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- PDB-3qc8: Crystal Structure of FAF1 UBX Domain In Complex with p97/VCP N Do... -

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Basic information

Entry
Database: PDB / ID: 3qc8
TitleCrystal 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
Components
  • FAS-associated factor 1
  • Transitional endoplasmic reticulum ATPase
KeywordsPROTEIN BINDING / UBX domain / FAF1 / p97 / VCP
Function / homology
Function and homology information


Fas signaling pathway / ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / BAT3 complex binding ...Fas signaling pathway / ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / BAT3 complex binding / cellular response to arsenite ion / protein kinase regulator activity / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / cytoplasm protein quality control / positive regulation of oxidative phosphorylation / : / aggresome assembly / deubiquitinase activator activity / mitotic spindle disassembly / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / regulation of protein catabolic process / positive regulation of ATP biosynthetic process / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / NF-kappaB binding / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / HSF1 activation / translesion synthesis / regulation of cell adhesion / interstrand cross-link repair / ATP metabolic process / endoplasmic reticulum unfolded protein response / Protein methylation / proteasomal protein catabolic process / Attachment and Entry / heat shock protein binding / ERAD pathway / lipid droplet / negative regulation of canonical NF-kappaB signal transduction / proteasome complex / viral genome replication / Josephin domain DUBs / positive regulation of DNA replication / ubiquitin binding / negative regulation of smoothened signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / establishment of protein localization / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / positive regulation of non-canonical NF-kappaB signal transduction / Translesion Synthesis by POLH / ADP binding / ABC-family proteins mediated transport / autophagy / cytoplasmic stress granule / Aggrephagy / positive regulation of protein catabolic process / azurophil granule lumen / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / nuclear envelope / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / cellular response to heat / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / secretory granule lumen / protein phosphatase binding / regulation of apoptotic process / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / Attachment and Entry / protein ubiquitination / ciliary basal body / positive regulation of apoptotic process
Similarity search - Function
FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / Vcp-like ATPase; Chain A, domain 2 - #10 / Domain present in ubiquitin-regulatory proteins / UBX domain ...FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / Vcp-like ATPase; Chain A, domain 2 - #10 / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / AAA ATPase, CDC48 family / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ubiquitin-like (UB roll) / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily / 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
Transitional endoplasmic reticulum ATPase / FAS-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, K.H. / Kang, W. / Suh, S.W. / Yang, J.K.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of FAF1 UBX domain in complex with p97/VCP N domain reveals a conformational change in the conserved FcisP touch-turn motif of UBX domain
Authors: Kim, K.H. / Kang, W. / Suh, S.W. / Yang, J.K.
History
DepositionJan 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
B: FAS-associated factor 1


Theoretical massNumber of molelcules
Total (without water)30,1222
Polymers30,1222
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-4 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.070, 72.740, 130.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 20286.295 Da / Num. of mol.: 1 / Fragment: N domain
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
#2: Protein FAS-associated factor 1 / hFAF1 / UBX domain-containing protein 12 / UBX domain-containing protein 3A


Mass: 9835.250 Da / Num. of mol.: 1 / Fragment: UBX domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNN5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25%(w/v) PEG3350, 0.2M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 14425 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.32 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.34 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.969 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24978 724 5 %RANDOM
Rwork0.21645 ---
all0.21813 14425 --
obs0.21813 13670 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.953 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 0 130 2148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222057
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9942780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9485248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06923.33396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96415382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5691521
X-RAY DIFFRACTIONr_chiral_restr0.1180.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211542
X-RAY DIFFRACTIONr_mcbond_it1.481.51255
X-RAY DIFFRACTIONr_mcangle_it2.59622054
X-RAY DIFFRACTIONr_scbond_it3.53802
X-RAY DIFFRACTIONr_scangle_it5.4824.5726
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 49 -
Rwork0.353 979 -
obs--100 %

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