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- PDB-9ln6: Structure of human NLRP14-UHRF1 complex -

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Basic information

Entry
Database: PDB / ID: 9ln6
TitleStructure of human NLRP14-UHRF1 complex
Components
  • Maltose/maltodextrin-binding periplasmic protein,E3 ubiquitin-protein ligase UHRF1
  • Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 14
KeywordsCYTOSOLIC PROTEIN / maternal complex / UHRF1 / NLRP14 / ubiquitylation
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / : / methyl-CpG binding / histone H3K9me2/3 reader activity / detection of maltose stimulus / negative regulation of gene expression via chromosomal CpG island methylation ...histone H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / : / methyl-CpG binding / histone H3K9me2/3 reader activity / detection of maltose stimulus / negative regulation of gene expression via chromosomal CpG island methylation / maltose transport complex / carbohydrate transport / positive regulation of protein metabolic process / carbohydrate transmembrane transporter activity / maltose binding / mitotic spindle assembly / maltose transport / maltodextrin transmembrane transport / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / heterochromatin / ATP-binding cassette (ABC) transporter complex / epigenetic regulation of gene expression / replication fork / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / cell chemotaxis / euchromatin / RING-type E3 ubiquitin transferase / double-strand break repair via homologous recombination / spindle / nuclear matrix / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / heterochromatin formation / outer membrane-bounded periplasmic space / regulation of inflammatory response / histone binding / spermatogenesis / ubiquitin-dependent protein catabolic process / nucleic acid binding / cell differentiation / periplasmic space / protein ubiquitination / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / : ...: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / : / 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 profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / PUA-like superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / PHD-finger / Bacterial extracellular solute-binding protein / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Death-like domain superfamily / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Leucine-rich repeat / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / NACHT, LRR and PYD domains-containing protein 14 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsQi, Q. / Chi, P. / Liu, S. / Lu, Y. / Li, J. / Li, J. / Wang, X. / Jiang, Y. / Deng, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971132 China
CitationJournal: To Be Published
Title: Structure of human NLRP14-UHRF1 complex
Authors: Qi, Q. / Chi, P. / Liu, S. / Lu, Y. / Li, J. / Li, J. / Wang, X. / Jiang, Y. / Deng, D.
History
DepositionJan 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 14
B: Maltose/maltodextrin-binding periplasmic protein,E3 ubiquitin-protein ligase UHRF1


Theoretical massNumber of molelcules
Total (without water)225,5132
Polymers225,5132
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 14 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Nucleotide-binding ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Nucleotide-binding oligomerization domain protein 5


Mass: 170249.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, NLRP14, NALP14, NOD5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0AEX9, UniProt: Q86W24
#2: Protein Maltose/maltodextrin-binding periplasmic protein,E3 ubiquitin-protein ligase UHRF1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Inverted CCAAT box-binding ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein Np95 / HuNp95 / hNp95 / RING finger protein 106 / RING-type E3 ubiquitin transferase UHRF1 / Transcription factor ICBP90 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / hUHRF1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 55263.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, UHRF1, ICBP90, NP95, RNF106 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P0AEX9, UniProt: Q96T88, RING-type E3 ubiquitin transferase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: binary complex of NLRP14 and UHRF1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenConc.: 1.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 55.13 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73160 / Symmetry type: POINT
RefinementHighest resolution: 3.49 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058287
ELECTRON MICROSCOPYf_angle_d0.59511189
ELECTRON MICROSCOPYf_dihedral_angle_d10.8753100
ELECTRON MICROSCOPYf_chiral_restr0.0391272
ELECTRON MICROSCOPYf_plane_restr0.0041421

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