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- EMDB-24304: p47-bound p97-R155H mutant with ADP -

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Basic information

Entry
Database: EMDB / ID: EMD-24304
Titlep47-bound p97-R155H mutant with ADP
Map datap47-bound p97-R155H mutant with ADP
Sample
  • Complex: p47-bound p97-R155H mutant with ADP
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: NSFL1 cofactor p47
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAAA+ ATPase / MOTOR PROTEIN / HYDROLASE / HYDROLASE-Lipid Binding Protein complex
Function / homology
Function and homology information


RHOH GTPase cycle / negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / spindle pole centrosome / : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control ...RHOH GTPase cycle / negative regulation of protein localization to centrosome / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / spindle pole centrosome / : / flavin adenine dinucleotide catabolic process / 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 / : / Golgi stack / aggresome assembly / deubiquitinase activator activity / mitotic spindle disassembly / 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 / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / Golgi organization / positive regulation of ATP biosynthetic process / MHC class I protein binding / ubiquitin-like protein ligase binding / establishment of mitotic spindle orientation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome assembly / autophagosome maturation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / HSF1 activation / translesion synthesis / interstrand cross-link repair / ATP metabolic process / proteasomal protein catabolic process / endoplasmic reticulum unfolded protein response / Protein methylation / Attachment and Entry / ERAD pathway / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of smoothened signaling pathway / macroautophagy / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / establishment of protein localization / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / positive regulation of non-canonical NF-kappaB signal transduction / Translesion Synthesis by POLH / ADP binding / ABC-family proteins mediated transport / autophagy / cytoplasmic stress granule / Aggrephagy / positive regulation of protein catabolic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / chromosome / cellular response to heat / Neddylation / ATPase binding / ubiquitin-dependent protein catabolic process / secretory granule lumen / protein phosphatase binding / regulation of apoptotic process / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / membrane fusion / Attachment and Entry / protein ubiquitination / ciliary basal body / protein domain specific 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
NSFL1 cofactor p47 / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsNandi P / Li S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS102279 United States
CitationJournal: Int J Mol Sci / Year: 2021
Title: Structural and Functional Analysis of Disease-Linked p97 ATPase Mutant Complexes.
Authors: Purbasha Nandi / Shan Li / Rod Carlo A Columbres / Feng Wang / Dewight R Williams / Yu-Ping Poh / Tsui-Fen Chou / Po-Lin Chiu /
Abstract: IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase ...IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase malfunction remains unclear. To understand how the mutation alters the ATPase regulation, we assembled a full-length p97 with its p47 cofactor and first visualized their structures using single-particle cryo-EM. More than one-third of the population was the dodecameric form. Nucleotide presence dissociates the dodecamer into two hexamers for its highly elevated function. The N-domains of the p97 mutant all show up configurations in ADP- or ATPS-bound states. Our functional and structural analyses showed that the p47 binding is likely to impact the p97 ATPase activities via changing the conformations of arginine fingers. These functional and structural analyses underline the ATPase dysregulation with the miscommunication between the functional modules of the p97.
History
DepositionJun 25, 2021-
Header (metadata) releaseAug 4, 2021-
Map releaseAug 4, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7r7t
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24304.png

Downloads & links

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Map

FileDownload / File: emd_24304.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationp47-bound p97-R155H mutant with ADP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 210 pix.
= 296.73 Å		1.41 Å/pix.
x 210 pix.
= 296.73 Å		1.41 Å/pix.
x 210 pix.
= 296.73 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.413 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0618 / Movie #1: 0.08
Minimum - Maximum-0.16823594 - 0.5576338
Average (Standard dev.)0.0014666901 (±0.024653394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 296.73 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4131.4131.413
M x/y/z210210210
origin x/y/z0.0000.0000.000
length x/y/z296.730296.730296.730
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ232232232
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS210210210
D min/max/mean-0.1680.5580.001

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Supplemental data

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Sample components

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Entire : p47-bound p97-R155H mutant with ADP

EntireName: p47-bound p97-R155H mutant with ADP
Components
  • Complex: p47-bound p97-R155H mutant with ADP
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: NSFL1 cofactor p47
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: p47-bound p97-R155H mutant with ADP

SupramoleculeName: p47-bound p97-R155H mutant with ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: p47-bound p97-R155H mutant with ADP
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 723 KDa

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Macromolecule #1: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.417773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVHGGMR A VEFKVVET ...String:
MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVHGGMR A VEFKVVET DPSPYCIVAP DTVIHCEGEP IKREDEEESL NEVGYDDIGG CRKQLAQIKE MVELPLRHPA LFKAIGVKPP RG ILLYGPP GTGKTLIARA VANETGAFFF LINGPEIMSK LAGESESNLR KAFEEAEKNA PAIIFIDELD AIAPKREKTH GEV ERRIVS QLLTLMDGLK QRAHVIVMAA TNRPNSIDPA LRRFGRFDRE VDIGIPDATG RLEILQIHTK NMKLADDVDL EQVA NETHG HVGADLAALC SEAALQAIRK KMDLIDLEDE TIDAEVMNSL AVTMDDFRWA LSQSNPSALR ETVVEVPQVT WEDIG GLED VKRELQELVQ YPVEHPDKFL KFGMTPSKGV LFYGPPGCGK TLLAKAIANE CQANFISIKG PELLTMWFGE SEANVR EIF DKARQAAPCV LFFDELDSIA KARGGNIGDG GGAADRVINQ ILTEMDGMST KKNVFIIGAT NRPDIIDPAI LRPGRLD QL IYIPLPDEKS RVAILKANLR KSPVAKDVDL EFLAKMTNGF SGADLTEICQ RACKLAIRES IESEIRRERE RQTNPSAM E VEEDDPVPEI RRDHFEEAMR FARRSVSDND IRKYEMFAQT LQQSRGFGSF RFPSGNQGGA GPSQGSGGGT GGSVYTEDN DDDLYG

UniProtKB: Transitional endoplasmic reticulum ATPase

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Macromolecule #2: NSFL1 cofactor p47

MacromoleculeName: NSFL1 cofactor p47 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 40.731855 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAEERQDALR EFVAVTGAEE DRARFFLESA GWDLQIALAS FYEDGGDEDI VTISQATPSS VSRGTAPSDN RVTSFRDLIH DQDEEEEEE EGQRFYAGGS ERSGQQIVGP PRKKSPNELV DDLFKGAKEH GAVAVERVTK SPGETSKPRP FAGGGYRLGA A PEEESAYV ...String:
MAEERQDALR EFVAVTGAEE DRARFFLESA GWDLQIALAS FYEDGGDEDI VTISQATPSS VSRGTAPSDN RVTSFRDLIH DQDEEEEEE EGQRFYAGGS ERSGQQIVGP PRKKSPNELV DDLFKGAKEH GAVAVERVTK SPGETSKPRP FAGGGYRLGA A PEEESAYV AGERRRHSGQ DVHVVLKLWK TGFSLDNGDL RSYQDPSNAQ FLESIRRGEV PAELRRLAHG GQVNLDMEDH RD EDFVKPK GAFKAFTGEG QKLGSTAPQV LNTSSPAQQA ENEAKASSSI LINEAEPTTN IQIRLADGGR LVQKFNHSHR ISD IRLFIV DARPAMAATS FVLMTTFPNK ELADENQTLK EANLLNAVIV QRLT

UniProtKB: NSFL1 cofactor p47

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 12 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
150.0 mMKClpotassium chloride
1.0 mMTCEPTCEP
GridModel: C-flat-2/1 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 292 K / Instrument: FEI VITROBOT MARK IV / Details: The grid was blotted for 6 seconds..
DetailsThe protein sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureComa free - Residual tilt: 0.001 mrad
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 3512 / Average electron dose: 44.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 48077
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1124232
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 160050
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.15)

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Atomic model buiding 1

Initial modelPDB ID:

5ftk


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 122.3 / Target criteria: CC
Output model

PDB-7r7t:
p47-bound p97-R155H mutant with ADP

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