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- PDB-9nef: Cryo-EM of NBD-L4pY filament at 5mM concentration -

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Basic information

Entry
Database: PDB / ID: 9nef
TitleCryo-EM of NBD-L4pY filament at 5mM concentration
Components(UQ4)LLLL(PTR)
KeywordsPROTEIN FIBRIL / peptide fiber / helical polymer
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZia, A. / Guo, J. / Xu, B. / Wang, F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA142746 United States
CitationJournal: To Be Published
Title: Cryo-EM of NBD-L4pY filament at 5mM concentration
Authors: Zia, A. / Guo, J. / Xu, B. / Wang, F.
History
DepositionFeb 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 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
8: (UQ4)LLLL(PTR)
9: (UQ4)LLLL(PTR)


Theoretical massNumber of molelcules
Total (without water)1,8962
Polymers1,8962
Non-polymers00
Water00
1
8: (UQ4)LLLL(PTR)
9: (UQ4)LLLL(PTR)
x 30


Theoretical massNumber of molelcules
Total (without water)56,87860
Polymers56,87860
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation29
MethodUCSF CHIMERA

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Components

#1: Protein/peptide (UQ4)LLLL(PTR)


Mass: 947.968 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: (UQ4)LLLL(PTR) / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7
SpecimenEmbedding 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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 43.07 ° / Axial rise/subunit: 0.39 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256561 / Symmetry type: HELICAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.018160
ELECTRON MICROSCOPYf_angle_d2.09411400
ELECTRON MICROSCOPYf_dihedral_angle_d26.8051200
ELECTRON MICROSCOPYf_chiral_restr0.11080
ELECTRON MICROSCOPYf_plane_restr0.0041080

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