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(-) Description

Title :  CRYSTAL STRUCTURE OF FAF1 UBX DOMAIN IN COMPLEX WITH P97/VCP N DOMAIN REVEALS THE CONSERVED FCISP TOUCH-TURN MOTIF OF UBX DOMAIN SUFFERING CONFORMATIONAL CHANGE
 
Authors :  K. H. Kim, W. Kang, S. W. Suh, J. K. Yang
Date :  15 Jan 11  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Ubx, Faf1, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Kang, J. K. Yang
Crystal Structure Of Human Faf1 Ubx Domain Reveals A Novel Fcisp Touch-Turn Motif In P97/Vcp-Binding Region
Biochem. Biophys. Res. Commun. V. 407 531 2011
PubMed-ID: 21414298  |  Reference-DOI: 10.1016/J.BBRC.2011.03.052

(-) Compounds

Molecule 1 - FAS-ASSOCIATED FACTOR 1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUBX DOMAIN
    GeneFAF1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHFAF1, UBX DOMAIN-CONTAINING PROTEIN 12, UBX DOMAIN- CONTAINING PROTEIN 3A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 3QCA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Phe A:619 -Pro A:620
2Phe A:639 -Pro A:640
3Phe B:619 -Pro B:620
4Phe B:639 -Pro B:640
5Phe C:619 -Pro C:620
6Phe C:639 -Pro C:640
7Phe D:619 -Pro D:620
8Phe D:639 -Pro D:640

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (2, 8)

Asymmetric Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003961531aENSE00001656216chr1:51425935-51425439497FAF1_HUMAN1-15150--
1.3ENST000003961533ENSE00001672468chr1:51323669-5132360169FAF1_HUMAN16-38230--
1.4ENST000003961534ENSE00001711667chr1:51267349-5126730347FAF1_HUMAN39-54160--
1.5ENST000003961535ENSE00001681390chr1:51253877-51253672206FAF1_HUMAN54-123700--
1.6ENST000003961536ENSE00001711552chr1:51210447-5121035692FAF1_HUMAN123-153310--
1.7ENST000003961537ENSE00001762864chr1:51204626-5120453592FAF1_HUMAN154-184310--
1.8cENST000003961538cENSE00001661954chr1:51171563-51171458106FAF1_HUMAN184-219360--
1.9ENST000003961539ENSE00001326285chr1:51121200-5112111487FAF1_HUMAN220-248290--
1.11ENST0000039615311ENSE00001323158chr1:51061888-5106179396FAF1_HUMAN249-280320--
1.12ENST0000039615312ENSE00001319113chr1:51050483-51050357127FAF1_HUMAN281-323430--
1.13aENST0000039615313aENSE00001294655chr1:51049387-5104932464FAF1_HUMAN323-344220--
1.14ENST0000039615314ENSE00001311843chr1:51048371-5104829082FAF1_HUMAN344-371280--
1.15ENST0000039615315ENSE00001295616chr1:51032903-51032749155FAF1_HUMAN372-423520--
1.16ENST0000039615316ENSE00001299544chr1:51005400-51005264137FAF1_HUMAN423-469470--
1.17ENST0000039615317ENSE00001293798chr1:51001129-5100104189FAF1_HUMAN469-498300--
1.18ENST0000039615318ENSE00001298822chr1:50957473-5095739381FAF1_HUMAN499-525270--
1.19ENST0000039615319ENSE00001302601chr1:50956337-5095626078FAF1_HUMAN526-551260--
1.20ENST0000039615320ENSE00001326948chr1:50941351-50941136216FAF1_HUMAN552-623724A:571-623
B:571-623
C:571-623
D:571-623
53
53
53
53
1.22cENST0000039615322cENSE00001819739chr1:50907195-509051502046FAF1_HUMAN624-650274A:624-650
B:624-650
C:624-650
D:624-650
27
27
27
27

(-) 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:80
 aligned with FAF1_HUMAN | Q9UNN5 from UniProtKB/Swiss-Prot  Length:650

    Alignment length:80
                                   580       590       600       610       620       630       640       650
           FAF1_HUMAN   571 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAKE 650
               SCOP domains d3qcaa_ A: automated matches                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeee...hhhhhhhhhhhh..hhh.eeeee....ee.hhh.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.20  PDB: A:571-623 UniProt: 552-623           Exon 1.22c  PDB: A:624-650  Transcript 1
                 3qca A 571 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAKE 650
                                   580       590       600       610       620       630       640       650

Chain B from PDB  Type:PROTEIN  Length:80
 aligned with FAF1_HUMAN | Q9UNN5 from UniProtKB/Swiss-Prot  Length:650

    Alignment length:80
                                   580       590       600       610       620       630       640       650
           FAF1_HUMAN   571 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAKE 650
               SCOP domains d3qcab_ B: automated matches                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeee...hhhhhhhhhhhh......eeeee....ee.................eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.20  PDB: B:571-623 UniProt: 552-623           Exon 1.22c  PDB: B:624-650  Transcript 1
                 3qca B 571 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAKE 650
                                   580       590       600       610       620       630       640       650

Chain C from PDB  Type:PROTEIN  Length:80
 aligned with FAF1_HUMAN | Q9UNN5 from UniProtKB/Swiss-Prot  Length:650

    Alignment length:80
                                   580       590       600       610       620       630       640       650
           FAF1_HUMAN   571 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAKE 650
               SCOP domains d3qcac_ C: automated matches                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeee...hhhhhhhhhhhh......eeee......hhhhh.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.20  PDB: C:571-623 UniProt: 552-623           Exon 1.22c  PDB: C:624-650  Transcript 1
                 3qca C 571 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAKE 650
                                   580       590       600       610       620       630       640       650

Chain D from PDB  Type:PROTEIN  Length:80
 aligned with FAF1_HUMAN | Q9UNN5 from UniProtKB/Swiss-Prot  Length:650

    Alignment length:80
                                   580       590       600       610       620       630       640       650
           FAF1_HUMAN   571 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAKE 650
               SCOP domains d3qcad_ D: automated matches                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) UBX-3qcaD01 D:571-648                                                         -- Pfam domains (1)
           Pfam domains (2) UBX-3qcaD02 D:571-648                                                         -- Pfam domains (2)
           Pfam domains (3) UBX-3qcaD03 D:571-648                                                         -- Pfam domains (3)
           Pfam domains (4) UBX-3qcaD04 D:571-648                                                         -- Pfam domains (4)
         Sec.struct. author ..eeeeeee.....eeeeeee...hhhhhhhhhhhh......eeeee....ee.hhh.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.20  PDB: D:571-623 UniProt: 552-623           Exon 1.22c  PDB: D:624-650  Transcript 1
                 3qca D 571 EPVSKLRIRTPSGEFLERRFLASNKLQIVFDFVASKGFPWDEYKLLSTFPRRDVTQLDPNKSLLEVKLFPQETLFLEAKE 650
                                   580       590       600       610       620       630       640       650

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Ubiquitin (279)
(-)
Family: UBX (7)
1aUBX-3qcaD01D:571-648
1bUBX-3qcaD02D:571-648
1cUBX-3qcaD03D:571-648
1dUBX-3qcaD04D:571-648

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (FAF1_HUMAN | Q9UNN5)
molecular function
    GO:0051059    NF-kappaB binding    Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.
    GO:0031072    heat shock protein binding    Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0019887    protein kinase regulator activity    Modulates the activity of a protein kinase, an enzyme which phosphorylates a protein.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0008219    cell death    Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
    GO:0007253    cytoplasmic sequestering of NF-kappaB    The selective interaction of the transcription factor NF-kappaB with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0010942    positive regulation of cell death    Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:1902043    positive regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    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:0030155    regulation of cell adhesion    Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
    GO:0042176    regulation of protein catabolic process    Any process that modulates 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:0045859    regulation of protein kinase activity    Any process that modulates the frequency, rate or extent of protein kinase activity.
cellular component
    GO:0031265    CD95 death-inducing signaling complex    A protein complex formed upon binding of Fas/CD95/APO-1 to its ligand. The complex includes FADD/Mort1, procaspase-8/10 and c-FLIP in addition to the ligand-bound receptor.
    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: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:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FAF1_HUMAN | Q9UNN51h8c 2dzm 2ec4 3e21 3qc8 3qq8 3qwz 3qx1 3r3m

(-) Related Entries Specified in the PDB File

3qc8