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- PDB-9qin: Human Mortalin (mitochondrial Hsp70) in complex with GrpE1 phosph... -

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Basic information

Entry
Database: PDB / ID: 9qin
TitleHuman Mortalin (mitochondrial Hsp70) in complex with GrpE1 phosphorylated at Ser-47
Components
  • GrpE protein homolog 1, mitochondrial
  • Stress-70 protein, mitochondrial
KeywordsCHAPERONE / HSP70 / mitochondria / Complex / ATP
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
ADENOSINE-5'-TRIPHOSPHATE / Stress-70 protein, mitochondrial / GrpE protein homolog 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsBauer, J.A. / Pinkas, M.
Funding support Slovakia, Czech Republic, European Union, 6items
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, J.A. / Kutejova, E. / Pevala, V.
History
DepositionMar 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stress-70 protein, mitochondrial
B: GrpE protein homolog 1, mitochondrial
C: GrpE protein homolog 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2295
Polymers117,6973
Non-polymers5312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Stress-70 protein, mitochondrial / 75 kDa glucose-regulated protein / GRP-75 / Heat shock 70 kDa protein 9 / Heat shock protein family ...75 kDa glucose-regulated protein / GRP-75 / Heat shock 70 kDa protein 9 / Heat shock protein family A member 9 / Mortalin / MOT / Peptide-binding protein 74 / PBP74


Mass: 70495.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA9, GRP75, HSPA9B, mt-HSP70 / Production host: Escherichia coli (E. coli) / References: UniProt: P38646
#2: Protein GrpE protein homolog 1, mitochondrial / HMGE / Mt-GrpE#1


Mass: 23600.844 Da / Num. of mol.: 2 / Mutation: S47(SEP)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRPEL1, GREPEL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HAV7
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human Mortalin (mitochondrial Hsp70) in complex with GrpE1 phosphorylated at Ser-47
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21rc1_5127model refinement
5cryoSPARCCTF correction
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224341 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 146.73 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00437311
ELECTRON MICROSCOPYf_angle_d0.55259865
ELECTRON MICROSCOPYf_chiral_restr0.0421141
ELECTRON MICROSCOPYf_plane_restr0.00371281
ELECTRON MICROSCOPYf_dihedral_angle_d3.58989

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