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- EMDB-63291: Structure of human dimeric NLRP7-TCL1A complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63291
TitleStructure of human dimeric NLRP7-TCL1A complex
Map data
Sample
  • Complex: Structure of human dimer NLRP7-TCL1A complex
    • Protein or peptide: Isoform 3 of NACHT, LRR and PYD domains-containing protein 7
    • Protein or peptide: T-cell leukemia/lymphoma protein 1A
Keywordssubcortical maternal complex / SIGNALING PROTEIN
Function / homology
Function and homology information


interleukin-1 binding / caspase binding / aspartic-type endopeptidase inhibitor activity / negative regulation of protein processing / negative regulation of interleukin-1 beta production / cellular response to interleukin-1 / negative regulation of cytokine production involved in inflammatory response / protein serine/threonine kinase activator activity / cellular response to lipopolysaccharide / regulation of inflammatory response ...interleukin-1 binding / caspase binding / aspartic-type endopeptidase inhibitor activity / negative regulation of protein processing / negative regulation of interleukin-1 beta production / cellular response to interleukin-1 / negative regulation of cytokine production involved in inflammatory response / protein serine/threonine kinase activator activity / cellular response to lipopolysaccharide / regulation of inflammatory response / intracellular signal transduction / protein kinase binding / endoplasmic reticulum / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
TCL1/MTCP1 / TCL1/MTCP1 superfamily / TCL1/MTCP1 family / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / NACHT nucleoside triphosphatase / NACHT domain ...TCL1/MTCP1 / TCL1/MTCP1 superfamily / TCL1/MTCP1 family / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
T-cell leukemia/lymphoma protein 1A / NACHT, LRR and PYD domains-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsLiu QT / Li JH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of human dimeric NLRP7-TCL1A complex
Authors: Liu QT / Li JH
History
DepositionJan 27, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63291.png

Downloads & links

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Map

FileDownload / File: emd_63291.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.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.3139812 - 0.6174438
Average (Standard dev.)0.0011928128 (±0.017934935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63291_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_63291_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 : Structure of human dimer NLRP7-TCL1A complex

EntireName: Structure of human dimer NLRP7-TCL1A complex
Components
  • Complex: Structure of human dimer NLRP7-TCL1A complex
    • Protein or peptide: Isoform 3 of NACHT, LRR and PYD domains-containing protein 7
    • Protein or peptide: T-cell leukemia/lymphoma protein 1A

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Supramolecule #1: Structure of human dimer NLRP7-TCL1A complex

SupramoleculeName: Structure of human dimer NLRP7-TCL1A complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 3 of NACHT, LRR and PYD domains-containing protein 7

MacromoleculeName: Isoform 3 of NACHT, LRR and PYD domains-containing protein 7
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.448906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTSPQLEWTL QTLLEQLNED ELKSFKSLLW AFPLEDVLQK TPWSEVEEAD GKKLAEILVN TSSENWIRNA TVNILEEMNL TELCKMAKA EMMEDGQVQE IDNPELGDAE EDSELAKPGE KEGWRNSMEK QSLVWKNTFW QGDIDNFHDD VTLRNQRFIP F LNPRTPRK ...String:
MTSPQLEWTL QTLLEQLNED ELKSFKSLLW AFPLEDVLQK TPWSEVEEAD GKKLAEILVN TSSENWIRNA TVNILEEMNL TELCKMAKA EMMEDGQVQE IDNPELGDAE EDSELAKPGE KEGWRNSMEK QSLVWKNTFW QGDIDNFHDD VTLRNQRFIP F LNPRTPRK LTPYTVVLHG PAGVGKTTLA KKCMLDWTDC NLSPTLRYAF YLSCKELSRM GPCSFAELIS KDWPELQDDI PS ILAQAQR ILFVVDGLDE LKVPPGALIQ DICGDWEKKK PVPVLLGSLL KRKMLPRAAL LVTTRPRALR DLQLLAQQPI YVR VEGFLE EDRRAYFLRH FGDEDQAMRA FELMRSNAAL FQLGSAPAVC WIVCTTLKLQ MEKGEDPVPT CLTRTGLFLR FLCS RFPQG AQLRGALRTL SLLAAQGLWA QMSVFHREDL ERLGVQESDL RLFLDGDILR QDRVSKGCYS FIHLSFQQFL TALFY ALEK EEGEDRDGHA WDIGDVQKLL SGEERLKNPD LIQVGHFLFG LANEKRAKEL EATFGCRMSP DIKQELLQCK AHLHAN KPL SVTDLKEVLG CLYESQEEEL AKVVVAPFKE ISIHLTNTSE VMHCSFSLKH CQDLQKLSLQ VAKGVFLENY MDFELDI EF ERCTYLTIPN WARQDLRSLR LWTDFCSLFS SNSNLKFLEV KQSFLSDSSV RILCDHVTRS TCHLQKVEIK NVTPDTAY R DFCLAFIGKK TLTHLTLAGH IEWERTMMLM LCDLLRNHKC NLQYLRLGGH CATPEQWAEF FYVLKANQSL KHLRLSANV LLDEGAMLLY KTMTRPKHFL QMLSLENCRL TEASCKDLAA VLVVSKKLTH LCLAKNPIGD TGVKFLCEGL SYPDCKLQTL VLQQCSITK LGCRYLSEAL QEACSLTNLD LSINQIARGL WILCQALENP NCNLKHLRLW SCSLMPFYCQ HLGSALLSNQ K LETLDLGQ NHLWKSGIIK LFGVLRQRTG SLKILRLKTY ETNLEIKKLL EEVKEKNPKL TIDCNASGAT APPCCDFFC

UniProtKB: NACHT, LRR and PYD domains-containing protein 7

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Macromolecule #2: T-cell leukemia/lymphoma protein 1A

MacromoleculeName: T-cell leukemia/lymphoma protein 1A / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.67258 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EAVTDHPDRL WAWEKFVYLD EKQHAWLPLT IEIKDRLQLR VLLRREDVVL GRPMTPTQIG PSLLPIMWQL YPDGRYRSSD SSFWRLVYH IKIDGVEDML LELLPDD

UniProtKB: T-cell leukemia/lymphoma protein 1A

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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

Concentration2.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMHepes4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
5.0 mMDTTDithiothreitol

Details: 25mM Hepes pH 7.5, 150mM NaCl,5 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Vitrification carried out in argon atmosphere.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.36 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: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1195156
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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