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- PDB-8hrz: Crystal structure of the p97-N/D1 hexamer in complex with six p47... -

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Basic information

Entry
Database: PDB / ID: 8hrz
TitleCrystal structure of the p97-N/D1 hexamer in complex with six p47-UBX domains
Components
  • NSFL1 cofactor p47
  • Transitional endoplasmic reticulum ATPase
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / positive regulation of Lys63-specific deubiquitinase activity / Golgi stack / 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 ...negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / positive regulation of Lys63-specific deubiquitinase activity / Golgi stack / 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 / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / MHC class I protein binding / Golgi organization / establishment of mitotic spindle orientation / RHOH GTPase cycle / autophagosome maturation / autophagosome assembly / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / Protein methylation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ERAD pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / lipid droplet / viral genome replication / proteasome complex / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / Hh mutants are degraded by ERAD / macroautophagy / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / ADP binding / autophagy / cytoplasmic stress granule / Aggrephagy / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / chromosome / Neddylation / site of double-strand break / cellular response to heat / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / Attachment and Entry / membrane fusion / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / centrosome / glutamatergic synapse / lipid binding
Similarity search - Function
SEP domain / NSFL1 cofactor p47, SEP domain superfamily / SEP domain / SEP domain profile. / Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain ...SEP domain / NSFL1 cofactor p47, SEP domain superfamily / SEP domain / SEP domain profile. / Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / 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 / UBA-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 / Ubiquitin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Transitional endoplasmic reticulum ATPase / NSFL1 cofactor p47
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNguyen, T.Q. / Kang, W.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A6A1A10044154 Korea, Republic Of
National Research Foundation (NRF, Korea)2022R1C1C1004221 Korea, Republic Of
CitationJournal: J. Korean Chem. Soc. / Year: 2024
Title: Crystal structure of the p97-N/D1 hexmaer in complex with six p47-UBX domains
Authors: Nguyen, T.Q. / Kang, W.
History
DepositionDec 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: NSFL1 cofactor p47
N: NSFL1 cofactor p47
O: NSFL1 cofactor p47
P: NSFL1 cofactor p47
Q: NSFL1 cofactor p47
R: NSFL1 cofactor p47
S: NSFL1 cofactor p47
T: NSFL1 cofactor p47
U: NSFL1 cofactor p47
V: NSFL1 cofactor p47
W: NSFL1 cofactor p47
X: NSFL1 cofactor p47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)706,87636
Polymers701,75024
Non-polymers5,12612
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.780, 178.850, 171.330
Angle α, β, γ (deg.)90.000, 119.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 48904.109 Da / Num. of mol.: 12 / Mutation: E294A, K295A
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
NSFL1 cofactor p47 / UBX domain-containing protein 2C / p97 cofactor p47


Mass: 9575.035 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSFL1C, UBXN2C / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNZ2
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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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: 3.25 Å3/Da / Density % sol: 62.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG 3350, 0.2M ammonium citrate tribasic (pH 7), 0.01M hexamine cobalt (III) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40.013 Å / Num. obs: 242685 / % possible obs: 99.3 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rpim(I) all: 0.038 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 11034 / CC1/2: 0.53 / Rpim(I) all: 0.54

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40.013 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: FREE R-VALUE / ESU R: 0.701 / ESU R Free: 0.325
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2558 11938 4.92 %
Rwork0.2132 230718 -
all0.215 --
obs-242656 99.301 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 71.106 Å2
Baniso -1Baniso -2Baniso -3
1--0.821 Å20 Å20.114 Å2
2--4.489 Å20 Å2
3----2.294 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48760 0 324 0 49084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01249828
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.64867408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.6756216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.7225452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.467109046
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.777102273
X-RAY DIFFRACTIONr_chiral_restr0.1260.27860
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0236516
X-RAY DIFFRACTIONr_nbd_refined0.2520.221634
X-RAY DIFFRACTIONr_nbtor_refined0.3140.234156
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.21407
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2580.213
X-RAY DIFFRACTIONr_mcbond_it8.256.75324972
X-RAY DIFFRACTIONr_mcangle_it12.29812.10831152
X-RAY DIFFRACTIONr_scbond_it10.0287.35824856
X-RAY DIFFRACTIONr_scangle_it14.59513.21336256
X-RAY DIFFRACTIONr_lrange_it19.43369.07471650
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.7-2.770.3858770.378157020.379179610.8720.8992.30550.361
2.77-2.8450.4078630.351164270.354175050.8960.91698.77180.33
2.845-2.9270.3818960.321160600.324169620.9120.93399.96460.296
2.927-3.0170.3587290.31158590.312165890.9170.9499.9940.286
3.017-3.1150.3238720.266151240.269159980.9320.95599.98750.243
3.115-3.2240.2877320.241148330.243155650.9420.9621000.224
3.224-3.3450.3047330.254141840.256149170.9410.9591000.242
3.345-3.480.2927180.239137190.242144370.9440.9651000.231
3.48-3.6340.2656260.223132270.225138530.9540.9711000.221
3.634-3.810.2865610.218127190.221132800.9480.9721000.222
3.81-4.0140.2246260.189118780.191125040.9680.9781000.2
4.014-4.2550.2274860.18114560.182119420.9670.981000.197
4.255-4.5450.226890.165105210.168112100.9710.9841000.189
4.545-4.9040.1965310.15899420.16104730.9770.9851000.184
4.904-5.3630.2195160.17391610.17696770.9690.9821000.202
5.363-5.9830.2164120.282880.20187010.9740.97999.98850.23
5.983-6.8830.2384010.21574260.21678270.9610.9761000.257
6.883-8.3680.1942720.17462840.17565560.9780.9831000.224
8.368-11.5840.2042470.15449470.15651970.9750.98799.94230.213
11.584-40.0130.2371510.22429620.22431190.9630.96699.80760.315

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