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- EMDB-53191: Human Mortalin (mitochondrial Hsp70) in complex with GrpE1 phosph... -

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Basic information

Entry
Database: EMDB / ID: EMD-53191
TitleHuman Mortalin (mitochondrial Hsp70) in complex with GrpE1 phosphorylated at Ser-47
Map data
Sample
  • Complex: Human Mortalin (mitochondrial Hsp70) in complex with GrpE1 phosphorylated at Ser-47
    • Protein or peptide: Stress-70 protein, mitochondrial
    • Protein or peptide: GrpE protein homolog 1, mitochondrial
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsHSP70 / mitochondria / Complex / ATP / CHAPERONE
Function / homology
Function and homology information


PAM complex, Tim23 associated import motor / negative regulation of hemopoiesis / MIB complex / negative regulation of hematopoietic stem cell differentiation / negative regulation of erythrocyte differentiation / SAM complex / TIM23 mitochondrial import inner membrane translocase complex / Cristae formation / inner mitochondrial membrane organization / Complex III assembly ...PAM complex, Tim23 associated import motor / negative regulation of hemopoiesis / MIB complex / negative regulation of hematopoietic stem cell differentiation / negative regulation of erythrocyte differentiation / SAM complex / TIM23 mitochondrial import inner membrane translocase complex / Cristae formation / inner mitochondrial membrane organization / Complex III assembly / adenyl-nucleotide exchange factor activity / calcium import into the mitochondrion / Complex I biogenesis / Mitochondrial protein import / iron-sulfur cluster assembly / protein import into mitochondrial matrix / non-chaperonin molecular chaperone ATPase / mitochondrial nucleoid / Regulation of HSF1-mediated heat shock response / Mitochondrial unfolded protein response (UPRmt) / heat shock protein binding / protein export from nucleus / protein folding chaperone / Mitochondrial protein degradation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / erythrocyte differentiation / ATP-dependent protein folding chaperone / regulation of erythrocyte differentiation / intracellular protein transport / : / protein refolding / protein-folding chaperone binding / protein folding / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / focal adhesion / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
GrpE nucleotide exchange factor / GrpE nucleotide exchange factor, head / GrpE nucleotide exchange factor, coiled-coil / GrpE / grpE protein signature. / Chaperone DnaK / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site ...GrpE nucleotide exchange factor / GrpE nucleotide exchange factor, head / GrpE nucleotide exchange factor, coiled-coil / GrpE / grpE protein signature. / Chaperone DnaK / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Stress-70 protein, mitochondrial / GrpE protein homolog 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsBauer JA / Pinkas M
Funding support Slovakia, Czech Republic, European Union, 6 items
OrganizationGrant numberCountry
Other government2/0069/23 Slovakia
Other governmentAPVV-19-0298 Slovakia
Other governmentAPVV-23-0407 Slovakia
Other government2/0081/24 Slovakia
Ministry of Education (MoE, Czech Republic)LM2023042 Czech Republic
European Regional Development FundCZ.02.01.01/00/23_015/0008175European Union
CitationJournal: To Be Published
Title: Human Mortalin (mitochondrial Hsp70) in complex with wild-type GrpE1
Authors: Havalova H / Ondrovicova G / Pinkas M / Bauer JA / Kutejova E / Pevala V
History
DepositionMar 17, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53191.png

Downloads & links

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Map

FileDownload / File: emd_53191.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.02 Å/pix.
x 256 pix.
= 261.786 Å		1.02 Å/pix.
x 256 pix.
= 261.786 Å		1.02 Å/pix.
x 256 pix.
= 261.786 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0226 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.21657236 - 0.63458407
Average (Standard dev.)0.00016291981 (±0.012808259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 261.7856 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53191_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53191_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Mortalin (mitochondrial Hsp70) in complex with GrpE1 phosph...

EntireName: Human Mortalin (mitochondrial Hsp70) in complex with GrpE1 phosphorylated at Ser-47
Components
  • Complex: Human Mortalin (mitochondrial Hsp70) in complex with GrpE1 phosphorylated at Ser-47
    • Protein or peptide: Stress-70 protein, mitochondrial
    • Protein or peptide: GrpE protein homolog 1, mitochondrial
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Human Mortalin (mitochondrial Hsp70) in complex with GrpE1 phosph...

SupramoleculeName: Human Mortalin (mitochondrial Hsp70) in complex with GrpE1 phosphorylated at Ser-47
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Stress-70 protein, mitochondrial

MacromoleculeName: Stress-70 protein, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.495734 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHSS GLEVLFQGTG AVVGIDLGTT NSCVAVMEGK QAKVLENAEG ARTTPSVVAF TADGERLVGM PAKRQAVTNP NNTFYATKR LIGRRYDDPE VQKDIKNVPF KIVRASNGDA WVEAHGKLYS PSQIGAFVLM KMKETAENYL GHTAKNAVIT V PAYFNDSQ ...String:
MAHHHHHHSS GLEVLFQGTG AVVGIDLGTT NSCVAVMEGK QAKVLENAEG ARTTPSVVAF TADGERLVGM PAKRQAVTNP NNTFYATKR LIGRRYDDPE VQKDIKNVPF KIVRASNGDA WVEAHGKLYS PSQIGAFVLM KMKETAENYL GHTAKNAVIT V PAYFNDSQ RQATKDAGQI SGLNVLRVIN EPTAAALAYG LDKSEDKVIA VYDLGGGTFD ISILEIQKGV FEVKSTNGDT FL GGEDFDQ ALLRHIVKEF KRETGVDLTK DNMALQRVRE AAEKAKCELS SSVQTDINLP YLTMDSSGPK HLNMKLTRAQ FEG IVTDLI RRTIAPCQKA MQDAEVSKSD IGEVILVGGM TRMPKVQQTV QDLFGRAPSK AVNPDEAVAI GAAIQGGVLA GDVT DVLLL DVTPLSLGIE TLGGVFTKLI NRNTTIPTKK SQVFSTAADG QTQVEIKVCQ GEREMAGDNK LLGQFTLIGI PPAPR GVPQ IEVTFDIDAN GIVHVSAKDK GTRREQQIVI QSSGGLSKDD IENMVKNAEK YAEEDRRKKE RVEAVNMAEG IIHDTE TKM EEFKDQLPAD ECNKLKEEIS KMRELLARKD SETGENIRQA ASSLQQASLK LFEMAYKKMA SEREGSGSSG TGEQKED QK EEKQ

UniProtKB: Stress-70 protein, mitochondrial

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Macromolecule #2: GrpE protein homolog 1, mitochondrial

MacromoleculeName: GrpE protein homolog 1, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.600844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHSS GLEVLFQGTC TATKQKNSGQ NLEEDMGQ(SEP)E QKADPPATEK TLLEEKVKLE EQLKETVEKY KRALAD TEN LRQRSQKLVE EAKLYGIQAF CKDLLEVADV LEKATQCVPK EEIKDDNPHL KNLYEGLVMT EVQIQKVFTK HGLLKLN PV GAKFDPYEHE ...String:
MAHHHHHHSS GLEVLFQGTC TATKQKNSGQ NLEEDMGQ(SEP)E QKADPPATEK TLLEEKVKLE EQLKETVEKY KRALAD TEN LRQRSQKLVE EAKLYGIQAF CKDLLEVADV LEKATQCVPK EEIKDDNPHL KNLYEGLVMT EVQIQKVFTK HGLLKLN PV GAKFDPYEHE ALFHTPVEGK EPGTVALVSK VGYKLHGRTL RPALVGVVKE A

UniProtKB: GrpE protein homolog 1, mitochondrial

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 224341
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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