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- PDB-3cf0: Structure of D2 subdomain of P97/VCP in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 3cf0
TitleStructure of D2 subdomain of P97/VCP in complex with ADP
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsTRANSPORT PROTEIN / AAA / P97/VCP / ERAD / CDC48 / ATP-binding / Lipid-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Transport / Ubl conjugation pathway
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 / VCP-NSFL1C complex / KEAP1-NFE2L2 pathway / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / protein-DNA covalent cross-linking repair / cytoplasm protein quality control / positive regulation of protein K63-linked deubiquitination / positive regulation of oxidative phosphorylation / : / aggresome assembly / deubiquitinase activator activity / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / cellular response to misfolded protein / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / stress granule disassembly / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / translesion synthesis / interstrand cross-link repair / proteasomal protein catabolic process / ATP metabolic 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 / cytosol / cytoplasm
Similarity search - Function
Vps4 C terminal oligomerisation domain / AAA ATPase, CDC48 family / Helicase, Ruva Protein; domain 3 - #60 / 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 ...Vps4 C terminal oligomerisation domain / AAA ATPase, CDC48 family / Helicase, Ruva Protein; domain 3 - #60 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / 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 Å
AuthorsDavies, J.M. / Brunger, A.T. / Weis, W.I.
CitationJournal: 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.
History
DepositionMar 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 21, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
G: Transitional endoplasmic reticulum ATPase
H: Transitional endoplasmic reticulum ATPase
I: Transitional endoplasmic reticulum ATPase
J: Transitional endoplasmic reticulum ATPase
K: Transitional endoplasmic reticulum ATPase
L: Transitional endoplasmic reticulum ATPase
M: Transitional endoplasmic reticulum ATPase
N: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)479,17528
Polymers473,19414
Non-polymers5,98114
Water00
1
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
G: Transitional endoplasmic reticulum ATPase
H: Transitional endoplasmic reticulum ATPase
M: Transitional endoplasmic reticulum ATPase
N: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,58814
Polymers236,5977
Non-polymers2,9907
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22870 Å2
ΔGint-119.4 kcal/mol
Surface area84390 Å2
MethodPISA
2
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
I: Transitional endoplasmic reticulum ATPase
J: Transitional endoplasmic reticulum ATPase
K: Transitional endoplasmic reticulum ATPase
L: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,58814
Polymers236,5977
Non-polymers2,9907
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23270 Å2
ΔGint-122.6 kcal/mol
Surface area84030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.317, 167.223, 209.465
Angle α, β, γ (deg.)90.00, 112.29, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ADP / End label comp-ID: ADP / Refine code: 1 / Auth seq-ID: 463 - 900 / Label seq-ID: 1

Dom-IDAuth asym-IDLabel asym-ID
1AA - O
2BB - P
3CC - Q
4DD - R
5EE - S
6FF - T
7GG - U
8HH - V
9II - W
10JJ - X
11KK - Y
12LL - Z
13MM - AA
14NN - BA

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Components

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


Mass: 33799.594 Da / Num. of mol.: 14 / Fragment: D2 subdomain OF P97/VCP (UNP residues 463-763)
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.: 14 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Nonpolymer detailsSOME OF THE C-N BONDS OF THE ADP MOLECULES ARE SHORTER THAN THE STANDARD VALUES.

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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: 2.97 Å3/Da / Density % sol: 58.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 100 mM Tris, pH 7.1, 2.45 M ammonium sulfate, and 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 108870 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.5
Reflection shellResolution: 3→3.078 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.905 / SU B: 50.172 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 9759 9.2 %SHELLS
Rwork0.243 ---
obs0.244 96556 98.1 %-
all-96556 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: MASK
Displacement parametersBiso mean: 89.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-1.35 Å2
2---0.45 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30786 0 378 0 31164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8331.519956
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.242231570
X-RAY DIFFRACTIONr_scbond_it7.333312926
X-RAY DIFFRACTIONr_scangle_it12.9684.511298
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2228 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.060.05
2Btight positional0.060.05
3Ctight positional0.070.05
4Dtight positional0.060.05
5Etight positional0.070.05
6Ftight positional0.060.05
7Gtight positional0.070.05
8Htight positional0.060.05
9Itight positional0.060.05
10Jtight positional0.060.05
11Ktight positional0.060.05
12Ltight positional0.060.05
13Mtight positional0.070.05
14Ntight positional0.060.05
1Atight thermal0.140.5
2Btight thermal0.150.5
3Ctight thermal0.140.5
4Dtight thermal0.130.5
5Etight thermal0.170.5
6Ftight thermal0.140.5
7Gtight thermal0.130.5
8Htight thermal0.150.5
9Itight thermal0.130.5
10Jtight thermal0.130.5
11Ktight thermal0.130.5
12Ltight thermal0.160.5
13Mtight thermal0.160.5
14Ntight thermal0.140.5
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 722 -
Rwork0.34 6346 -
obs--99.3 %
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)
10.02110.19040.02081.71750.18750.0205-0.0938-0.39750.35470.02590.01180.40390.0697-0.35920.082-0.04130.2449-0.04740.4196-0.26580.2757-35.615715.701521.3127
20.1383-0.2502-0.27920.99541.56262.62380.03240.11290.11170.0656-0.0725-0.2837-0.18760.00110.04010.04820.1113-0.1694-0.05390.00770.121-22.710337.0451-3.0395
30.2440.3689-0.17640.9128-0.34440.1874-0.1285-0.08520.16150.0732-0.0672-0.0544-0.34710.14040.19570.0997-0.0544-0.1110.10420.0806-0.0673-6.732829.0426-32.1623
40.626-0.07730.3284.69832.33621.6836-0.20630.30710.3243-0.12310.4163-0.5347-0.05910.4604-0.21-0.08180.08480.09730.38150.11750.1967-9.96820.247-122.6746
50.1112-0.11160.15840.9542-0.18841.3579-0.1081-0.0796-0.0399-0.23280.03520.04680.29690.33160.0728-0.1309-0.1477-0.0448-0.07190.0951-0.0227-16.742230.545-109.0426
60.89161.1335-0.2751.4411-0.35341.13270.2476-0.53090.22810.2759-0.1050.3961-0.07170.0608-0.1426-0.0747-0.09650.00420.1466-0.20620.2042-32.008938.005-78.9834
70.55810.6351-0.38081.034-0.72981.77360.0741-0.0584-0.077-0.3327-0.11190.06250.31060.38770.03770.09950.14-0.02670.1409-0.0113-0.174-0.5129-2.5154-44.7498
82.7163-1.2944-0.92492.4089-0.4752.8570.003-0.2744-0.15850.03790.3506-0.03550.5125-0.2179-0.35360.1558-0.0096-0.1536-0.1079-0.0261-0.0026-7.4938-33.0671-31.2014
90.8727-1.39650.44343.38020.08680.77870.0552-0.05970.02870.0677-0.0107-0.26340.0007-0.1924-0.0446-0.12430.0286-0.02250.0434-0.0291-0.1956-44.037815.8549-55.6106
101.548-1.2969-0.94571.6220.67451.85620.0603-0.2158-0.28980.23440.16690.0530.5166-0.0763-0.22720.0882-0.1202-0.15070.07630.1866-0.0475-43.7553-18.5448-55.9719
110.02390.14820.00350.99730.23660.58140.1424-0.1096-0.01590.02630.09560.16430.3520.1549-0.2380.1140.0937-0.20070.0195-0.0250.3112-31.646-39.5921-79.6947
121.24590.6224-0.03051.80110.21510.03630.17070.328-0.0807-0.1494-0.28380.0866-0.0404-0.06050.1131-0.08060.1733-0.07080.0935-0.13880.074-16.3159-31.0093-109.5045
130.7871-0.2875-0.13743.4567-0.74850.84520.1802-0.01560.0946-0.0457-0.0856-0.2630.0976-0.0779-0.0947-0.0894-0.1992-0.0796-0.00230.13960.0046-23.1012-40.3294-2.0196
140.9445-1.41351.48014.7704-2.91352.5030.2911-0.00230.15610.4001-0.21230.4969-0.45130.0561-0.0788-0.1125-0.21080.13260.3770.0252-0.0357-35.9568-18.076821.3017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A463 - 763
2X-RAY DIFFRACTION2B463 - 763
3X-RAY DIFFRACTION3C463 - 763
4X-RAY DIFFRACTION4D463 - 763
5X-RAY DIFFRACTION5E463 - 763
6X-RAY DIFFRACTION6F463 - 763
7X-RAY DIFFRACTION7G463 - 763
8X-RAY DIFFRACTION8H463 - 763
9X-RAY DIFFRACTION9I463 - 763
10X-RAY DIFFRACTION10J463 - 763
11X-RAY DIFFRACTION11K463 - 763
12X-RAY DIFFRACTION12L463 - 763
13X-RAY DIFFRACTION13M463 - 763
14X-RAY DIFFRACTION14N463 - 763

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