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- EMDB-22919: Full-length human mitochondrial Hsp90 (TRAP1) SpyCatcher/SpyTag-S... -

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Basic information

Entry
Database: EMDB / ID: EMD-22919
TitleFull-length human mitochondrial Hsp90 (TRAP1) SpyCatcher/SpyTag-SdhB heterodimer in the presence of AMP-PNP
Map data
Sample
  • Complex: Full-length human mitochondrial Hsp90 (TRAP1) SpyCatcher/SpyTag-SdhB heterodimer in the presence of AMP-PNP
    • Protein or peptide: Heat shock protein 75 kDa, mitochondrial, SpyCatcherHeat shock response
    • Protein or peptide: Heat shock protein 75 kDa, mitochondrial, SpyTag, Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (chimera)Heat shock response
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM IONPotassium
Function / homology
Function and homology information


translational attenuation / negative regulation of cellular respiration / mitochondrial electron transport, succinate to ubiquinone / mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone) / succinate dehydrogenase (quinone) activity / : / Citric acid cycle (TCA cycle) / succinate dehydrogenase / Respiratory electron transport / tumor necrosis factor receptor binding ...translational attenuation / negative regulation of cellular respiration / mitochondrial electron transport, succinate to ubiquinone / mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone) / succinate dehydrogenase (quinone) activity / : / Citric acid cycle (TCA cycle) / succinate dehydrogenase / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquinone binding / 3 iron, 4 sulfur cluster binding / proton motive force-driven mitochondrial ATP synthesis / chaperone-mediated protein folding / aerobic respiration / negative regulation of reactive oxygen species biosynthetic process / tricarboxylic acid cycle / respiratory electron transport chain / cell periphery / mitochondrial membrane / ATP-dependent protein folding chaperone / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / unfolded protein binding / protein folding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family ...4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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 analysis of human mitochondrial Hsp90 in multiple tetrameric states
Authors: Liu YX / Agard DA / Elnatan D / Sun M / Larson AG
History
DepositionNov 1, 2020-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateNov 3, 2021-
Current statusNov 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7klv
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22919.png

Downloads & links

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Map

FileDownload / File: emd_22919.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8488 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.04762115 - 0.13262628
Average (Standard dev.)-5.492763e-05 (±0.0029190695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.616 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.84880.84880.8488
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z271.616271.616271.616
α/β/γ90.00090.00090.000
start NX/NY/NZ799196
NX/NY/NZ149138117
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0480.133-0.000

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Supplemental data

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Sample components

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Entire : Full-length human mitochondrial Hsp90 (TRAP1) SpyCatcher/SpyTag-S...

EntireName: Full-length human mitochondrial Hsp90 (TRAP1) SpyCatcher/SpyTag-SdhB heterodimer in the presence of AMP-PNP
Components
  • Complex: Full-length human mitochondrial Hsp90 (TRAP1) SpyCatcher/SpyTag-SdhB heterodimer in the presence of AMP-PNP
    • Protein or peptide: Heat shock protein 75 kDa, mitochondrial, SpyCatcherHeat shock response
    • Protein or peptide: Heat shock protein 75 kDa, mitochondrial, SpyTag, Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (chimera)Heat shock response
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM IONPotassium

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Supramolecule #1: Full-length human mitochondrial Hsp90 (TRAP1) SpyCatcher/SpyTag-S...

SupramoleculeName: Full-length human mitochondrial Hsp90 (TRAP1) SpyCatcher/SpyTag-SdhB heterodimer in the presence of AMP-PNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 180 KDa

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Macromolecule #1: Heat shock protein 75 kDa, mitochondrial, SpyCatcher

MacromoleculeName: Heat shock protein 75 kDa, mitochondrial, SpyCatcher / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 87.094617 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEME IHLQTNAEKG TITIQDTGIG MTQEELVSNL GTIARSGSKA FLDALQNQAE ASSKIIGQFG VGFYSAFMVA D RVEVYSRS ...String:
GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEME IHLQTNAEKG TITIQDTGIG MTQEELVSNL GTIARSGSKA FLDALQNQAE ASSKIIGQFG VGFYSAFMVA D RVEVYSRS AAPGSLGYQW LSDGSGVFEI AEASGVRTGT KIIIHLKSDC KEFSSEARVR DVVTKYSNFV SFPLYLNGRR MN TLQAIWM MDPKDVGEWQ HEEFYRYVAQ AHDKPRYTLH YKTDAPLNIR SIFYVPDMKP SMFDVSRELG SSVALYSRKV LIQ TKATDI LPKWLRFIRG VVDSEDIPLN LSRELLQESA LIRKLRDVLQ QRLIKFFIDQ SKKDAEKYAK FFEDYGLFMR EGIV TATEQ EVKEDIAKLL RYESSALPSG QLTSLSEYAS RMRAGTRNIY YLCAPNRHLA EHSPYYEAMK KKDTEVLFCF EQFDE LTLL HLREFDKKKL ISVETDIVVD HYKEEKFEDR SPAAECLSEK ETEELMAWMR NVLGSRVTNV KVTLRLDTHP AMVTVL EMG AARHFLRMQQ LAKTQEERAQ LLQPTLEINP RHALIKKLNQ LRASEPGLAQ LLVDQIYENA MIAAGLVDDP RAMVGRL NE LLVKALERHG GSGSGSSAMV DTLSGLSSEQ GQSGDMTIEE DSATHIKFSK RDEDGKELAG ATMELRDSSG KTISTWIS D GQVKDFYLYP GKYTFVETAA PDGYEVATAI TFTVNEQGQV TVNGKATKGD AHI

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Macromolecule #2: Heat shock protein 75 kDa, mitochondrial, SpyTag, Succinate dehyd...

MacromoleculeName: Heat shock protein 75 kDa, mitochondrial, SpyTag, Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (chimera)
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.121344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEME IHLQTNAEKG TITIQDTGIG MTQEELVSNL GTIARSGSKA FLDALQNQAE ASSKIIGQFG VGFYSAFMVA D RVEVYSRS ...String:
GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEME IHLQTNAEKG TITIQDTGIG MTQEELVSNL GTIARSGSKA FLDALQNQAE ASSKIIGQFG VGFYSAFMVA D RVEVYSRS AAPGSLGYQW LSDGSGVFEI AEASGVRTGT KIIIHLKSDC KEFSSEARVR DVVTKYSNFV SFPLYLNGRR MN TLQAIWM MDPKDVGEWQ HEEFYRYVAQ AHDKPRYTLH YKTDAPLNIR SIFYVPDMKP SMFDVSRELG SSVALYSRKV LIQ TKATDI LPKWLRFIRG VVDSEDIPLN LSRELLQESA LIRKLRDVLQ QRLIKFFIDQ SKKDAEKYAK FFEDYGLFMR EGIV TATEQ EVKEDIAKLL RYESSALPSG QLTSLSEYAS RMRAGTRNIY YLCAPNRHLA EHSPYYEAMK KKDTEVLFCF EQFDE LTLL HLREFDKKKL ISVETDIVVD HYKEEKFEDR SPAAECLSEK ETEELMAWMR NVLGSRVTNV KVTLRLDTHP AMVTVL EMG AARHFLRMQQ LAKTQEERAQ LLQPTLEINP RHALIKKLNQ LRASEPGLAQ LLVDQIYENA MIAAGLVDDP RAMVGRL NE LLVKALERHG GSGSGSSAHI VMVDAYKPTK GGGGSGGGGS GGGGSLEVLF QGPGSAQTAA ATAPRIKKFA IYRWDPDK A GDKPHMQTYE VDLNKCGPMV LDALIKIKNE VDSTLTFRRS CREGICGSCA MNINGGNTLA CTRRIDTNLN KVSKIYPLP HMYVIKDLVP DLSNFYAQYK SIEPYLKKK

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 66.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

6xg6

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162653
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6xg6

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7klv:
Full-length human mitochondrial Hsp90 (TRAP1) SpyCatcher/SpyTag-SdhB heterodimer in the presence of AMP-PNP

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