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- PDB-5b6c: Structural Details of Ufd1 binding to p97 -

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Basic information

Entry
Database: PDB / ID: 5b6c
TitleStructural Details of Ufd1 binding to p97
Components
  • Peptide from Ubiquitin fusion degradation protein 1 homolog
  • Transitional endoplasmic reticulum ATPase
KeywordsHYDROLASE/PROTEIN BINDING / Ufd1 / SHP box / p97 / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion ...UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / negative regulation of type I interferon production / regulation of aerobic respiration / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / ERAD pathway / ubiquitin-like protein ligase binding / MHC class I protein binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / translesion synthesis / Protein methylation / endoplasmic reticulum to Golgi vesicle-mediated transport / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ATP metabolic process / Attachment and Entry / endoplasmic reticulum unfolded protein response / viral genome replication / lipid droplet / proteasome complex / proteasomal protein catabolic process / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / skeletal system development / Hh mutants are degraded by ERAD / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / macroautophagy / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / ABC-family proteins mediated transport / establishment of protein localization / ADP binding / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / positive regulation of canonical Wnt signaling pathway / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / cellular response to heat / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / cysteine-type deubiquitinase activity / Attachment and Entry / Ub-specific processing proteases / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / glutamatergic synapse / lipid binding / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm
Similarity search - Function
Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / Ubiquitin fusion degradation protein UFD1 / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain ...Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / Ubiquitin fusion degradation protein UFD1 / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ubiquitin recognition factor in ER-associated degradation protein 1 / Transitional endoplasmic reticulum ATPase / Ubiquitin recognition factor in ER-associated degradation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLe, L.T.M. / Yang, J.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2014R1A2A2A01006834 Korea, Republic Of
CitationJournal: PLoS ONE / Year: 2016
Title: Structural Details of Ufd1 Binding to p97 and Their Functional Implications in ER-Associated Degradation
Authors: Le, L.T.M. / Kang, W. / Kim, J.Y. / Le, O.T.T. / Lee, S.Y. / Yang, J.K.
History
DepositionMay 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
B: Peptide from Ubiquitin fusion degradation protein 1 homolog


Theoretical massNumber of molelcules
Total (without water)20,9392
Polymers20,9392
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-9 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.270, 107.270, 44.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 19725.830 Da / Num. of mol.: 1 / Fragment: UNP residues 21-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli (E. coli) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein/peptide Peptide from Ubiquitin fusion degradation protein 1 homolog /


Mass: 1213.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UFD1L / Production host: Escherichia coli (E. coli) / References: UniProt: C9JNP9, UniProt: Q92890*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 21%(w/v) PEG 8000, 2.9mM n-nonyl-beta-thiomaltoside, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 25310 / % possible obs: 97 % / Redundancy: 10.7 % / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→26.83 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.256 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 1315 4.9 %RANDOM
Rwork0.15797 ---
obs0.16 25310 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.623 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.09 Å20 Å2
2--0.09 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.55→26.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 0 274 1740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191489
X-RAY DIFFRACTIONr_bond_other_d0.0010.021479
X-RAY DIFFRACTIONr_angle_refined_deg2.2351.9882009
X-RAY DIFFRACTIONr_angle_other_deg1.0133398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1735183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37622.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47515273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7491518
X-RAY DIFFRACTIONr_chiral_restr0.150.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02331
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 82 -
Rwork0.168 1506 -
obs--77.65 %

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