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- EMDB-64858: Cryo-EM structure of renal amyloid fibril from an immunoglobulin ... -

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Basic information

Entry
Database: EMDB / ID: EMD-64858
TitleCryo-EM structure of renal amyloid fibril from an immunoglobulin light chain amyloidosis patient in polymorph B
Map data
Sample
  • Organelle or cellular component: immunoglobulin light chain IGLV1-44
    • Protein or peptide: IG c956_light_IGLV1-44_IGLJ3
KeywordsAmyloid fibril / PROTEIN 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)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhao K / Yu CY / Ma YY / Huang H
Funding support1 items
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 B
Authors: Zhao K / Yu CY / Ma YY / Huang H
History
DepositionMay 30, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64858.png

Downloads & links

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Map

FileDownload / File: emd_64858.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.027117647 - 0.046710506
Average (Standard dev.)0.000117536256 (±0.0013849513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64858_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64858_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64858_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 : immunoglobulin light chain IGLV1-44

EntireName: immunoglobulin light chain IGLV1-44
Components
  • Organelle or cellular component: immunoglobulin light chain IGLV1-44
    • Protein or peptide: IG c956_light_IGLV1-44_IGLJ3

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Supramolecule #1: immunoglobulin light chain IGLV1-44

SupramoleculeName: immunoglobulin light chain IGLV1-44 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: IG c956_light_IGLV1-44_IGLJ3

MacromoleculeName: IG c956_light_IGLV1-44_IGLJ3 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.364423 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVVTQPPSA SGTPGQRVTI SCSGSTSNIG GNTVNWFQHL PGTAPKLLIY SNNQRPSGVP DRFSASKSGT SASLAISGLQ SEDEAHYYC AAWDDSLNGP LFGGGTKVTV L

UniProtKB: IG c956_light_IGLV1-44_IGLJ3

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.91514 Å
Applied symmetry - Helical parameters - Δ&Phi: 0.87006 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15120
CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ic3

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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