3VWW - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A0-DOMAIN OF P5 FROM H. SAPIENS

Authors :   K. Inaba, M. Suzuki

Date :   03 Sep 12 (Deposition) - 04 Sep 13 (Release) - 04 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

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

Keywords :   Pdi Family Member, Thioredoxin Fold, Protein Disulfide Isomerase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Sato, R. Kojima, M. Okumura, M. Hagiwara, S. Masui, K. Maegawa, M. Saiki, T. Horibe, M. Suzuki, K. Inaba
Synergistic Cooperation Of Pdi Family Members In Peroxiredoxin 4-Driven Oxidative Protein Folding
Sci Rep V. 3 2456 2013
PubMed-ID: 23949117 | Reference-DOI: 10.1038/SREP02456

Molecule 1 - PROTEIN DISULFIDE-ISOMERASE A6
	Chains	:	A, B
	EC Number	:	5.3.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	A0 DOMAIN, UNP RESIDUES 25-140
	Gene	:	PDIA6, ERP5, P5, TXNDC7
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ENDOPLASMIC RETICULUM PROTEIN 5, ER PROTEIN 5, ERP5, PROTEIN DISULFIDE ISOMERASE P5, THIOREDOXIN DOMAIN-CONTAINING PROTEIN 7

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MLY	2	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	MLY	2	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:59 , PRO A:101 , ARG A:120 , HOH A:368 , HOH A:380 , SER B:35	BINDING SITE FOR RESIDUE PO4 A 201
2	AC2	SOFTWARE	HIS A:59 , ARG A:62 , ASN B:38 , GLN B:43	BINDING SITE FOR RESIDUE PO4 B 201

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

Asymmetric Unit

No.	Residues
1	Phe A:100	-	Pro A:101
2	Phe B:100	-	Pro B:101

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	PDIA6_HUMAN	47-65 182-200	2	A:49-67 B:49-67 -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	PDIA6_HUMAN	47-65 182-200	1	A:49-67 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	PDIA6_HUMAN	47-65 182-200	1	- B:49-67 -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	PDIA6_HUMAN	47-65 182-200	2	A:49-67 B:49-67 -

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.8a	ENST00000272227	8a	ENSE00001401250	chr2:10952970-10952804	167	PDIA6_HUMAN	1-7	7	0	-	-
1.10	ENST00000272227	10	ENSE00000996575	chr2:10942766-10942625	142	PDIA6_HUMAN	7-54	48	2	A:27-56 B:27-56	30 30
1.11	ENST00000272227	11	ENSE00000962411	chr2:10937883-10937826	58	PDIA6_HUMAN	54-73	20	2	A:56-75 B:56-75	20 20
1.12b	ENST00000272227	12b	ENSE00000962412	chr2:10937333-10937207	127	PDIA6_HUMAN	74-116	43	2	A:76-118 B:76-118	43 43
1.13	ENST00000272227	13	ENSE00000962413	chr2:10933328-10933222	107	PDIA6_HUMAN	116-151	36	2	A:118-142 B:118-142	25 25
1.14	ENST00000272227	14	ENSE00000962414	chr2:10932051-10931921	131	PDIA6_HUMAN	152-195	44	0	-	-
1.15	ENST00000272227	15	ENSE00000962415	chr2:10930959-10930845	115	PDIA6_HUMAN	195-233	39	0	-	-
1.16	ENST00000272227	16	ENSE00000962416	chr2:10930015-10929875	141	PDIA6_HUMAN	234-280	47	0	-	-
1.17	ENST00000272227	17	ENSE00000962418	chr2:10929107-10929023	85	PDIA6_HUMAN	281-309	29	0	-	-
1.18	ENST00000272227	18	ENSE00000962419	chr2:10928895-10928823	73	PDIA6_HUMAN	309-333	25	0	-	-
1.19	ENST00000272227	19	ENSE00000962420	chr2:10927565-10927407	159	PDIA6_HUMAN	333-386	54	0	-	-
1.20	ENST00000272227	20	ENSE00000962421	chr2:10925156-10925060	97	PDIA6_HUMAN	386-418	33	0	-	-
1.21c	ENST00000272227	21c	ENSE00001893291	chr2:10924452-10923517	936	PDIA6_HUMAN	419-440	22	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:116
 aligned with PDIA6_HUMAN | Q15084 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:116
                                    34        44        54        64        74        84        94       104       114       124       134      
          PDIA6_HUMAN    25 DDVIELTPSNFNREVIQSDSLWLVEFYAPWCGHCQRLTPEWKKAATALKDVVKVGAVDADKHHSLGGQYGVQGFPTIKIFGSNKNRPEDYQGGRTGEAIVDAALSALRQLVKDRLG 140
               SCOP domains d3vwwa_ A: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....hhhhhh......eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeee.......eee....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------THIOREDOXIN_1      --------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:27-56       -------------------Exon 1.12b  PDB: A:76-118 UniProt: 74-116  ------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.11           ------------------------------------------Exon 1.13  PDB: A:118-142 Transcript 1 (2)
                 3vww A  27 DDVIELTPSNFNREVIQSDSLWLVEFYAPWCGHCQRLTPEWKKAATALKDVVKVGAVDADKHHSLGGQYGVQGFPTIkIFGSNKNRPEDYQGGRTGEAIVDAALSALRQLVKDRLG 142
                                    36        46        56        66        76        86        96       106       116       126       136      
                                                                                                       104-MLY

Chain B from PDB  Type:PROTEIN  Length:116
 aligned with PDIA6_HUMAN | Q15084 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:116
                                    34        44        54        64        74        84        94       104       114       124       134      
          PDIA6_HUMAN    25 DDVIELTPSNFNREVIQSDSLWLVEFYAPWCGHCQRLTPEWKKAATALKDVVKVGAVDADKHHSLGGQYGVQGFPTIKIFGSNKNRPEDYQGGRTGEAIVDAALSALRQLVKDRLG 140
               SCOP domains d3vwwb_ B: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...hhhhhh......eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeee.......ee.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------THIOREDOXIN_1      --------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: B:27-56       -------------------Exon 1.12b  PDB: B:76-118 UniProt: 74-116  ------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.11           ------------------------------------------Exon 1.13  PDB: B:118-142 Transcript 1 (2)
                 3vww B  27 DDVIELTPSNFNREVIQSDSLWLVEFYAPWCGHCQRLTPEWKKAATALKDVVKVGAVDADKHHSLGGQYGVQGFPTIkIFGSNKNRPEDYQGGRTGEAIVDAALSALRQLVKDRLG 142
                                    36        46        56        66        76        86        96       106       116       126       136      
                                                                                                       104-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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: automated matches (347)

Protein domain: automated matches (347)

Human (Homo sapiens) [TaxId: 9606] (87)

1a	d3vwwa_	A:
1b	d3vwwb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PDIA6_HUMAN | Q15084)

molecular function
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	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:0003756	protein disulfide isomerase activity	Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
biological process
	GO:0036498	IRE1-mediated unfolded protein response	A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
	GO:0043277	apoptotic cell clearance	The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	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.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0034663	endoplasmic reticulum chaperone complex	A protein complex that is located in the endoplasmic reticulum and is composed of chaperone proteins, including BiP, GRP94; CaBP1, protein disulfide isomerase (PDI), ERdj3, cyclophilin B, ERp72, GRP170, UDP-glucosyltransferase, and SDF2-L1.
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005793	endoplasmic reticulum-Golgi intermediate compartment	A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
	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:0042470	melanosome	A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

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	3vww
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	PDIA6_HUMAN \| Q15084	:	1x5d 3w8j 4ef0 4gwr

2dml	NMR STRUCTURE OF P5 A0-DOMAIN
3vwu
3vwv
3w8j

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (4, 8)

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