EMDB-8707: Negative stain reconstruction of Endoplasmic Reticulum HSP40 co-c...

Basic information

• Entry: Database: EMDB / ID: EMD-8707
• Title: Negative stain reconstruction of Endoplasmic Reticulum HSP40 co-chaperone native ERdj3 tetramer.
• Map data: Negative stain reconstruction of native ERdj3 tetramer

Sample

• Complex: Tetrameric complex of native ERdj3 protein complex

Function / homology

Function:

endoplasmic reticulum chaperone complex / XBP1(S) activates chaperone genes / misfolded protein binding / positive regulation of ATP-dependent activity / mRNA modification / protein folding chaperone complex / : / protein maturation / negative regulation of neurogenesis / protein folding / endoplasmic reticulum lumen / signaling receptor binding / endoplasmic reticulum / : / membrane / nucleus

Domain/homology:

: / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain

Component:

DnaJ homolog subfamily B member 11

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / negative staining / Resolution: 16.9 Å
• Authors: Chowdhury S / Lander GC / Chen K-C / Qu S / Noxon IC / Schonhoft JD / Plate L / Powers ET / Kelly JW / Wiseman RL

Funding support

United States, 1 items

Organization	Grant number	Country
National Institutes of Health/National Institute of Neurological Disorders and Stroke	NS092829, DK107604, DK102635, DP2 EB020401, DK046335	United States

• Citation: Journal: Proc Natl Acad Sci U S A / Year: 2017; Title: Structures of Qβ virions, virus-like particles, and the Qβ-MurA complex reveal internal coat proteins and the mechanism of host lysis.; Authors: Zhicheng Cui / Karl V Gorzelnik / Jeng-Yih Chang / Carrie Langlais / Joanita Jakana / Ry Young / Junjie Zhang / ; Abstract: In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the canonical Qβ the maturation protein, A, has an additional role as the lysis protein, by its ability to bind and inhibit MurA, which is involved in peptidoglycan biosynthesis. Here, we determined structures of Qβ virions, virus-like particles, and the Qβ-MurA complex using single-particle cryoelectron microscopy, at 4.7-Å, 3.3-Å, and 6.1-Å resolutions, respectively. We identified the outer surface of the β-region in A as the MurA-binding interface. Moreover, the pattern of MurA mutations that block Qβ lysis and the conformational changes of MurA that facilitate A binding were found to be due to the intimate fit between A and the region encompassing the closed catalytic cleft of substrate-liganded MurA. Additionally, by comparing the Qβ virion with Qβ virus-like particles that lack a maturation protein, we observed a structural rearrangement in the capsid coat proteins that is required to package the viral gRNA in its dominant conformation. Unexpectedly, we found a coat protein dimer sequestered in the interior of the virion. This coat protein dimer binds to the gRNA and interacts with the buried α-region of A, suggesting that it is sequestered during the early stage of capsid formation to promote the gRNA condensation required for genome packaging. These internalized coat proteins are the most asymmetrically arranged major capsid proteins yet observed in virus structures.

History

Deposition	Apr 26, 2017	-
Header (metadata) release	May 24, 2017	-
Map release	May 24, 2017	-
Update	Sep 23, 2026	-
Current status	Sep 23, 2026	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_8707.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Negative stain reconstruction of native ERdj3 tetramer
• Voxel size: X=Y=Z: 4.1 Å

Density

Contour Level	By AUTHOR: 0.0179 / Movie #1: 0.0179
Minimum - Maximum	-0.08225489 - 0.2763727
Average (Standard dev.)	0.000801101 (±0.014040019)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 26 26 26 Dimensions 60 60 60 Spacing 60 60 60
Cell	A=B=C: 246.0 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	4.1	4.1	4.1
M x/y/z	60	60	60
origin x/y/z	0.000	0.000	0.000
length x/y/z	246.000	246.000	246.000
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	-15	2	-37
NX/NY/NZ	99	82	71
MAP C/R/S	1	2	3
start NC/NR/NS	26	26	26
NC/NR/NS	60	60	60
D min/max/mean	-0.082	0.276	0.001

Supplemental data

Sample components

Entire : Tetrameric complex of native ERdj3 protein complex

• Entire: Name: Tetrameric complex of native ERdj3 protein complex

Components

• Complex: Tetrameric complex of native ERdj3 protein complex

Supramolecule #1: Tetrameric complex of native ERdj3 protein complex

• Supramolecule: Name: Tetrameric complex of native ERdj3 protein complex / type: complex / ID: 1 / Parent: 0
• Source (natural): Organism: Homo sapiens (human) / Location in cell: Endoplasmic reticulum
• Molecular weight: Theoretical: 153 KDa

Experimental details

Structure determination

• Method: negative staining
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.025 mg/mL
• Buffer: pH: 7.5 / Details: 50 mM HEPES, 300 mM NaCl, 1% (v/v)Glycerol
• Staining: Type: NEGATIVE / Material: Uranyl Formate; Details: Sample absorbed on carbon surface was stained with 2% (w/v) Uranyl Formate solution, and finally air-dried after blotting off excess stain.
• Grid: Model: 400 mesh Cu-Rh maxtaform grids (Electron Microscopy Sciences) that were coated with a thin layer of amorphous carbon.; Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Details: 15mA current
• Details: Mono dispersed protein solution

Electron microscopy

• Microscope: FEI TECNAI 12
• Temperature: Min: 293.0 K / Max: 295.0 K
• Image recording: Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 980 / Average exposure time: 0.79 sec. / Average electron dose: 35.0 e/Ų; Details: Automated image acquisition software Leginon was used for data collection.
• Electron beam: Acceleration voltage: 120 kV / Electron source: LAB6
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000
• Sample stage: Specimen holder model: SIDE ENTRY, EUCENTRIC

Image processing

• Details: Automated image acquisition software Leginon was used for data collection.
• Particle selection: Number selected: 385141 ; Details: Difference of Gaussian (DOG)-based automated particle picker, implemented in Appion processing package was used for particle selection.
• CTF correction: Software - Name: CTFFIND4; Details: Ctffind4 was used for determining the CTF of each micrograph. Phases of each micrographs were flipped before particle extraction.; Type: PHASE FLIPPING ONLY

Startup model

Type of model: PDB ENTRY
PDB model - PDB ID:

2qld

Details: Four copies of PDB 2QLD were overlaid on 2D classes and low pass filtered to generate an initial 3D model.

• Final reconstruction: Number classes used: 2 / Applied symmetry - Point group: C₂ (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 16.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 17405
• Initial angle assignment: Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
• Final angle assignment: Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
• Final 3D classification: Number classes: 10 / Software - Name: RELION (ver. 1.4)