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- PDB-3cf2: Structure of P97/vcp in complex with ADP/AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 3cf2
TitleStructure of P97/vcp in complex with ADP/AMP-PNP
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsTRANSPORT PROTEIN / AAA / CDC48 / ERAD / ATPASE
Function / homology
Function and homology information


RHOH GTPase cycle / HSF1 activation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Protein methylation / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / ABC-family proteins mediated transport / Neddylation ...RHOH GTPase cycle / HSF1 activation / Translesion Synthesis by POLH / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Protein methylation / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / ABC-family proteins mediated transport / Neddylation / flavin adenine dinucleotide catabolic process / KEAP1-NFE2L2 pathway / 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-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 / 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 / retrograde protein transport, ER to cytosol / stress granule disassembly / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / MHC class I protein binding / polyubiquitin modification-dependent protein binding / autophagosome maturation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / ATP metabolic process / proteasomal protein catabolic process / ERAD pathway / lipid droplet / Neutrophil degranulation / proteasome complex / viral genome replication / negative regulation of smoothened signaling pathway / macroautophagy / positive regulation of protein-containing complex assembly / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / autophagy / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / myelin sheath / site of double-strand break / cellular response to heat / ubiquitin-dependent protein catabolic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / ciliary basal body / protein domain specific binding / DNA repair / synapse / lipid binding / ubiquitin protein ligase binding / DNA damage response / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / protein-containing complex / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Arc Repressor Mutant, subunit A - #150 / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Arc Repressor Mutant, subunit A / Vps4 C terminal oligomerisation domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain ...Arc Repressor Mutant, subunit A - #150 / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Arc Repressor Mutant, subunit A / Vps4 C terminal oligomerisation domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Helicase, Ruva Protein; domain 3 - #60 / 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. / Helicase, Ruva Protein; domain 3 / Helix non-globular / Special / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsDavies, J.M. / Delabarre, B. / Brunger, A.T. / Weis, W.I.
Citation
Journal: Structure / Year: 2008
Title: Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change.
Authors: Davies, J.M. / Brunger, A.T. / Weis, W.I.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2003
Title: Complete Structure of P97/Valosin-Containing Protein Reveals Communication between Nucleotide Domains
Authors: DelaBarre, B. / Brunger, A.T.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Nucleotide Dependent Motion and Mechanism of Action of P97/Vcp
Authors: DelaBarre, B. / Brunger, A.T.
History
DepositionMar 1, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionApr 22, 2008ID: 1YPW
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Other
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,48112
Polymers357,7474
Non-polymers3,7348
Water00
1
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
hetero molecules

A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
hetero molecules

A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)542,22118
Polymers536,6216
Non-polymers5,60012
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
Buried area48840 Å2
ΔGint-143 kcal/mol
Surface area168700 Å2
MethodPISA
2
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
hetero molecules

C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
hetero molecules

C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)542,22118
Polymers536,6216
Non-polymers5,60012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area48800 Å2
ΔGint-145.3 kcal/mol
Surface area168890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.900, 144.900, 164.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.49775, -0.86732, 0.00264), (0.8673, 0.49775, 0.00496), (-0.00562, -0.00018, 0.99998)0.32735, 0.09298, 0.51914
3given(0.49986, 0.86611, 3.0E-5), (0.86611, -0.49986, -4.0E-5), (-2.0E-5, 4.0E-5, -1)0.01307, -0.00354, -0.0864
4given(0.99999, -0.00239, 0.00489), (-0.00238, -1, -0.0014), (0.00489, 0.00139, -0.99999)0.20857, 0.14125, -0.49491

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Components

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


Mass: 89436.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vcp / Production host: Escherichia coli (E. coli) / References: UniProt: Q01853
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*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: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: AMMONIUM FLUORIDE, CITRATE BUFFER, SODIUM DIHYDROGEN PHOSPHATE, PEG 400, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 177 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.0316
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0316 Å / Relative weight: 1
ReflectionResolution: 3.1→23 Å / Num. obs: 60820 / % possible obs: 85 % / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 8.8

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Processing

Software
NameClassification
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→23 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5634593.88 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED OTHER REFINEMENT REMARKS: THE DIFFRACTION WAS ANISOTROPIC - IT EXTENDED TO 3.1 A (AS IN FILE) IN THE BEST DIRECTION BUT REFINEMENT WAS ONLY DONE TO 3.5 A (THE WORST DIRECTION).
RfactorNum. reflection% reflectionSelection details
Rfree0.285 4798 5 %RANDOM
Rwork0.271 ---
obs0.271 60820 99.6 %-
all-60820 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.1 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 147.8 Å2
Baniso -1Baniso -2Baniso -3
1--41.08 Å20 Å20 Å2
2---41.08 Å20 Å2
3---82.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a1.15 Å1.09 Å
Refinement stepCycle: LAST / Resolution: 3.5→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20685 0 232 0 20917
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.33
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.456 788 4.8 %
Rwork0.429 15487 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP_CNS.PARADP_CNS.TOP
X-RAY DIFFRACTION3AXP_CNS.PAR

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