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- PDB-5epp: Structural Insights into the Interaction of p97 N-terminus Domain... -

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Basic information

Entry
Database: PDB / ID: 5epp
TitleStructural Insights into the Interaction of p97 N-terminus Domain and VBM Motif in Rhomboid Protease, RHBDL4
Components
  • Rhomboid-related protein 4
  • Transitional endoplasmic reticulum ATPase
KeywordsHYDROLASE / BETA-BARREL / ATPASE / RHBDL4 VBM motif / UBIQUITIN
Function / homology
Function and homology information


membrane protein proteolysis involved in retrograde protein transport, ER to cytosol / positive regulation of secretion / rhomboid protease / spermatid differentiation / membrane protein proteolysis / endoplasmic reticulum quality control compartment / membrane protein intracellular domain proteolysis / positive regulation of protein processing / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex ...membrane protein proteolysis involved in retrograde protein transport, ER to cytosol / positive regulation of secretion / rhomboid protease / spermatid differentiation / membrane protein proteolysis / endoplasmic reticulum quality control compartment / membrane protein intracellular domain proteolysis / positive regulation of protein processing / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cytoplasmic ubiquitin ligase complex / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / cytoplasm protein quality control / positive regulation of oxidative phosphorylation / aggresome assembly / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / cellular response to misfolded protein / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / NAD+ metabolic process / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / ATPase complex / ubiquitin-specific protease binding / regulation of synapse organization / ciliary transition zone / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / RHOH GTPase cycle / intracellular membrane-bounded organelle / MHC class I protein binding / cellular response to unfolded protein / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / interstrand cross-link repair / ATP metabolic process / translesion synthesis / Attachment and Entry / Protein methylation / endoplasmic reticulum unfolded protein response / ERAD pathway / negative regulation of protein localization to chromatin / proteasomal protein catabolic process / lipid droplet / ciliary tip / post-translational protein modification / proteasome complex / viral genome replication / Josephin domain DUBs / macroautophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of smoothened signaling pathway / establishment of protein localization / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / ABC-family proteins mediated transport / autophagy / mitochondrial membrane / cytoplasmic stress granule / Aggrephagy / positive regulation of protein catabolic process / azurophil granule lumen / cellular response to UV / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / positive regulation of canonical Wnt signaling pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / secretory granule lumen / protein phosphatase binding / endopeptidase activity / regulation of apoptotic process / ficolin-1-rich granule lumen / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / Attachment and Entry
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #10 / Peptidase S54, rhomboid domain / Rhomboid domain / Rhomboid-like superfamily / 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 / : ...Vcp-like ATPase; Chain A, domain 2 - #10 / Peptidase S54, rhomboid domain / Rhomboid domain / Rhomboid-like superfamily / 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. / 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
Transitional endoplasmic reticulum ATPase / Rhomboid-related protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsLim, J.J. / Lee, Y. / Ly, T.T. / Kang, J.Y. / Lee, J.-G. / An, J.Y. / Youn, H.-S. / Park, K.R. / Kim, T.G. / Yang, J.K. ...Lim, J.J. / Lee, Y. / Ly, T.T. / Kang, J.Y. / Lee, J.-G. / An, J.Y. / Youn, H.-S. / Park, K.R. / Kim, T.G. / Yang, J.K. / Jun, Y. / Eom, S.H.
CitationJournal: Biochem.J. / Year: 2016
Title: Structural insights into the interaction of p97 N-terminus domain and VBM in rhomboid protease, RHBDL4.
Authors: Lim, J.J. / Lee, Y. / Ly, T.T. / Kang, J.Y. / Lee, J.G. / An, J.Y. / Youn, H.S. / Park, K.R. / Kim, T.G. / Yang, J.K. / Jun, Y. / Eom, S.H.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references / Structure summary
Revision 1.2Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
B: Rhomboid-related protein 4


Theoretical massNumber of molelcules
Total (without water)22,8092
Polymers22,8092
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint0 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.999, 96.999, 50.902
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: 20859.961 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-199
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 Rhomboid-related protein 4 / RRP4 / Rhomboid domain-containing protein 1 / Rhomboid-like protein 4


Mass: 1949.179 Da / Num. of mol.: 1 / Fragment: VBM motif (RESIDUES 300-314) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8TEB9, rhomboid protease
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.1 M Bis-Tris Propane pH 6.5, 0.2 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 22279 / % possible obs: 99.4 % / Redundancy: 5.8 % / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Cootmodel building
HKL-2000data processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ7

3qq7


Resolution: 1.88→42.002 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 1143 5.13 %
Rwork0.1768 --
obs0.1784 22279 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→42.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 0 127 1617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071514
X-RAY DIFFRACTIONf_angle_d0.9892043
X-RAY DIFFRACTIONf_dihedral_angle_d20.598952
X-RAY DIFFRACTIONf_chiral_restr0.065230
X-RAY DIFFRACTIONf_plane_restr0.009270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8797-1.96520.31841300.23532620X-RAY DIFFRACTION99
1.9652-2.06880.24681410.19132634X-RAY DIFFRACTION99
2.0688-2.19850.19531390.18222625X-RAY DIFFRACTION99
2.1985-2.36820.20971560.18032601X-RAY DIFFRACTION99
2.3682-2.60650.22561470.18362638X-RAY DIFFRACTION100
2.6065-2.98350.24181620.19192631X-RAY DIFFRACTION100
2.9835-3.75860.22381310.17632670X-RAY DIFFRACTION100
3.7586-42.01230.14891370.14822717X-RAY DIFFRACTION99

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