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- EMDB-53186: Human Mortalin (mitochondrial Hsp70) in complex with wild-type GrpE1 -

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Basic information

Entry
Database: EMDB / ID: EMD-53186
TitleHuman Mortalin (mitochondrial Hsp70) in complex with wild-type GrpE1
Map data
Sample
  • Complex: Human Mortalin (mitochondrial Hsp70) in complex with wild-type GrpE1
    • 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: 2.73 Å
AuthorsBauer JA / Pinkas M
Funding support Slovakia, Czech Republic, European Union, 6 items
OrganizationGrant numberCountry
Other governmentVEGA-2/0069/23 Slovakia
Other governmentAPVV-19-0298 Slovakia
Other governmentAPVV-23-0407 Slovakia
Other governmentVEGA-2/0081/24 Slovakia
Ministry of Education (MoE, Czech Republic)LM2023042 Czech Republic
European Regional Development FundCZ.02.01.01/00/23_015/0008175European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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_53186.png

Downloads & links

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Map

FileDownload / File: emd_53186.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: 0.07
Minimum - Maximum-0.25113112 - 0.5848502
Average (Standard dev.)0.00013730282 (±0.012478727)
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_53186_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_53186_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 wild-type GrpE1

EntireName: Human Mortalin (mitochondrial Hsp70) in complex with wild-type GrpE1
Components
  • Complex: Human Mortalin (mitochondrial Hsp70) in complex with wild-type GrpE1
    • 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 wild-type GrpE1

SupramoleculeName: Human Mortalin (mitochondrial Hsp70) in complex with wild-type GrpE1
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: 23.520863 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHSS GLEVLFQGTC TATKQKNSGQ NLEEDMGQSE QKADPPATEK TLLEEKVKLE EQLKETVEKY KRALADTENL RQRSQKLVE EAKLYGIQAF CKDLLEVADV LEKATQCVPK EEIKDDNPHL KNLYEGLVMT EVQIQKVFTK HGLLKLNPVG A KFDPYEHE ...String:
MAHHHHHHSS GLEVLFQGTC TATKQKNSGQ NLEEDMGQSE QKADPPATEK TLLEEKVKLE EQLKETVEKY KRALADTENL RQRSQKLVE EAKLYGIQAF CKDLLEVADV LEKATQCVPK EEIKDDNPHL KNLYEGLVMT EVQIQKVFTK HGLLKLNPVG A KFDPYEHE 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: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 175318
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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