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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE OF THE UBL-DOMAIN OF HERP

Authors :   T. Nakanishi, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   28 May 04 (Deposition) - 28 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Endplasmic Reticulum Stress, Ubl Domain, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nakanishi, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Ubl-Domain Of Herp
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HOMOCYSTEINE-RESPONSIVE ENDOPLASMIC RETICULUM- RESIDENT UBIQUITIN-LIKE DOMAIN MEMBER 1 PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P030609-57
	Expression System Vector Type	:	PLASMID
	Fragment	:	UBL-DOMAIN
	Gene	:	KAZUSA CDNA HA00594
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	HOMOCYSTEINE-RESPONSIVE ENDPLASMIC RETICULUM RESIDENT PROTEIN, HERP, METHYL METHANESULFONATE (MMF)- INDUCIBLE FRAGMENT PROTEIN 1


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1WGD)

(no "Site" information available for 1WGD)

(no "SS Bond" information available for 1WGD)

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

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024277	R	50	H	HERP1_HUMAN	Polymorphism	2217332	A	R	48	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UBIQUITIN_2	PS50053	Ubiquitin domain profile.	HERP1_HUMAN	10-72	1	A:8-70

(no "Exon" information available for 1WGD)

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:93
 aligned with HERP1_HUMAN | Q15011 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:112
                                    12        22        32        42        52        62        72        82        92       102       112  
          HERP1_HUMAN     3 SETEPEPVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVKSPSKMPEINAKVAESTEEPAGSNRG 114
               SCOP domains d1wgda_ A:                                                                                                       SCOP domains
               CATH domains 1wgdA00 A:1-93 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee........eeee......hhhhhhhhhhh..........eeee..ee......hhhh.......eeeeee.....-------------------..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------H---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------UBIQUITIN_2  PDB: A:8-70 UniProt: 10-72                        ------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1wgd A   1 GSSGSSGVTLLVKSPNQRHRDLELSGDRGWSVGHLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVKS-------------------GPSSG  93
                                    10        20        30        40        50        60        70        80       | -         -       |91  
                                                                                                                  88                  89

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	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 '\|'

NMR Structure

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 (286)

Human (Homo sapiens) (177)

1wgdA00

A:1-93

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

NMR Structure(hide GO term definitions)

Chain A (HERP1_HUMAN | Q15011)

molecular function
	GO:0044325	ion channel binding	Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	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).
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:0006874	cellular calcium ion homeostasis	Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
	GO:0032469	endoplasmic reticulum calcium ion homeostasis	Any process involved in the maintenance of an internal steady state of calcium ions within the endoplasmic reticulum of a cell or between the endoplasmic reticulum and its surroundings.
	GO:0030968	endoplasmic reticulum unfolded protein response	The series of molecular signals generated as a consequence of the presence of unfolded proteins in the endoplasmic reticulum (ER) or other ER-related stress; results in changes in the regulation of transcription and translation.
	GO:0043154	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
	GO:1902236	negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of an endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway.
	GO:2001243	negative regulation of intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway.
	GO:1903071	positive regulation of ER-associated ubiquitin-dependent protein catabolic process	Any process that activates or increases the frequency, rate or extent of ER-associated ubiquitin-dependent protein catabolic process.
	GO:0032092	positive regulation of protein binding	Any process that activates or increases the frequency, rate or extent of protein binding.
	GO:1903069	regulation of ER-associated ubiquitin-dependent protein catabolic process	Any process that modulates the frequency, rate or extent of ER-associated ubiquitin-dependent protein catabolic process.
	GO:1902235	regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	Any process that modulates the frequency, rate or extent of an endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway.
	GO:0031396	regulation of protein ubiquitination	Any process that modulates the frequency, rate or extent of the addition of ubiquitin groups to a protein.
	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:0006986	response to unfolded protein	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus.
	GO:0030970	retrograde protein transport, ER to cytosol	The directed movement of unfolded or misfolded proteins from the endoplasmic reticulum to the cytosol through the translocon.
	GO:0006511	ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
	GO:1990037	Lewy body core	The center portion of a Lewy body. In Parkinson's disease, it contains a matted meshwork of filaments.
	GO:0034704	calcium channel complex	An ion channel complex through which calcium ions pass.
	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:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

NMR Structure
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