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3.A.16.1.1
Mammalian ER retrotranslocon. The Grp170 protein plays a role during ERAD, positioning this client-release factor at the retrotranslocation site, allowing a mechanism to couple client release from BiP and retrotranslocation (Inoue and Tsai, 2016). The cryo-EM structure of the ERAD protein channel, formed by tetrameric human Derlin-1, has been solved (Rao et al. 2021).  The structure shows that Derlin-1 forms a homotetramer that encircles a large tunnel traversing the ER membrane. The tunnel has a diameter of about 12 to 15 angstroms, large enough to allow an α-helix to pass through. The structure shows a lateral gate within the membrane, providing access of transmembrane proteins to the tunnel. Thus, Derlin-1 forms a protein channel for translocation of misfolded proteins. This structure is different from the monomeric yeast Derlin structure previously reported, which forms a semichannel with another protein (Rao et al. 2021).

Accession Number:P55072
Protein Name:p97 ATPase aka TER ATPase
Length:806
Molecular Weight:89322.00
Species:Homo sapiens (Human) [9606]
Location1 / Topology2 / Orientation3: Cytoplasm1
Substrate

Cross database links:

DIP: DIP-33543N
RefSeq: NP_009057.1   
Entrez Gene ID: 7415   
Pfam: PF00004    PF02933    PF02359    PF09336   
OMIM: 167320  phenotype
601023  gene
KEGG: hsa:7415   

Gene Ontology

GO:0005829 C:cytosol
GO:0005783 C:endoplasmic reticulum
GO:0005792 C:microsome
GO:0005634 C:nucleus
GO:0000502 C:proteasome complex
GO:0005524 F:ATP binding
GO:0016887 F:ATPase activity
GO:0008289 F:lipid binding
GO:0031593 F:polyubiquitin binding
GO:0019904 F:protein domain specific binding
GO:0019903 F:protein phosphatase binding
GO:0006919 P:activation of caspase activity
GO:0006302 P:double-strand break repair
GO:0030968 P:endoplasmic reticulum unfolded protein resp...
GO:0030433 P:ER-associated protein catabolic process
GO:0032436 P:positive regulation of proteasomal ubiquiti...
GO:0016567 P:protein ubiquitination
GO:0030970 P:retrograde protein transport, ER to cytosol

References (27)

[1] “Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning.”  Hu R.-M.et.al.   10931946
[2] “Complete sequencing and characterization of 21,243 full-length human cDNAs.”  Ota T.et.al.   14702039
[3] “DNA sequence and analysis of human chromosome 9.”  Humphray S.J.et.al.   15164053
[4] “The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).”  The MGC Project Teamet.al.   15489334
[5] “Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides.”  Gevaert K.et.al.   12665801
[6] “A novel UBA and UBX domain protein that binds polyubiquitin and VCP and is a substrate for SAPKs.”  McNeill H.et.al.   15362974
[7] “Physical and functional interaction between dorfin and valosin-containing protein that are colocalized in ubiquitylated inclusions in neurodegenerative disorders.”  Ishigaki S.et.al.   15456787
[8] “A membrane protein complex mediates retro-translocation from the ER lumen into the cytosol.”  Ye Y.et.al.   15215856
[9] “The ubiquitin-domain protein HERP forms a complex with components of the endoplasmic reticulum associated degradation pathway.”  Schulze A.et.al.   16289116
[10] “Phosphoproteome analysis of HeLa cells using stable isotope labeling with amino acids in cell culture (SILAC).”  Amanchy R.et.al.   16212419
[11] “Immunoaffinity profiling of tyrosine phosphorylation in cancer cells.”  Rush J.et.al.   15592455
[12] “Recruitment of the p97 ATPase and ubiquitin ligases to the site of retrotranslocation at the endoplasmic reticulum membrane.”  Ye Y.et.al.   16186510
[13] “Multiprotein complexes that link dislocation, ubiquitination, and extraction of misfolded proteins from the endoplasmic reticulum membrane.”  Lilley B.N.et.al.   16186509
[14] “Calcium-sensing receptor ubiquitination and degradation mediated by the E3 ubiquitin ligase dorfin.”  Huang Y.et.al.   16513638
[15] “Derlin-2 and Derlin-3 are regulated by the mammalian unfolded protein response and are required for ER-associated degradation.”  Oda Y.et.al.   16449189
[16] “Characterization of erasin (UBXD2): a new ER protein that promotes ER-associated protein degradation.”  Liang J.et.al.   16968747
[17] “ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.”  Matsuoka S.et.al.   17525332
[18] “Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column.”  Imami K.et.al.   18187866
[19] “Ubxd1 is a novel co-factor of the human p97 ATPase.”  Madsen L.et.al.   18656546
[20] “Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle.”  Daub H.et.al.   18691976
[21] “Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.”  Gauci S.et.al.   19413330
[22] “The otubain YOD1 is a deubiquitinating enzyme that associates with p97 to facilitate protein dislocation from the ER.”  Ernst R.et.al.   19818707
[23] “Large-scale proteomics analysis of the human kinome.”  Oppermann F.S.et.al.   19369195
[24] “Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.”  Mayya V.et.al.   19690332
[25] “Inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia is caused by mutant valosin-containing protein.”  Watts G.D.J.et.al.   15034582
[26] “Mutant valosin-containing protein causes a novel type of frontotemporal dementia.”  Schroeder R.et.al.   15732117
[27] “Inclusion body myopathy and Paget disease is linked to a novel mutation in the VCP gene.”  Haubenberger D.et.al.   16247064
Structure:
3EBB   3HU1   3HU2   3HU3   3QC8   3QQ7   3QQ8   3QWZ   3TIW   4KDI   [...more]

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Predict TMSs (Predict number of transmembrane segments)
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FASTA formatted sequence
1:	MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK 
61:	GKKRREAVCI VLSDDTCSDE KIRMNRVVRN NLRVRLGDVI SIQPCPDVKY GKRIHVLPID 
121:	DTVEGITGNL FEVYLKPYFL EAYRPIRKGD IFLVRGGMRA VEFKVVETDP SPYCIVAPDT 
181:	VIHCEGEPIK REDEEESLNE VGYDDIGGCR KQLAQIKEMV ELPLRHPALF KAIGVKPPRG 
241:	ILLYGPPGTG KTLIARAVAN ETGAFFFLIN GPEIMSKLAG ESESNLRKAF EEAEKNAPAI 
301:	IFIDELDAIA PKREKTHGEV ERRIVSQLLT LMDGLKQRAH VIVMAATNRP NSIDPALRRF 
361:	GRFDREVDIG IPDATGRLEI LQIHTKNMKL ADDVDLEQVA NETHGHVGAD LAALCSEAAL 
421:	QAIRKKMDLI DLEDETIDAE VMNSLAVTMD DFRWALSQSN PSALRETVVE VPQVTWEDIG 
481:	GLEDVKRELQ ELVQYPVEHP DKFLKFGMTP SKGVLFYGPP GCGKTLLAKA IANECQANFI 
541:	SIKGPELLTM WFGESEANVR EIFDKARQAA PCVLFFDELD SIAKARGGNI GDGGGAADRV 
601:	INQILTEMDG MSTKKNVFII GATNRPDIID PAILRPGRLD QLIYIPLPDE KSRVAILKAN 
661:	LRKSPVAKDV DLEFLAKMTN GFSGADLTEI CQRACKLAIR ESIESEIRRE RERQTNPSAM 
721:	EVEEDDPVPE IRRDHFEEAM RFARRSVSDN DIRKYEMFAQ TLQQSRGFGS FRFPSGNQGG 
781:	AGPSQGSGGG TGGSVYTEDN DDDLYG