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- EMDB-63559: Cryo-EM structrue of kpNLRL filament -

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Basic information

Entry
Database: EMDB / ID: EMD-63559
TitleCryo-EM structrue of kpNLRL filament
Map data
Sample
  • Complex: kpNLRL filament
    • Protein or peptide: Tetratricopeptide repeat protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsbacterial immune system / NLR-like / IMMUNE SYSTEM
Function / homologyTIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Tetratricopeptide-like helical domain superfamily / signal transduction / P-loop containing nucleoside triphosphate hydrolase / Tetratricopeptide repeat protein
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsWang L / Wang H / Li J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structrue of kpNLRL filament
Authors: Wang L / Wang H / Li J
History
DepositionFeb 25, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63559.png

Downloads & links

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Map

FileDownload / File: emd_63559.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 480 pix.
= 395.52 Å		0.82 Å/pix.
x 480 pix.
= 395.52 Å		0.82 Å/pix.
x 480 pix.
= 395.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-1.044869 - 1.9613959
Average (Standard dev.)0.00041892403 (±0.0327118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 395.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63559_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63559_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 : kpNLRL filament

EntireName: kpNLRL filament
Components
  • Complex: kpNLRL filament
    • Protein or peptide: Tetratricopeptide repeat protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: kpNLRL filament

SupramoleculeName: kpNLRL filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Klebsiella pneumoniae (bacteria)

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Macromolecule #1: Tetratricopeptide repeat protein

MacromoleculeName: Tetratricopeptide repeat protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 96.072984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIKAFLSHSS KDKEHYVRNV ANWLGKENII YDEFTFEEGE RTLDQIMEGL GDSELFVLFI SNSALESEWV KKEITESKKL LDEGKILKI FPIIIDNNIN HEDQRIPDWL RKDYNLQPIT RARTAASRIK NHLYKISWQK HPKLEKISSL FVGRNDKLEE F EERINDYT ...String:
MIKAFLSHSS KDKEHYVRNV ANWLGKENII YDEFTFEEGE RTLDQIMEGL GDSELFVLFI SNSALESEWV KKEITESKKL LDEGKILKI FPIIIDNNIN HEDQRIPDWL RKDYNLQPIT RARTAASRIK NHLYKISWQK HPKLEKISSL FVGRNDKLEE F EERINDYT KKKPTVIFAS GLIGVGRRSF LSKALIKCNI QKNQITPYAI YLDRNESIED FILKLNDLGI TDLKESALSL SE KTIEEKQ KIISNILNEA YKAKETIFFL DDGCIINYKR ELTPWFKMII EEYNDINFPV LCIASRYRVN FANRPRDDRF YFI ELPELN VKERRRLLSQ LLEIENIDDL DPSNFSSVCD LLTGLPEQVR FAIELIKDKN IIPFENKLPI LSDFNNDKAS IQLQ RYAHN ETVLDFIRLI AQFEVITLDF IFSIVDKDKY LPVLEALIAE SICELVGSDG EMIRLNDIVR DYIKRNRLKI NDEHN KKLN LVVKEIVNNE DLTEANSSVY IFTIKEMLKS DEYIDPKHLI PSHYLRCMKD LYNAKGSLEK VISLADTILQ KEKNMD NGV VQDIRYYLCL ALAKKSDSRL LTEVQKIRGD EHKFLLGFYY RKCGRLSDAL SQFESIINAP YVESRAKREL VQVYTQL EE YDKALSYAKK NYEENRSNQF HCQAYFNCLI NSQHRVDSDN IVLKDIITTL INIDSEQSNE MAKIADAMYS AKIENDVV K SITIINDCIA TYPESPYPLL AKCDVGLKFK SIQTLEEALS SLDKMKRRKV VSERTLTTYQ AYLMALKGDE NSANQIISN DIKKYPQEAR ERILKRIKEY AGKN

UniProtKB: Tetratricopeptide repeat protein

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / 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 statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 380130
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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