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- PDB-9x45: Cryo-EM structure of renal amyloid fibril from an immunoglobulin ... -

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Basic information

Entry
Database: PDB / ID: 9x45
TitleCryo-EM structure of renal amyloid fibril from an immunoglobulin light chain amyloidosis patient in polymorph A
ComponentsIG c956_light_IGLV1-44_IGLJ3
KeywordsPROTEIN FIBRIL / Amyloid fibril
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IG c956_light_IGLV1-44_IGLJ3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsZhao, K. / Yu, C.Y. / Ma, Y.Y. / Huang, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of renal amyloid fibril from an immunoglobulin light chain amyloidosis patient in polymorph A
Authors: Zhao, K. / Yu, C.Y. / Ma, Y.Y. / Huang, H.
History
DepositionOct 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data 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: IG c956_light_IGLV1-44_IGLJ3
B: IG c956_light_IGLV1-44_IGLJ3
C: IG c956_light_IGLV1-44_IGLJ3
D: IG c956_light_IGLV1-44_IGLJ3
E: IG c956_light_IGLV1-44_IGLJ3
F: IG c956_light_IGLV1-44_IGLJ3


Theoretical massNumber of molelcules
Total (without water)68,1876
Polymers68,1876
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: Antibody
IG c956_light_IGLV1-44_IGLJ3


Mass: 11364.423 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: A0A5C2GJC2
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: immunoglobulin light chain IGLV1-44 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: 1500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.20.1_4487model refinement
13RELION3D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -179.58 ° / Axial rise/subunit: 2.46 Å / Axial symmetry: C1
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15120 / Symmetry type: HELICAL
RefinementHighest resolution: 2.93 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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