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- PDB-1r7r: The crystal structure of murine p97/VCP at 3.6A -

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Basic information

Entry
Database: PDB / ID: 1r7r
TitleThe crystal structure of murine p97/VCP at 3.6A
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsTRANSPORT PROTEIN / p97 / VCP / AAA / CDC48
Function / homology
Function and homology information


RHOH GTPase cycle / HSF1 activation / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport ...RHOH GTPase cycle / HSF1 activation / Protein methylation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport / Neddylation / 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 / positive regulation of ubiquitin-dependent protein catabolic process / 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 / NADH metabolic process / regulation of protein localization to chromatin / vesicle-fusing ATPase / : / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / ERAD pathway / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / autophagosome maturation / polyubiquitin modification-dependent protein binding / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / interstrand cross-link repair / negative regulation of smoothened signaling pathway / : / ATP metabolic process / Neutrophil degranulation / lipid droplet / proteasome complex / viral genome replication / proteasomal protein catabolic process / ADP binding / positive regulation of protein-containing complex assembly / macroautophagy / autophagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / myelin sheath / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / protein ubiquitination / protein domain specific binding / DNA repair / synapse / lipid binding / glutamatergic synapse / DNA damage response / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Vps4 C terminal oligomerisation domain / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / 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 ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Vps4 C terminal oligomerisation domain / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / 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. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsHuyton, T. / Pye, V.E. / Briggs, L.C. / Flynn, T.C. / Beuron, F. / Kondo, H. / Ma, J. / Zhang, X. / Freemont, P.S.
CitationJournal: J.Struct.Biol. / Year: 2003
Title: The crystal structure of murine p97/VCP at 3.6A
Authors: Huyton, T. / Pye, V.E. / Briggs, L.C. / Flynn, T.C. / Beuron, F. / Kondo, H. / Ma, J. / Zhang, X. / Freemont, P.S.
History
DepositionOct 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 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
Remark 999SEQUENCE This model consists of residues 17-464 (ND1 domains) and a poly-alanine model for residues ...SEQUENCE This model consists of residues 17-464 (ND1 domains) and a poly-alanine model for residues 465-735 (D2 domain) due to the less well-defined density for the D2 domain which can be ascribed to the inherent flexibility of D2. The following residues are missing in the coordinates as they could not be seen in the electron density: 337-338, 610-615, 665-668, 703-726, 736-806.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0632
Polymers90,6361
Non-polymers4271
Water0
1
A: Transitional endoplasmic reticulum ATPase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)546,38012
Polymers543,8176
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation4_755-x+2,-y,z1
crystal symmetry operation5_665y+1,-x+y+1,z1
crystal symmetry operation6_545x-y,x-1,z1
Buried area29300 Å2
ΔGint-121 kcal/mol
Surface area188080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)145.200, 145.200, 167.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the crystallographic 6-fold axis.

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Components

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


Mass: 90636.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: VCP / Plasmid: pET22b (Novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q01853
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.0-1.4M ammonium phosphate (monobasic), 1-5% PEG 400, 2mM BMe, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17 mg/mlprotein1drop
225 mMHEPES1drop
3250 mM1dropKCl
42 mg/mlbeta-mercaptoethanol1drop
51 mM1dropMgCl2
610 mMAMP-PNP1dropor 2'-BrAMP-PNP
71.0-1.4 Mammonium phosphate1reservoir
81-5 %PEG4001reservoir
92 mMbeta-mercaptoethanol1reservoir
100.1 sodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9292 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2002 / Details: Toroidal Zerodur mirror
RadiationMonochromator: Si111 or Si311 crystals, LN2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9292 Å / Relative weight: 1
ReflectionResolution: 3.6→25 Å / Num. all: 12554 / Num. obs: 12461 / % possible obs: 99.25 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.66 % / Biso Wilson estimate: 100 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.4
Reflection shellResolution: 3.6→3.66 Å / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1858 / % possible all: 99.8
Reflection
*PLUS
% possible obs: 99.8 % / Num. measured all: 133872
Reflection shell
*PLUS
Highest resolution: 3.6 Å / % possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
ProDCdata collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1E32

1e32


Resolution: 3.6→19.99 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 6776409.1 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.358 1266 10.3 %RANDOM
Rwork0.327 ---
all0.327 ---
obs0.327 12312 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.7476 Å2 / ksol: 0.194102 e/Å3
Displacement parametersBiso mean: 104.4 Å2
Baniso -1Baniso -2Baniso -3
1--34.27 Å2-11.27 Å20 Å2
2---34.27 Å20 Å2
3---68.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 0 27 0 4680
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.6→3.82 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 184 9.9 %
Rwork0.342 1674 -
obs-1858 90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP.PARAMADP.TOP
Refinement
*PLUS
Highest resolution: 3.6 Å / Lowest resolution: 25 Å / Rfactor Rwork: 0.329
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.95
LS refinement shell
*PLUS
Highest resolution: 3.6 Å / Lowest resolution: 3.8 Å / Rfactor Rwork: 0.341

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