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- EMDB-38770: Cryo-EM map of p97 cross-linked with ZFAND1 with three of the six... -

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Basic information

Entry
Database: EMDB / ID: EMD-38770
TitleCryo-EM map of p97 cross-linked with ZFAND1 with three of the six NTDs resolved in the NTD-up conformation.
Map dataCryo-EM map of p97 cross-linked with ZFAND1 with three of the six NTDs resolved in the NTD-up 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 / 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 ...positive regulation of intracellular protein transport / : / 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 / 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 / : / mitotic spindle disassembly / 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 / regulation of aerobic respiration / stress granule disassembly / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / proteasome binding / ubiquitin-specific protease binding / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / negative regulation of hippo signaling / HSF1 activation / translesion synthesis / interstrand cross-link repair / proteasomal protein catabolic process / ATP metabolic process / Protein methylation / endoplasmic reticulum unfolded protein response / ERAD pathway / Attachment and Entry / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / 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 / Hedgehog ligand biogenesis / establishment of protein localization / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of non-canonical NF-kappaB signal transduction / ADP binding / ABC-family proteins mediated transport / autophagy / positive regulation of protein catabolic process / cytoplasmic stress granule / Aggrephagy / 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 / Neddylation / cellular response to heat / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / ciliary basal body / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / lipid binding / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / protein-containing complex
Similarity search - Function
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 / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 ...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 / 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. / 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: 3.8 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_38770.png

Downloads & links

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Map

FileDownload / File: emd_38770.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 three of the six NTDs resolved in the NTD-up 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-0.47585365 - 1.8706226
Average (Standard dev.)0.0010993103 (±0.07783969)
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_38770_additional_1.map
AnnotationSharpened cryo-EM map of p97 cross-linked with ZFAND1 with three of the six NTDs resolved in the NTD-up 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_38770_half_map_1.map
AnnotationCryo-EM half-map of p97 cross-linked with ZFAND1 with three of the six NTDs resolved in the NTD-up 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_38770_half_map_2.map
AnnotationCryo-EM half-map of p97 cross-linked with ZFAND1 with three of the six NTDs resolved in the NTD-up 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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 40000
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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