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- EMDB-68158: Cryo-EM structure of A-H(M) complex (one ADP) -

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Basic information

Entry
Database: EMDB / ID: EMD-68158
TitleCryo-EM structure of A-H(M) complex (one ADP)
Map data
Sample
  • Complex: ATPase-HNH complex
    • Protein or peptide: AAA family ATPase
    • Protein or peptide: TIGR02646 family protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
Keywordsimmune / complex / IMMUNE SYSTEM
Function / homology: / :
Function and homology information
Biological speciesLigilactobacillus acidipiscis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLin Z / Guo M / Zhu Y / Huang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of A-H(M) complex (one ADP)
Authors: Lin Z / Guo M / Zhu Y / Huang Z
History
DepositionJan 6, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68158.png

Downloads & links

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Map

FileDownload / File: emd_68158.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å		0.96 Å/pix.
x 256 pix.
= 245.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.194
Minimum - Maximum-0.5969133 - 1.2891666
Average (Standard dev.)0.00089142116 (±0.03524103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 245.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68158_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68158_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATPase-HNH complex

EntireName: ATPase-HNH complex
Components
  • Complex: ATPase-HNH complex
    • Protein or peptide: AAA family ATPase
    • Protein or peptide: TIGR02646 family protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: ATPase-HNH complex

SupramoleculeName: ATPase-HNH complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Ligilactobacillus acidipiscis (bacteria)

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Macromolecule #1: AAA family ATPase

MacromoleculeName: AAA family ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Ligilactobacillus acidipiscis (bacteria)
Molecular weightTheoretical: 63.13343 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VTKQLERKAK GGSLLSAFEL YQQEKNNNLH DLNNKSDQWF ELCWNYLQQP AHDGNLDIYH PENQFCLRSM SFTDFRRFPQ LDINFEEDL TIIIGNNGQG KTSILYAIAK TLSWFTANIL KEDSSGQRLN EYSDIRNDSD NNFSDVSSNF FFGKGLKNIS I RLSRSTLG ...String:
VTKQLERKAK GGSLLSAFEL YQQEKNNNLH DLNNKSDQWF ELCWNYLQQP AHDGNLDIYH PENQFCLRSM SFTDFRRFPQ LDINFEEDL TIIIGNNGQG KTSILYAIAK TLSWFTANIL KEDSSGQRLN EYSDIRNDSD NNFSDVSSNF FFGKGLKNIS I RLSRSTLG ASERRESIIK PAKEVADIWR IINERRMVNL PIFALYSVER SHPFSKPAKE SIEKREDRFD AYNHALTGAG RF DHFVEWF IYLHKRAEAQ GASAIELLEE QVNHLKQSVE NGLTSMVPLL EETQKKLLTA QMRKESLQSV NMLTETAQMD IVS RAITTV VPSISRIWVE TASGADIIKV TNDLQDVTIE QLSDGQRVFL ALVADLARRM IMLNPLLKNP LEGRGIVLID EIEL HLHPK WQQEVIIVLR TVFPNIQFVI TTHSPIVLST TEIRCIREFK QNSESGELFL DSPPIQTKGS ENSDILEQVM GVLST PPNI AESYLVSNFE KSIIDDSEEL SAESRRLYNK IISHFGQHSS ELKKADSLIR LHRMKNKINK AKREKDS

UniProtKB: UNIPROTKB: A0A921F998

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Macromolecule #2: TIGR02646 family protein

MacromoleculeName: TIGR02646 family protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ligilactobacillus acidipiscis (bacteria)
Molecular weightTheoretical: 24.501613 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSLNRTAGP AHLHQFRAGR DPWMSVEQSN IWPHLLEMQG EFCAYCECSL NRKHIEAFRP RGKFPALTFA WGNLFGSCGD SSKTGGWQR CGIFKDNGAG NYNPDHLIKP DDDNPDDYLL FLTTGHVVPA KDISGTKLLK AQETIRVFNL NGDPSLLGSR K KALNYIME ...String:
MKSLNRTAGP AHLHQFRAGR DPWMSVEQSN IWPHLLEMQG EFCAYCECSL NRKHIEAFRP RGKFPALTFA WGNLFGSCGD SSKTGGWQR CGIFKDNGAG NYNPDHLIKP DDDNPDDYLL FLTTGHVVPA KDISGTKLLK AQETIRVFNL NGDPSLLGSR K KALNYIME EVILLHESYE DLGDALWHEM RDAEIQEIGN KEFYTALKHA WLHNSEY

UniProtKB: UNIPROTKB: A0A921FAL0

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI MORGAGNI
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 159202
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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