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- EMDB-38771: Cryo-EM map of p97 cross-linked with ZFAND1 with one of the six N... -

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Basic information

Entry
Database: EMDB / ID: EMD-38771
TitleCryo-EM map of p97 cross-linked with ZFAND1 with one of the six NTDs resolved in the NTD-down conformation.
Map dataCryo-EM map of p97 cross-linked with ZFAND1 with one of the six NTDs resolved in the NTD-down conformation.
Sample
  • Complex: p97 (Transitional endoplasmic reticulum ATPase) bound with ZFAND1 (AN1-type zinc finger protein 1).
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: AN1-type zinc finger protein 1
KeywordsATPase / hexameric AAA / protein homeostasis / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


positive regulation of intracellular protein transport / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cellular response to arsenite ion / cytoplasmic ubiquitin ligase complex / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination ...positive regulation of intracellular protein transport / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cellular response to arsenite ion / cytoplasmic ubiquitin ligase complex / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / deubiquitinase activator activity / ATPase complex / positive regulation of oxidative phosphorylation / cytoplasm protein quality control / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / cellular response to misfolded protein / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / NAD+ metabolic process / retrograde protein transport, ER to cytosol / stress granule disassembly / ubiquitin-specific protease binding / regulation of synapse organization / proteasome binding / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / intracellular membrane-bounded organelle / RHOH GTPase cycle / autophagosome maturation / MHC class I protein binding / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / polyubiquitin modification-dependent protein binding / mitophagy / interstrand cross-link repair / ATP metabolic process / protein unfolding / proteasome complex / ribosome-associated ubiquitin-dependent protein catabolic process / Attachment and Entry / endoplasmic reticulum unfolded protein response / Protein methylation / ERAD pathway / negative regulation of smoothened signaling pathway / viral genome replication / translesion synthesis / negative regulation of protein localization to chromatin / macroautophagy / rescue of stalled cytosolic ribosome / lipid droplet / Josephin domain DUBs / establishment of protein localization / proteasomal protein catabolic process / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of protein-containing complex assembly / positive regulation of non-canonical NF-kappaB signal transduction / Hh mutants are degraded by ERAD / ADP binding / Dengue Virus Genome Translation and Replication / Translesion Synthesis by POLH / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / ABC-family protein mediated transport / autophagy / cytoplasmic stress granule / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / positive regulation of protein catabolic process / Aggrephagy / positive regulation of canonical Wnt signaling pathway / double-strand break repair / azurophil granule lumen / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / KEAP1-NFE2L2 pathway / site of double-strand break / cellular response to heat / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / secretory granule lumen / protein phosphatase binding / ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / Attachment and Entry / protein ubiquitination / protein domain specific binding / ubiquitin protein ligase binding / DNA repair / Neutrophil degranulation / DNA damage response / lipid binding
Similarity search - Function
: / ZFAND1-like ubiquitin-like domain / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger / AAA ATPase, CDC48 family / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48), N-terminal domain ...: / ZFAND1-like ubiquitin-like domain / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger / AAA ATPase, CDC48 family / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48), N-terminal domain / 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. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transitional endoplasmic reticulum ATPase / AN1-type zinc finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsDraczkowski P / Hsu STD / Ko KT
Funding support Taiwan, 6 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-CDA-109-L08 Taiwan
Other government110-2113-M-001-050-MY3
Other government110-2311-B-001-013-MY3
Academia Sinica (Taiwan)AS-CFII-111-214 Taiwan
Academia Sinica (Taiwan)AS-CFII-111-210 Taiwan
Other governmentAS-KPQ-109-TPP2
CitationJournal: To Be Published
Title: Structural Insight into ZFAND1-p97 Interaction
Authors: Lai CH / Ko KT / Fan PJ / Yu TA / Chang CF / Draczkowski P / Hsu STD
History
DepositionJan 19, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38771.png

Downloads & links

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Map

FileDownload / File: emd_38771.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of p97 cross-linked with ZFAND1 with one of the six NTDs resolved in the NTD-down conformation.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 200 pix.
= 328. Å		1.64 Å/pix.
x 200 pix.
= 328. Å		1.64 Å/pix.
x 200 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.47613955 - 1.8208404
Average (Standard dev.)0.00037780768 (±0.07695978)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened cryo-EM map of p97 cross-linked with ZFAND1...

Fileemd_38771_additional_1.map
AnnotationSharpened cryo-EM map of p97 cross-linked with ZFAND1 with one of the six NTDs resolved in the NTD-down conformation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half-map of p97 cross-linked with ZFAND1 with...

Fileemd_38771_half_map_1.map
AnnotationCryo-EM half-map of p97 cross-linked with ZFAND1 with one of the six NTDs resolved in the NTD-down conformation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half-map of p97 cross-linked with ZFAND1 with...

Fileemd_38771_half_map_2.map
AnnotationCryo-EM half-map of p97 cross-linked with ZFAND1 with one of the six NTDs resolved in the NTD-down conformation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : p97 (Transitional endoplasmic reticulum ATPase) bound with ZFAND1...

EntireName: p97 (Transitional endoplasmic reticulum ATPase) bound with ZFAND1 (AN1-type zinc finger protein 1).
Components
  • Complex: p97 (Transitional endoplasmic reticulum ATPase) bound with ZFAND1 (AN1-type zinc finger protein 1).
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: AN1-type zinc finger protein 1

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Supramolecule #1: p97 (Transitional endoplasmic reticulum ATPase) bound with ZFAND1...

SupramoleculeName: p97 (Transitional endoplasmic reticulum ATPase) bound with ZFAND1 (AN1-type zinc finger protein 1).
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Chemical cross-linking of p97 and ZFAND1 was necessary to maintain complex formation during grid preparation
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 1 / Details: 6xHis-tag at N-term / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH GSSGENLYFQ GSMASGADSK GDDLSTAILK QKNRPNRLIV DEAINEDNSV VSLSQPKMDE LQLFRGDTVL LKGKKRREAV CIVLSDDTCS DEKIRMNRVV RNNLRVRLGD VISIQPCPDV KYGKRIHVLP IDDTVEGITG NLFEVYLKPY FLEAYRPIRK ...String:
MGSSHHHHHH GSSGENLYFQ GSMASGADSK GDDLSTAILK QKNRPNRLIV DEAINEDNSV VSLSQPKMDE LQLFRGDTVL LKGKKRREAV CIVLSDDTCS DEKIRMNRVV RNNLRVRLGD VISIQPCPDV KYGKRIHVLP IDDTVEGITG NLFEVYLKPY FLEAYRPIRK GDIFLVRGGM RAVEFKVVET DPSPYCIVAP DTVIHCEGEP IKREDEEESL NEVGYDDIGG CRKQLAQIKE MVELPLRHPA LFKAIGVKPP RGILLYGPPG TGKTLIARAV ANETGAFFFL INGPEIMSKL AGESESNLRK AFEEAEKNAP AIIFIDELDA IAPKREKTHG EVERRIVSQL LTLMDGLKQR AHVIVMAATN RPNSIDPALR RFGRFDREVD IGIPDATGRL EILQIHTKNM KLADDVDLEQ VANETHGHVG ADLAALCSEA ALQAIRKKMD LIDLEDETID AEVMNSLAVT MDDFRWALSQ SNPSALRETV VEVPQVTWED IGGLEDVKRE LQELVQYPVE HPDKFLKFGM TPSKGVLFYG PPGCGKTLLA KAIANECQAN FISIKGPELL TMWFGESEAN VREIFDKARQ AAPCVLFFDE LDSIAKARGG NIGDGGGAAD RVINQILTEM DGMSTKKNVF IIGATNRPDI IDPAILRPGR LDQLIYIPLP DEKSRVAILK ANLRKSPVAK DVDLEFLAKM TNGFSGADLT EICQRACKLA IRESIESEIR RERERQTNPS AMEVEEDDPV PEIRRDHFEE AMRFARRSVS DNDIRKYEMF AQTLQQSRGF GSFRFPSGNQ GGAGPSQGSG GGTGGSVYTE DNDDDLYG

UniProtKB: Transitional endoplasmic reticulum ATPase

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Macromolecule #2: AN1-type zinc finger protein 1

MacromoleculeName: AN1-type zinc finger protein 1 / type: protein_or_peptide / ID: 2 / Details: GST-tag at N-term / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKERA EISMLEGAVL DIRYGVSRIA YSKDFETLKV DFLSKLPEML KMFEDRLCHK TYLNGDHVTH PDFMLYDALD VVLYMDPMCL ...String:
MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKERA EISMLEGAVL DIRYGVSRIA YSKDFETLKV DFLSKLPEML KMFEDRLCHK TYLNGDHVTH PDFMLYDALD VVLYMDPMCL DAFPKLVCFK KRIEAIPQID KYLKSSKYIA WPLQGWQATF GGGDHPPKSD LVPRGSENLY FQGGSMAELD IGQHCQVEHC RQRDFLPFVC DDCSGIFCLE HRSRESHGCP EVTVINERLK TDQHTSYPCS FKDCAERELV AVICPYCEKN FCLRHRHQSD HECEKLEIPK PRMAATQKLV KDIIDSKTGE TASKRWKGAK NSETAAKVAL MKLKMHADGD KSLPQTERIY FQVFLPKGSK EKSKPMFFCH RWSIGKAIDF AASLARLKND NNKFTAKKLR LCHITSGEAL PLDHTLETWI AKEDCPLYNG GNIILEYLND EEQFCKNVES YLE

UniProtKB: AN1-type zinc finger protein 1

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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

BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3TRIS
150.0 mMNaClSodium chloride
0.5 mMC9H15O6PTCEP
1.0 mMC10H12N5O12P3S-4ATPgammaS
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 3s blotting time.
DetailsThe sample was chemically cross-linked using 0.0625% (v/v) glutaraldehyde. The sample was supplemented with 1 mM ATPgammaS before vitrification.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number real images: 5693 / Average exposure time: 4.5 sec. / Average electron dose: 58.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 957000
Startup modelType of model: OTHER
Details: Ab initio reconstruction in CryoSparc using Stochastic Gradient Descent method.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 38000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 31000 / Software - Name: cryoSPARC (ver. 3.1)
Details: 3D Variability Analysis followed by Heterogenous Refinement
FSC plot (resolution estimation)

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