[English] 日本語
Yorodumi
- EMDB-22813: Mitochondrial Hsp90 (TRAP1) in complex with SdhB folding intermed... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22813
TitleMitochondrial Hsp90 (TRAP1) in complex with SdhB folding intermediate state in the presence of AMP-PNP
Map data
Sample
  • Complex: human Trap1 in complex with SdhB in the presence of AMP-PNP
    • Protein or peptide: TRAP1
    • Protein or peptide: TRAP1
    • Protein or peptide: Succinate dehydrogenase iron-sulfur subunit, mitochondrial SDHB
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsLiu YX / Agard DA
Funding support United States, 6 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
American Heart Association18POST33990362 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118099 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U54CA209891 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)U01MH115747 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI135990 United States
CitationJournal: To Be Published
Title: Cryo-EM reveals the dynamic interplay between mitochondrial Hsp90 and SdhB folding intermediates
Authors: Liu YX / Agard DA / Elnatan D / Sun M / Myasnikov AG
History
DepositionOct 6, 2020-
Header (metadata) releaseOct 13, 2021-
Map releaseOct 13, 2021-
UpdateOct 13, 2021-
Current statusOct 13, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22813.png

Downloads & links

-
Map

FileDownload / File: emd_22813.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 320 pix.
= 260.48 Å		0.81 Å/pix.
x 320 pix.
= 260.48 Å		0.81 Å/pix.
x 320 pix.
= 260.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.814 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.03216292 - 0.08874026
Average (Standard dev.)-4.9679682e-05 (±0.0021533123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 260.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8140.8140.814
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z260.480260.480260.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0320.089-0.000

-
Supplemental data

-
Additional map: #1

Fileemd_22813_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : human Trap1 in complex with SdhB in the presence of AMP-PNP

EntireName: human Trap1 in complex with SdhB in the presence of AMP-PNP
Components
  • Complex: human Trap1 in complex with SdhB in the presence of AMP-PNP
    • Protein or peptide: TRAP1
    • Protein or peptide: TRAP1
    • Protein or peptide: Succinate dehydrogenase iron-sulfur subunit, mitochondrial SDHB

-
Supramolecule #1: human Trap1 in complex with SdhB in the presence of AMP-PNP

SupramoleculeName: human Trap1 in complex with SdhB in the presence of AMP-PNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 162 KDa

-
Macromolecule #1: TRAP1

MacromoleculeName: TRAP1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEMEI HLQTNAEKGT ITIQDTGIGM TQEELVSNLG TIARSGSKAF LDALQNQAEA SSKIIGQFGV GFYSAFMVAD RVEVYSRSAA ...String:
GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEMEI HLQTNAEKGT ITIQDTGIGM TQEELVSNLG TIARSGSKAF LDALQNQAEA SSKIIGQFGV GFYSAFMVAD RVEVYSRSAA PGSLGYQWLS DGSGVFEIAE ASGVRTGTKI IIHLKSDCKE FSSEARVRDV VTKYSNFVSF PLYLNGRRMN TLQAIWMMDP KDVGEWQHEE FYRYVAQAHD KPRYTLHYKT DAPLNIRSIF YVPDMKPSMF DVSRELGSSV ALYSRKVLIQ TKATDILPKW LRFIRGVVDS EDIPLNLSRE LLQESALIRK LRDVLQQRLI KFFIDQSKKD AEKYAKFFED YGLFMREGIV TATEQEVKED IAKLLRYESS ALPSGQLTSL SEYASRMRAG TRNIYYLCAP NRHLAEHSPY YEAMKKKDTE VLFCFEQFDE LTLLHLREFD KKKLISVETD IVVDHYKEEK FEDRSPAAEC LSEKETEELM AWMRNVLGSR VTNVKVTLRL DTHPAMVTVL EMGAARHFLR MQQLAKTQEE RAQLLQPTLE INPRHALIKK LNQLRASEPG LAQLLVDQIY ENAMIAAGLV DDPRAMVGRL NELLVKALER H

-
Macromolecule #2: TRAP1

MacromoleculeName: TRAP1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEMEI HLQTNAEKGT ITIQDTGIGM TQEELVSNLG TIARSGSKAF LDALQNQAEA SSKIIGQFGV GFYSAFMVAD RVEVYSRSAA ...String:
GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEMEI HLQTNAEKGT ITIQDTGIGM TQEELVSNLG TIARSGSKAF LDALQNQAEA SSKIIGQFGV GFYSAFMVAD RVEVYSRSAA PGSLGYQWLS DGSGVFEIAE ASGVRTGTKI IIHLKSDCKE FSSEARVRDV VTKYSNFVSF PLYLNGRRMN TLQAIWMMDP KDVGEWQHEE FYRYVAQAHD KPRYTLHYKT DAPLNIRSIF YVPDMKPSMF DVSRELGSSV ALYSRKVLIQ TKATDILPKW LRFIRGVVDS EDIPLNLSRE LLQESALIRK LRDVLQQRLI KFFIDQSKKD AEKYAKFFED YGLFMREGIV TATEQEVKED IAKLLRYESS ALPSGQLTSL SEYASRMRAG TRNIYYLCAP NRHLAEHSPY YEAMKKKDTE VLFCFEQFDE LTLLHLREFD KKKLISVETD IVVDHYKEEK FEDRSPAAEC LSEKETEELM AWMRNVLGSR VTNVKVTLRL DTHPAMVTVL EMGAARHFLR MQQLAKTQEE RAQLLQPTLE INPRHALIKK LNQLRASEPG LAQLLVDQIY ENAMIAAGLV DDPRAMVGRL NELLVKALER H

-
Macromolecule #3: Succinate dehydrogenase iron-sulfur subunit, mitochondrial SDHB

MacromoleculeName: Succinate dehydrogenase iron-sulfur subunit, mitochondrial SDHB
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSAQTAAATA PRIKKFAIYR WDPDKAGDKP HMQTYEVDLN KCGPMVLDAL IKIKNEVDST LTFRRSCREG ICGSCAMNIN GGNTLACTRR IDTNLNKVSK IYPLPHMYVI KDLVPDLSNF YAQYKSIEPY LKKK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xg6

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80304
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

6xg6


1zoy

chain_id: B
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

+
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