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- PDB-3qq8: Crystal structure of p97-N in complex with FAF1-UBX -

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Basic information

Entry
Database: PDB / ID: 3qq8
TitleCrystal structure of p97-N in complex with FAF1-UBX
Components
  • FAS-associated factor 1
  • Transitional endoplasmic reticulum ATPase
KeywordsTRANSPORT PROTEIN/APOPTOSIS / beta-barrel / beta-grasp / ATPase / ubiquitin / phosphorylation / TRANSPORT PROTEIN-APOPTOSIS complex
Function / homology
Function and homology information


ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / cytoplasmic sequestering of NF-kappaB / CD95 death-inducing signaling complex / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control / endosome to lysosome transport via multivesicular body sorting pathway ...ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / cytoplasmic sequestering of NF-kappaB / CD95 death-inducing signaling complex / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / protein-DNA covalent cross-linking repair / positive regulation of protein K63-linked deubiquitination / protein kinase regulator activity / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / aggresome assembly / NADH metabolic process / vesicle-fusing ATPase / cellular response to misfolded protein / stress granule disassembly / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / retrograde protein transport, ER to cytosol / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / regulation of synapse organization / positive regulation of ATP biosynthetic process / ATPase complex / regulation of protein catabolic process / ubiquitin-specific protease binding / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / NF-kappaB binding / autophagosome maturation / HSF1 activation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / regulation of cell adhesion / translesion synthesis / proteasomal protein catabolic process / Protein methylation / interstrand cross-link repair / ATP metabolic process / negative regulation of smoothened signaling pathway / endoplasmic reticulum unfolded protein response / ERAD pathway / heat shock protein binding / Attachment and Entry / proteasome complex / viral genome replication / lipid droplet / Josephin domain DUBs / positive regulation of DNA replication / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / positive regulation of protein-containing complex assembly / ADP binding / Translesion Synthesis by POLH / establishment of protein localization / ABC-family proteins mediated transport / : / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / positive regulation of canonical Wnt signaling pathway / Ovarian tumor domain proteases / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / nuclear envelope / site of double-strand break / Neddylation / cellular response to heat / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / positive regulation of apoptotic process / protein domain specific binding
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 / molecular replacement / Resolution: 2 Å
AuthorsHaenzelmann, P. / Schindelin, H.
CitationJournal: Structure / Year: 2011
Title: Hierarchical Binding of Cofactors to the AAA ATPase p97.
Authors: Hanzelmann, P. / Buchberger, A. / Schindelin, H.
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,8873
Polymers30,8512
Non-polymers351
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-15 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.080, 88.080, 66.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 20904.055 Da / Num. of mol.: 1 / Fragment: unp residues 2-187
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: 9947.401 Da / Num. of mol.: 1 / Fragment: unp residues 568-650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAF1, UBXD12, UBXN3A, CGI-03 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNN5
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16-20% PEG MME 2000, 0.2 M Trimethyl-N-oxide, 0.1 M Tris, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→76.279 Å / Num. all: 19757 / Num. obs: 19757 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2-2.117.70.5341.40.534197.8
2.11-2.247.80.3532.20.353197.7
2.24-2.397.70.2442.90.244198.1
2.39-2.587.80.1764.30.176198.4
2.58-2.837.70.1235.90.123198.8
2.83-3.167.70.0759.60.075198.9
3.16-3.657.70.05311.90.053199.2
3.65-4.477.60.04413.50.044199.3
4.47-6.327.60.04113.10.041199.6
6.32-38.147.30.03614.60.036199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASERphasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1S3S, 1H8C

1s3s

1h8c


Resolution: 2→33.135 Å / Occupancy max: 1 / Occupancy min: 0.16 / SU ML: 0.21 / σ(F): 0 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 987 5.09 %
Rwork0.1664 --
obs0.1686 19395 96.76 %
all-19394 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.264 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1141 Å2-0 Å2-0 Å2
2--1.1141 Å20 Å2
3----2.2281 Å2
Refinement stepCycle: LAST / Resolution: 2→33.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 1 146 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072160
X-RAY DIFFRACTIONf_angle_d1.1032931
X-RAY DIFFRACTIONf_dihedral_angle_d14.623844
X-RAY DIFFRACTIONf_chiral_restr0.073335
X-RAY DIFFRACTIONf_plane_restr0.005380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10550.25931490.18952479X-RAY DIFFRACTION93
2.1055-2.23740.23711260.1852553X-RAY DIFFRACTION95
2.2374-2.41010.211410.17592607X-RAY DIFFRACTION96
2.4101-2.65250.24861390.17982640X-RAY DIFFRACTION98
2.6525-3.03610.21791720.17822642X-RAY DIFFRACTION98
3.0361-3.82430.20531180.15592734X-RAY DIFFRACTION99
3.8243-33.13930.18371420.15472753X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.65730.3175-0.19531.5952-0.80380.41520.5905-0.06240.7552-0.4518-0.47410.53340.25750.3928-0.02760.23730.1690.04520.58480.10520.412451.7302-32.3075-8.8078
22.84330.6476-0.1972.6228-0.84432.58740.0493-0.2038-0.00080.0376-0.1186-0.1807-0.05470.11590.05840.1075-0.0480.00870.1692-0.00640.125532.7648-29.1652-6.2741
31.7362-0.07011.87311.515-0.41192.60530.1597-0.0811-0.1931-0.13730.10370.04260.4334-0.3313-0.24280.1973-0.0819-0.01950.19770.04030.155418.2359-44.2467-11.0843
42.7831.50230.48142.22991.65962.9011-0.1268-0.13860.3985-0.2373-0.1080.5605-0.5596-0.12290.21440.26770.0212-0.02810.2057-0.00110.305415.9499-19.9791-22.8188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:20)
2X-RAY DIFFRACTION2(chain A and resid 21:108)
3X-RAY DIFFRACTION3(chain A and resid 109:186)
4X-RAY DIFFRACTION4(chain B and resid 570:649)

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