[English] 日本語
Yorodumi
- EMDB-12304: SRP54 and SRP RNA proximal site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12304
TitleSRP54 and SRP RNA proximal site
Map datafocused refinement of state A
Sample
  • Complex: ribosome nascent chain complex with SRP and SRP receptor
    • RNA: SRP RNA and SRP54
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsJomaa A / Ban N
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Sci Adv / Year: 2021
Title: Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER.
Authors: Jae Ho Lee / Ahmad Jomaa / SangYoon Chung / Yu-Hsien Hwang Fu / Ruilin Qian / Xuemeng Sun / Hao-Hsuan Hsieh / Sowmya Chandrasekar / Xiaotian Bi / Simone Mattei / Daniel Boehringer / Shimon ...Authors: Jae Ho Lee / Ahmad Jomaa / SangYoon Chung / Yu-Hsien Hwang Fu / Ruilin Qian / Xuemeng Sun / Hao-Hsuan Hsieh / Sowmya Chandrasekar / Xiaotian Bi / Simone Mattei / Daniel Boehringer / Shimon Weiss / Nenad Ban / Shu-Ou Shan /
Abstract: The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP ...The conserved signal recognition particle (SRP) cotranslationally delivers ~30% of the proteome to the eukaryotic endoplasmic reticulum (ER). The molecular mechanism by which eukaryotic SRP transitions from cargo recognition in the cytosol to protein translocation at the ER is not understood. Here, structural, biochemical, and single-molecule studies show that this transition requires multiple sequential conformational rearrangements in the targeting complex initiated by guanosine triphosphatase (GTPase)-driven compaction of the SRP receptor (SR). Disruption of these rearrangements, particularly in mutant SRP54 linked to severe congenital neutropenia, uncouples the SRP/SR GTPase cycle from protein translocation. Structures of targeting intermediates reveal the molecular basis of early SRP-SR recognition and emphasize the role of eukaryote-specific elements in regulating targeting. Our results provide a molecular model for the structural and functional transitions of SRP throughout the targeting cycle and show that these transitions provide important points for biological regulation that can be perturbed in genetic diseases.
History
DepositionFeb 8, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJun 2, 2021-
Current statusJun 2, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12304.png

Downloads & links

-
Map

FileDownload / File: emd_12304.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfocused refinement of state A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 448 pix.
= 475.776 Å		1.06 Å/pix.
x 448 pix.
= 475.776 Å		1.06 Å/pix.
x 448 pix.
= 475.776 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.062 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.028176036 - 0.057955813
Average (Standard dev.)-1.2989796e-05 (±0.0005650009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 475.776 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0621.0621.062
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z475.776475.776475.776
α/β/γ90.00090.00090.000
start NX/NY/NZ7297100
NX/NY/NZ181127145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.0280.058-0.000

-
Supplemental data

-
Sample components

-
Entire : ribosome nascent chain complex with SRP and SRP receptor

EntireName: ribosome nascent chain complex with SRP and SRP receptor
Components
  • Complex: ribosome nascent chain complex with SRP and SRP receptor
    • RNA: SRP RNA and SRP54

-
Supramolecule #1: ribosome nascent chain complex with SRP and SRP receptor

SupramoleculeName: ribosome nascent chain complex with SRP and SRP receptor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 3.5 MDa

-
Macromolecule #1: SRP RNA and SRP54

MacromoleculeName: SRP RNA and SRP54 / type: rna / ID: 1
Source (natural)Organism: Homo sapiens (human)
SequenceString: LADLGRKITS ALRSLSNATI INEEVLNAML KEVCTALLEA DVNIKLVKQL RENVKSAIDL EEMASGLNK RKMIQHAVFK ELVKLVDPGV KAWTPTKGKQ NVIMFVGLQG SGKTTTCSKL AYYYQRKGWK TCLICADTFR AGAFDQLKQ NATKARIPFY GSYTEMDPVI ...String:
LADLGRKITS ALRSLSNATI INEEVLNAML KEVCTALLEA DVNIKLVKQL RENVKSAIDL EEMASGLNK RKMIQHAVFK ELVKLVDPGV KAWTPTKGKQ NVIMFVGLQG SGKTTTCSKL AYYYQRKGWK TCLICADTFR AGAFDQLKQ NATKARIPFY GSYTEMDPVI IASEGVEKFK NENFEIIIVD TSGRHKQEDS LFEEMLQVAN A IQPDNIVY VMDASIEQAC EAQAKAFKDK VDVASVIVTK LDGHAKGGGA LSAVAATKSP IIFIGTGEHI DD FEPFKTQ PFISKLLGMG DIEGLIDKVN ELKLDDNEAL IEKLKHGQFT LRDMYEQFQN IMKMGPGNEQ ESM ARLKKL MTIMDSMNDQ ELDSTDGAKV FSKQPGRIQR VARGSGVSTR DVQELLTQYT KFAQMVKKMG GI

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV
Detailsin-vitro translation system

-
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 / Cs: 2.7 mm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: INSILICO MODEL / In silico model: using SGD from particles
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33821
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more