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- EMDB-56583: XBP1u-stalled RPL4 RNC in complex with NAC (locally refined on 40... -

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Basic information

Entry
Database: EMDB / ID: EMD-56583
TitleXBP1u-stalled RPL4 RNC in complex with NAC (locally refined on 40S head)
Map data
Sample
  • Complex: XBP1u-stalled RPL4 RNC in complex with NAC
KeywordsNAC / chaperone / cotranslational folding / RNC / human 80S / TRANSLATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPredin M / Jang J / Ban N
Funding supportEuropean Union, Germany, United States, Switzerland, 7 items
OrganizationGrant numberCountry
European Research Council (ERC)SyG-101072047European Union
German Research Foundation (DFG)KR3593/4-1 Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136321 United States
National Science Foundation (NSF, United States)2219287 United States
Swiss National Science Foundation310030_212308 Switzerland
European Molecular Biology Organization (EMBO)European Union
Boehringer Ingelheim Fonds (BIF) Germany
CitationJournal: Mol.Cell / Year: 2026
Title: NAC promotes co-translational protein folding at the ribosomal tunnel exit
Authors: Santos J / Gunnigmann M / Gora RJ / Iljina M / Predin M / Kotan IE / De P / Choudhary D / Jang J / Tippmann F / Hins C / Ban N / Tans SJ / Shan SO / Kramer G / Bukau B
History
DepositionFeb 5, 2026-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56583.png

Downloads & links

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Map

FileDownload / File: emd_56583.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 560 pix.
= 586.32 Å		1.05 Å/pix.
x 560 pix.
= 586.32 Å		1.05 Å/pix.
x 560 pix.
= 586.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.45321313 - 0.96588105
Average (Standard dev.)0.000100097255 (±0.024988959)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 586.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_56583_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_56583_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 : XBP1u-stalled RPL4 RNC in complex with NAC

EntireName: XBP1u-stalled RPL4 RNC in complex with NAC
Components
  • Complex: XBP1u-stalled RPL4 RNC in complex with NAC

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Supramolecule #1: XBP1u-stalled RPL4 RNC in complex with NAC

SupramoleculeName: XBP1u-stalled RPL4 RNC in complex with NAC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#86
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.3 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8qoi

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 104588
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

8qoi

source_name: PDB, initial_model_type: experimental model80S

6r7q

source_name: PDB, initial_model_type: experimental modeltRNA-Xbp1u

7qwr

source_name: PDB, initial_model_type: experimental modelNAC
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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