[English] 日本語
Yorodumi
- PDB-3cf2: Structure of P97/vcp in complex with ADP/AMP-PNP -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / cytoplasm protein quality control / Derlin-1 retrotranslocation complex / protein-DNA covalent cross-linking repair / positive regulation of protein K63-linked deubiquitination / positive regulation of oxidative phosphorylation / deubiquitinase activator activity / NADH metabolic process / aggresome assembly / 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 / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / stress granule disassembly / regulation of synapse organization / positive regulation of ATP biosynthetic process / ATPase complex / ubiquitin-specific protease binding / 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 / proteasomal protein catabolic process / ATP metabolic process / negative regulation of smoothened signaling pathway / ERAD pathway / lipid droplet / Neutrophil degranulation / proteasome complex / viral genome replication / positive regulation of protein-containing complex assembly / macroautophagy / 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 / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / protein domain specific binding / DNA repair / ubiquitin protein ligase binding / lipid binding / synapse / 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
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 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Helicase, Ruva Protein; domain 3 - #60 / 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 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / 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 / Helix non-globular / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Special / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more