3W1Y - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF T BRUCEI ATG8.2 IN COMPLEX WITH E COLI S10

Authors :   Y. A. Yuan, C. Wang

Date :   23 Nov 12 (Deposition) - 27 Nov 13 (Release) - 27 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Autophage Protein 8, Autophage Protein 12, Ubiquitin Fold, Transport Protein-Ribosomal Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. A. Yuan, C. Wang
Crystal Structure Of T Brucei Atg8. 2
To Be Published
PubMed: search

Molecule 1 - MICROTUBULE-ASSOCIATED PROTEIN 1A/1B, LIGHT CHAIN 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	TB927.7.3320
	Organism Scientific	:	TRYPANOSOMA BRUCEI BRUCEI
	Organism Taxid	:	999953
	Strain	:	927/4 GUTAT10.1

Molecule 2 - 30S RIBOSOMAL PROTEIN S10
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RPSJ, NUSE, B3321, JW3283
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3W1Y)

(no "Site" information available for 3W1Y)

(no "SS Bond" information available for 3W1Y)

Asymmetric Unit

No.	Residues
1	Gly C:38	-	Pro C:39

(no "SAP(SNP)/Variant" information available for 3W1Y)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S10	PS00361	Ribosomal protein S10 signature.	RS10_ECOLI	29-44	1	C:29-44

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S10	PS00361	Ribosomal protein S10 signature.	RS10_ECOLI	29-44	1	C:29-44

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S10	PS00361	Ribosomal protein S10 signature.	RS10_ECOLI	29-44	1	C:29-44

(no "Exon" information available for 3W1Y)

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:120
 aligned with Q57WE7_TRYB2 | Q57WE7 from UniProtKB/TrEMBL  Length:134

    Alignment length:129
                                    13        23        33        43        53        63        73        83        93       103       113       123         
         Q57WE7_TRYB2     4 HYRYQYTRSFAERAKETESARLRYPKHIPILCEPTSAASASTPRDVRLFSTRQQVQRELDCNKFLLPETATVMEFMMALRQRLLLEEGQAVFVFIGNELPPNSACLGDIYARAKDPDGFLYVSYGVENT 132
               SCOP domains d3w1ya_ A: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..---------......hhhhhhhhhheeeeee...hhhhhhhhhhhhh......eeeee..........hhhhhhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w1y A   4 HYRYQYTRSFAERAKETESARLRYPKHIPILCEPTS---------VRLFSTRQQVQRELDCNKFLLPETATVMEFMMALRQRLLLEEGQAVFVFIGNELPPNSACLGDIYARAKDPDGFLYVSYGVENT 132
                                    13        23        33     |   -     |  53        63        73        83        93       103       113       123         
                                                              39        49

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with Q57WE7_TRYB2 | Q57WE7 from UniProtKB/TrEMBL  Length:134

    Alignment length:127
                                    14        24        34        44        54        64        74        84        94       104       114       124       
         Q57WE7_TRYB2     5 YRYQYTRSFAERAKETESARLRYPKHIPILCEPTSAASASTPRDVRLFSTRQQVQRELDCNKFLLPETATVMEFMMALRQRLLLEEGQAVFVFIGNELPPNSACLGDIYARAKDPDGFLYVSYGVEN 131
               SCOP domains d3w1yb_ B: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..-----------------------..eeeeee...hhhhhhhhhhhhh......eeeee..........hhhhhhhhhh.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w1y B   5 YRYQYTRSFAERAKETESARLRYPKHIPILCEPTS-----------------------DCNKFLLPETATVMEFMMALRQRLLLEEGQAVFVFIGNELPPNSACLGDIYARAKDPDGFLYVSYGVEN 131
                                    14        24        34    |    -         -        64        74        84        94       104       114       124       
                                                             39                      63

Chain C from PDB  Type:PROTEIN  Length:90
 aligned with RS10_ECOLI | P0A7R5 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:99
                                    14        24        34        44        54        64        74        84        94         
           RS10_ECOLI     5 RIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG 103
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeee...---------.eeeeeeeeeeeeee..hhhhhhhhhh.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------RIBOSOMAL_S10   ----------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 3w1y C   5 RIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLI---------DQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG 103
                                    14        24        34        44        |-        64        74        84        94         
                                                                           53        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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: beta-Grasp (ubiquitin-like) (1032)

Superfamily: Ubiquitin-like (546)

Family: automated matches (55)

Protein domain: automated matches (55)

Trypanosoma brucei [TaxId: 999953] (2)

1a	d3w1ya_	A:
1b	d3w1yb_	B:

(no "CATH Domain" information available for 3W1Y)

(no "Pfam Domain" information available for 3W1Y)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q57WE7_TRYB2 | Q57WE7)

biological process
	GO:0006914		autophagy		The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0006995		cellular response to nitrogen 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 nitrogen.

Chain C (RS10_ECOLI | P0A7R5)

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:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	GO:0001072	transcription antitermination factor activity, RNA binding	Binds to RNA, typically within the nascent RNA transcript, to promote readthrough of a transcription termination site and thus extending the length of the RNA transcript produced. Examples of antitermination factors which bind the nascent RNA include the lambda N protein and the HIV-1 tat protein.
biological process
	GO:0031564	transcription antitermination	Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
	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.
cellular component
	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:0022627	cytosolic small ribosomal subunit	The small subunit of a ribosome located in the cytosol.
	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:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	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.

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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3w1y)

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(no "Sites" information available for 3w1y)

	Cis Peptide Bonds
		Gly C:38 - Pro C:39	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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