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(-) Description

Title :  CRYSTAL STRUCTURE OF P97N IN COMPLEX WITH THE C-TERMINUS OF GP78
 
Authors :  P. Haenzelmann, H. Schindelin
Date :  22 Aug 11  (Deposition) - 14 Sep 11  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Beta-Barrel Alpha-Helix, Transport Protein Atpase Ubiquitin Ligase, Ubiquitin, Phosphorylation, Cytoplasm Endoplasmic Reticulum, Protein Transport-Ligase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Hanzelmann, H. Schindelin
The Structural And Functional Basis Of The P97/Valosin-Containing Protein (Vcp)-Interacting Motif (Vim): Mutually Exclusive Binding Of Cofactors To The N-Terminal Domain Of P97.
J. Biol. Chem. V. 286 38679 2011
PubMed-ID: 21914798  |  Reference-DOI: 10.1074/JBC.M111.274506

(-) Compounds

Molecule 1 - TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEX_HTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-187
    GeneVCP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTER ATPASE, 15S MG(2+)-ATPASE P97 SUBUNIT, VALOSIN- CONTAINING PROTEIN, VCP
 
Molecule 2 - E3 UBIQUITIN-PROTEIN LIGASE AMFR
    ChainsC, D
    EC Number6.3.2.-
    EngineeredYES
    FragmentUNP RESIDUES 622-640
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAUTOCRINE MOTILITY FACTOR RECEPTOR, ISOFORM 2, AMF RECEPTOR, ISOFORM 2, RING FINGER PROTEIN 45, GP78
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:53 , HOH A:318 , ARG C:626 , ARG C:627BINDING SITE FOR RESIDUE CL A 188
2AC2SOFTWAREHOH C:100 , HOH C:296 , THR C:623 , LEU C:624 , ARG C:627BINDING SITE FOR RESIDUE CL C 2
3AC3SOFTWAREARG B:53 , ARG D:626 , ARG D:627BINDING SITE FOR RESIDUE CL B 188
4AC4SOFTWAREHOH D:356 , LEU D:624 , ARG D:627BINDING SITE FOR RESIDUE CL D 4

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:169 -Pro A:170
2Ser A:171 -Pro A:172
3Asp B:169 -Pro B:170
4Ser B:171 -Pro B:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 18)

Asymmetric Unit (9, 18)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033016R95GTERA_HUMANDisease (IBMPFD1)121909332A/BR95G
2UniProtVAR_076464G97ETERA_HUMANDisease (CMT2Y)864309502A/BG97E
3UniProtVAR_033017R155CTERA_HUMANDisease (IBMPFD1)121909330A/BR155C
4UniProtVAR_033018R155HTERA_HUMANDisease (IBMPFD1)121909329A/BR155H
5UniProtVAR_033019R155PTERA_HUMANDisease (IBMPFD1)121909329A/BR155P
6UniProtVAR_076466R155STERA_HUMANDisease (IBMPFD1)  ---A/BR155S
7UniProtVAR_065910R159GTERA_HUMANDisease (ALS14)387906789A/BR159G
8UniProtVAR_033020R159HTERA_HUMANDisease (IBMPFD1)121909335A/BR159H
9UniProtVAR_076467E185KTERA_HUMANDisease (CMT2Y)864309501A/BE185K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (9, 9) Biological Unit 2 (9, 9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TIW)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002906491ENSE00001233636chr16:56459448-56458985464AMFR_HUMAN1-85850--
1.2ENST000002906492ENSE00001108665chr16:56448256-5644816493AMFR_HUMAN86-116310--
1.3ENST000002906493ENSE00001108651chr16:56443500-56443336165AMFR_HUMAN117-171550--
1.4ENST000002906494ENSE00001108659chr16:56442028-56441876153AMFR_HUMAN172-222510--
1.5ENST000002906495ENSE00001108663chr16:56439156-5643911641AMFR_HUMAN223-236140--
1.6ENST000002906496ENSE00001108656chr16:56438953-56438821133AMFR_HUMAN236-280450--
1.7aENST000002906497aENSE00001045776chr16:56437030-56436897134AMFR_HUMAN281-325450--
1.8ENST000002906498ENSE00001292782chr16:56435755-56435645111AMFR_HUMAN325-362380--
1.9ENST000002906499ENSE00001045783chr16:56423287-56423097191AMFR_HUMAN362-426650--
1.10ENST0000029064910ENSE00001045791chr16:56419934-56419831104AMFR_HUMAN426-460350--
1.11ENST0000029064911ENSE00001204463chr16:56403239-56403105135AMFR_HUMAN461-505450--
1.12ENST0000029064912ENSE00001204457chr16:56401439-5640135684AMFR_HUMAN506-533280--
1.13aENST0000029064913aENSE00001204449chr16:56398017-56397833185AMFR_HUMAN534-595620--
1.14cENST0000029064914cENSE00001204531chr16:56396968-563953641605AMFR_HUMAN595-643492C:622-639
D:622-640
18
19

(-) Sequences/Alignments

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:160
 aligned with TERA_HUMAN | P55072 from UniProtKB/Swiss-Prot  Length:806

    Alignment length:165
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181     
           TERA_HUMAN    22 RPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEG 186
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......eeeehhhhhhhhh.....eeeee.....eeeeeeee.......eeeehhhhhhhh......eeeeee....ee..eeeeee...-----..hhhhhhhhhhhh....eee...eeeee....eeeeeeeeee...eee.....eee... Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------------------------------G-E---------------------------------------------------------C---G-------------------------K- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------H---H--------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------------------------------------------------------------------------------------------------------P------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) -------------------------------------------------------------------------------------------------------------------------------------S------------------------------- SAPs(SNPs) (4)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tiw A  22 RPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDD-----TGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEG 186
                                    31        41        51        61        71        81        91       101       111       121     | 131       141       151       161       171       181     
                                                                                                                             121   127                                                           

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with TERA_HUMAN | P55072 from UniProtKB/Swiss-Prot  Length:806

    Alignment length:165
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182     
           TERA_HUMAN    23 PNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGE 187
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........eeeehhhhhhhhh.....eeeee.hhh.eeeeeeee.......eee.hhhhhhhh......eeeeee........eeeeee....----..hhhhhhhhhhhh...eeee...eeeeee..eeeeeeeeeee...eeee....eeee... Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------------------------------------------G-E---------------------------------------------------------C---G-------------------------K-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------H---H---------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ------------------------------------------------------------------------------------------------------------------------------------P-------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) ------------------------------------------------------------------------------------------------------------------------------------S-------------------------------- SAPs(SNPs) (4)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tiw B  23 PNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDT----TGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGE 187
                                    32        42        52        62        72        82        92       102       112       122    |  132       142       152       162       172       182     
                                                                                                                             122  127                                                            

Chain C from PDB  Type:PROTEIN  Length:18
 aligned with AMFR_HUMAN | Q9UKV5 from UniProtKB/Swiss-Prot  Length:643

    Alignment length:18
                                   631        
           AMFR_HUMAN   622 VTLRRRMLAAAAERRLQK 639
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
               Transcript 1 Exon 1.14c         Transcript 1
                 3tiw C 622 VTLRRRMLAAAAERRLQK 639
                                   631        

Chain D from PDB  Type:PROTEIN  Length:19
 aligned with AMFR_HUMAN | Q9UKV5 from UniProtKB/Swiss-Prot  Length:643

    Alignment length:19
                                   631         
           AMFR_HUMAN   622 VTLRRRMLAAAAERRLQKQ 640
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
               Transcript 1 Exon 1.14c          Transcript 1
                 3tiw D 622 VTLRRRMLAAAAERRLQKQ 640
                                   631         

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3TIW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (99, 114)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TERA_HUMAN | P55072)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:1904288    BAT3 complex binding    Interacting selectively and non-covalently with a BAT3 complex.
    GO:0036435    K48-linked polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 48 in the target protein.
    GO:0042288    MHC class I protein binding    Interacting selectively and non-covalently with major histocompatibility complex class I molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
    GO:0035800    deubiquitinase activator activity    Increases the activity of deubiquitinase, an enzyme that catalyzes the hydrolysis of various forms of polymeric ubiquitin sequences.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0031593    polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0044389    ubiquitin-like protein ligase binding    Interacting selectively and non-covalently with a ubiquitin-like protein ligase, such as ubiquitin-ligase.
    GO:1990381    ubiquitin-specific protease binding    Interacting selectively and non-covalently with a ubiquitin-specific protease.
biological process
    GO:0046034    ATP metabolic process    The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0071712    ER-associated misfolded protein catabolic process    The chemical reactions and pathways resulting in the breakdown of misfolded proteins transported from the endoplasmic reticulum and targeted to cytoplasmic proteasomes for degradation.
    GO:0036503    ERAD pathway    The protein catabolic pathway which targets endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. It begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein modifications necessary for correct substrate transfer (e.g. ubiquitination), transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
    GO:0006734    NADH metabolic process    The chemical reactions and pathways involving reduced nicotinamide adenine dinucleotide (NADH), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0070842    aggresome assembly    The aggregation, arrangement and bonding together of a set of components to form an aggresome; requires the microtubule cytoskeleton and dynein.
    GO:0006974    cellular response to DNA damage stimulus    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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006302    double-strand break repair    The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
    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:0070987    error-free translesion synthesis    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.
    GO:0045184    establishment of protein localization    The directed movement of a protein to a specific location.
    GO:0072389    flavin adenine dinucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of flavin adenine dinucleotide, which acts as a coenzyme or prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:2001171    positive regulation of ATP biosynthetic process    Any process that activates or increases the frequency, rate or extent of ATP biosynthetic process.
    GO:1903007    positive regulation of Lys63-specific deubiquitinase activity    Any process that activates or increases the frequency, rate or extent of Lys63-specific deubiquitinase activity.
    GO:0010918    positive regulation of mitochondrial membrane potential    Any process that activates or increases the frequency, rate or extent of establishment or extent of a mitochondrial membrane potential, the electric potential existing across any mitochondrial membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane.
    GO:1903862    positive regulation of oxidative phosphorylation    Any process that activates or increases the frequency, rate or extent of oxidative phosphorylation.
    GO:0032436    positive regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:1903006    positive regulation of protein K63-linked deubiquitination    Any process that activates or increases the frequency, rate or extent of protein K63-linked deubiquitination.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0031334    positive regulation of protein complex assembly    Any process that activates or increases the frequency, rate or extent of protein complex assembly.
    GO:0043161    proteasome-mediated 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 ubiquitin, and mediated by the proteasome.
    GO:0018279    protein N-linked glycosylation via asparagine    The glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine and N4 glucosyl asparagine also occur. This modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification.
    GO:0034214    protein hexamerization    The formation of a protein hexamer, a macromolecular structure consisting of six noncovalently associated identical or nonidentical subunits.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:1903715    regulation of aerobic respiration    Any process that modulates the frequency, rate or extent of aerobic respiration.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    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:0019985    translesion synthesis    The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
    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.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
cellular component
    GO:0036513    Derlin-1 retrotranslocation complex    A protein complex that functions in the retrotranslocation step of ERAD (ER-associated protein degradation), and includes at its core Derlin-1 oligomers forming a retrotranslocation channel.
    GO:0034098    VCP-NPL4-UFD1 AAA ATPase complex    A multiprotein ATPase complex required for the efficient dislocation of ER-lumenal degradation substrates, and their subsequent proteolysis by the proteasome. In budding yeast, this complex includes Cdc48p, Npl4p and Ufd1p proteins. In mammals, this complex includes a hexamer of VCP/p97 (a cytosolic ATPase) and trimers of each of its cofactors UFD1L and NPL4 (NPLOC4) (e.g. a 6:3:3 stoichiometry).
    GO:1990730    VCP-NSFL1C complex    A protein complex between the ATPase VCP (p97) and its cofactor p47 (NSFL1C). In human, the protein complex consists of one homotrimer of NSFL1C/p47 per homohexamer of VCP/p97.
    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: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: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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005811    lipid droplet    An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0000502    proteasome complex    A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0035861    site of double-strand break    A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix.

Chain C,D   (AMFR_HUMAN | Q9UKV5)
molecular function
    GO:1904288    BAT3 complex binding    Interacting selectively and non-covalently with a BAT3 complex.
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:1904264    ubiquitin protein ligase activity involved in ERAD pathway    Any ubiquitin protein ligase activity that is involved in the ERAD pathway (the targeting of endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome).
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:1990381    ubiquitin-specific protease binding    Interacting selectively and non-covalently with a ubiquitin-specific protease.
    GO:0034450    ubiquitin-ubiquitin ligase activity    Isoenergetic transfer of ubiquitin from one protein to an existing ubiquitin chain via the reaction X-ubiquitin + Y-ubiquitin -> Y-ubiquitin-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0036503    ERAD pathway    The protein catabolic pathway which targets endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. It begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein modifications necessary for correct substrate transfer (e.g. ubiquitination), transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    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:0007611    learning or memory    The acquisition and processing of information and/or the storage and retrieval of this information over time.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:0070936    protein K48-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is added to a protein. K48-linked ubiquitination targets the substrate protein for degradation.
    GO:0051865    protein autoubiquitination    The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
    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:0036513    Derlin-1 retrotranslocation complex    A protein complex that functions in the retrotranslocation step of ERAD (ER-associated protein degradation), and includes at its core Derlin-1 oligomers forming a retrotranslocation channel.
    GO:0000838    Hrd1p ubiquitin ligase ERAD-M complex    A multiprotein complex that recognizes and ubiquitinates proteins with misfolded membrane domains during ER-associated protein degradation (ERAD). In S. cerevisiae, this complex contains the ubiquitin ligase Hrd1p.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0030176    integral component of endoplasmic reticulum membrane    The component of the endoplasmic reticulum 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: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.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AMFR_HUMAN | Q9UKV52ejs 2lvn 2lvo 2lvp 2lvq 2lxh 2lxp 3fsh 3h8k 4g3o 4lad
        TERA_HUMAN | P550723ebb 3hu1 3hu2 3hu3 3qc8 3qq7 3qq8 3qwz 4kdi 4kdl 4kln 4ko8 4kod 4p0a 5b6c 5c18 5c19 5c1a 5c1b 5dyg 5dyi 5epp 5ftj 5ftk 5ftl 5ftm 5ftn 5glf 5ifs 5ifw 5x4l

(-) Related Entries Specified in the PDB File

3qq7 CRYSTAL STRUCTURE OF THE P97 N-TERMINAL DOMAIN
3qq8 CRYSTAL STRUCTURE OF P97N IN COMPLEX WITH FAF1-UBX