                                                                                                                                                                    177-MLY                                          226-MLY

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(

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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: Tandem AAA-ATPase domain (59)

Protein domain: Initiation factor 4a (6)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2g9na1	A:21-238
1b	d2g9nb_	B:

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)

Human (Homo sapiens) (413)

1a	2g9nA00	A:21-236
1b	2g9nB00	B:23-236

(no "Pfam Domain" information available for 2G9N)

Asymmetric Unit(hide GO term definitions)

Chain A,B (IF4A1_HUMAN | P60842)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004004	ATP-dependent RNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	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:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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).
	GO:0008135	translation factor activity, RNA binding	Functions during translation by interacting selectively and non-covalently with RNA during polypeptide synthesis at the ribosome.
	GO:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
	GO:0010501	RNA secondary structure unwinding	The process in which a secondary structure of RNA are broken or 'melted'.
	GO:0031100	animal organ regeneration	The regrowth of a lost or destroyed animal organ.
	GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0006446	regulation of translational initiation	Any process that modulates the frequency, rate or extent of translational initiation.
	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: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: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: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: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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(no "Related Entries Specified in the PDB File" available for 2G9N)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 27)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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Exons (6, 12)

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