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- PDB-7x84: Cryo-EM structure of the TMEM106B fibril from Parkinson's disease... -

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Basic information

Entry
Database: PDB / ID: 7x84
TitleCryo-EM structure of the TMEM106B fibril from Parkinson's disease dementia
ComponentsTransmembrane protein 106B
KeywordsPROTEIN FIBRIL / amyloid
Function / homology
Function and homology information


lysosomal protein catabolic process / lysosomal lumen acidification / regulation of lysosome organization / lysosome localization / positive regulation of dendrite development / lysosomal transport / lysosome organization / dendrite morphogenesis / neuron cellular homeostasis / late endosome membrane ...lysosomal protein catabolic process / lysosomal lumen acidification / regulation of lysosome organization / lysosome localization / positive regulation of dendrite development / lysosomal transport / lysosome organization / dendrite morphogenesis / neuron cellular homeostasis / late endosome membrane / ATPase binding / lysosome / endosome / lysosomal membrane / plasma membrane
Similarity search - Function
Transmembrane protein 106 / : / : / TM106 protein C-terminal domain / Transmembrane protein 106 N-terminal region
Similarity search - Domain/homology
Transmembrane protein 106B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsZhao, Q.Y. / Xia, W.C. / Fan, Y. / Sun, Y.P. / Tao, Y.Q. / Liu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2022
Title: Generic amyloid fibrillation of TMEM106B in patient with Parkinson's disease dementia and normal elders.
Authors: Yun Fan / Qinyue Zhao / Wencheng Xia / Youqi Tao / Wenbo Yu / Mingjia Chen / Yiqi Liu / Jue Zhao / Yan Shen / Yunpeng Sun / Chenfang Si / Shenqing Zhang / Yaoyang Zhang / Wensheng Li / Cong ...Authors: Yun Fan / Qinyue Zhao / Wencheng Xia / Youqi Tao / Wenbo Yu / Mingjia Chen / Yiqi Liu / Jue Zhao / Yan Shen / Yunpeng Sun / Chenfang Si / Shenqing Zhang / Yaoyang Zhang / Wensheng Li / Cong Liu / Jian Wang / Dan Li /
History
DepositionMar 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Transmembrane protein 106B
A: Transmembrane protein 106B
C: Transmembrane protein 106B


Theoretical massNumber of molelcules
Total (without water)46,5083
Polymers46,5083
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Transmembrane protein 106B


Mass: 15502.680 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NUM4
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: the fibril formed by TMEM106B from Parkinson's disease dementia
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.15.2_3472refinement
PHENIX1.15.2_3472refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -0.45 ° / Axial rise/subunit: 4.83 Å / Axial symmetry: C1
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17752 / Symmetry type: HELICAL
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00843312
ELECTRON MICROSCOPYf_angle_d0.77324503
ELECTRON MICROSCOPYf_chiral_restr0.0535543
ELECTRON MICROSCOPYf_plane_restr0.0031558
ELECTRON MICROSCOPYf_dihedral_angle_d8.14751986

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