[English] 日本語
Yorodumi
- EMDB-18674: Structure of nPBD of human SRP68/72 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18674
TitleStructure of nPBD of human SRP68/72
Map dataPostprocessed EM map
Sample
  • Complex: SRP68/72
    • Protein or peptide: Signal recognition particle subunit SRP68
    • Protein or peptide: Signal recognition particle subunit SRP72
KeywordsSignal recognition particle / TPR / protein translocation / TRANSLATION
Function / homology
Function and homology information


signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / endoplasmic reticulum signal peptide binding / signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / TPR domain binding / SRP-dependent cotranslational protein targeting to membrane / ribosome binding / ribosome ...signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / endoplasmic reticulum signal peptide binding / signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / TPR domain binding / SRP-dependent cotranslational protein targeting to membrane / ribosome binding / ribosome / response to xenobiotic stimulus / protein domain specific binding / focal adhesion / nucleolus / endoplasmic reticulum / RNA binding / cytosol
Similarity search - Function
Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Putative TPR-like repeat / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Tetratricopeptide repeat ...Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Putative TPR-like repeat / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Signal recognition particle subunit SRP72 / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhong Y / Feng J / Koh AF / Kotecha A / Greber BJ / Ataide SF
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V009354/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of nPBD of human SRP68/72
Authors: Zhong Y / Feng J / Koh AF / Kotecha A / Greber BJ / Ataide SF
History
DepositionOct 18, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18674.png

Downloads & links

-
Map

FileDownload / File: emd_18674.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed EM map
Voxel sizeX=Y=Z: 1.14 Å
Density
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.047912624 - 0.088216074
Average (Standard dev.)0.000019769173 (±0.00197382)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 205.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18674_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered half-map

Fileemd_18674_half_map_1.map
AnnotationUnfiltered half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered half-map

Fileemd_18674_half_map_2.map
AnnotationUnfiltered half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SRP68/72

EntireName: SRP68/72
Components
  • Complex: SRP68/72
    • Protein or peptide: Signal recognition particle subunit SRP68
    • Protein or peptide: Signal recognition particle subunit SRP72

-
Supramolecule #1: SRP68/72

SupramoleculeName: SRP68/72 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140 KDa

-
Macromolecule #1: Signal recognition particle subunit SRP68

MacromoleculeName: Signal recognition particle subunit SRP68 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.617305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKEFGDSLSL EILQIIKESQ QQHGLRHGDF QRYRGYCSRR QRRLRKTLNF KMGNRHKFTG KKVTEELLTD NRYLLLVLMD AERAWSYAM QLKQEANTEP RKRFHLLSRL RKAVKHAEEL ERLCESNRVD AKTKLEAQAY TAYLSGMLRF EHQEWKAAIE A FNKCKTIY ...String:
MKEFGDSLSL EILQIIKESQ QQHGLRHGDF QRYRGYCSRR QRRLRKTLNF KMGNRHKFTG KKVTEELLTD NRYLLLVLMD AERAWSYAM QLKQEANTEP RKRFHLLSRL RKAVKHAEEL ERLCESNRVD AKTKLEAQAY TAYLSGMLRF EHQEWKAAIE A FNKCKTIY EKLASAFTEE QAVLYNQRVE EISPNIRYCA YNIGDQSAIN ELMQMRLRSG GTEGLLAEKL EALITQTRAK QA ATMSEVE WRGRTVPVKI DKVRIFLLGL ADNEAAIVQA ESEETKERLF ESMLSECRDA IQVVREELKP DQKQRDYILE GEP GKVSNL QYLHSYLTYI KLSTAIKRNE NMAKGLQRAL LQQQPEDDSK RSPRPQDLIR LYDIILQNLV ELLQLPGLEE DKAF QKEIG LKTLVFKAYR CFFIAQSYVL VKKWSEALVL YDRVLKYANE VNSDAGAFKN SLKDLPDVQE LITQVRSEKC SLQAA AILD ANDAHQTETS SSQVKDNKPL VERFETFCLD PSLVTKQANL VHFPPGFQPI PCKPLFFDLA LNHVAFPPLE DKLEQK TKS GLTGYIKGIF GFRS

UniProtKB: Signal recognition particle subunit SRP68

-
Macromolecule #2: Signal recognition particle subunit SRP72

MacromoleculeName: Signal recognition particle subunit SRP72 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.992531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMASGGSG GVSVPALWSE VNRYGQNGDF TRALKTVNKI LQINKDDVTA LHCKVVCLIQ NGSFKEALNV INTHTKVLAN NSLSFEKAY CEYRLNRIEN ALKTIESANQ QTDKLKELYG QVLYRLERYD ECLAVYRDLV RNSQDDYDEE RKTNLSAVVA A QSNWEKVV ...String:
SNAMASGGSG GVSVPALWSE VNRYGQNGDF TRALKTVNKI LQINKDDVTA LHCKVVCLIQ NGSFKEALNV INTHTKVLAN NSLSFEKAY CEYRLNRIEN ALKTIESANQ QTDKLKELYG QVLYRLERYD ECLAVYRDLV RNSQDDYDEE RKTNLSAVVA A QSNWEKVV PENLGLQEGT HELCYNTACA LIGQGQLNQA MKILQKAEDL CRRSLSEDTD GTEEDPQAEL AIIHGQMAYI LQ LQGRTEE ALQLYNQIIK LKPTDVGLLA VIANNIITIN KDQNVFDSKK KVKLTNAEGV EFKLSKKQLQ AIEFNKALLA MYT NQAEQC RKISASLQSQ SPEHLLPVLI QAAQLCREKQ HTKAIELLQE FSDQHPENAA EIKLTMAQLK ISQGNISKAC LILR SIEEL KHKPGMVSAL VTMYSHEEDI DSAIEVFTQA IQWYQNHQPK SPAHLSLIRE AANFKLKYGR KKEAISDLQQ LWKQN PKDI HTLAQLISAY SLVDPEKAKA LSKHLPSSDS MSLKVDVEAL ENSAGATYIR KKGGKVTGDS QPKEQGQGDL KKKKKK KKG KLPKNYDPKV TPDPERWLPM RERSYYRGRK KGKKKDQIGK GTQGATAGAS SELDASKTVS SPPTSPRPGS AATVSAS TS NIIPPRHQKP AGAPATKKKQ QQKKKKGGKG GW

UniProtKB: Signal recognition particle subunit SRP72

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMKClPotassium Chloride
400.0 mMNaClSodium Chloride
10.0 mMMgCl2Magnesium Chloride
50.0 mMHEPES-KOH
0.5 mMTCEP
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 18601 / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 245614 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsCollected movies in EER format.
Startup modelType of model: OTHER
Details: Initial reference generated from refining of a particle subset against a rod-like density.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Details: BLUSH regularisation in RELION 5 used. / Number images used: 38514
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5) / Details: BLUSH regularisation in RELION 5 used.
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 5) / Details: BLUSH regularisation in RELION 5 used.

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8qvw:
Cryo-EM structure of the peptide binding domain of human SRP68/72

+
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://pdbjlvh1.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