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- PDB-9qid: Human Mortalin (mitochondrial Hsp70) in complex with wild-type GrpE1 -

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Basic information

Entry
Database: PDB / ID: 9qid
TitleHuman Mortalin (mitochondrial Hsp70) in complex with wild-type GrpE1
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: 2.73 Å
AuthorsBauer, J.A. / Pinkas, M.
Funding support Slovakia, Czech Republic, European Union, 6items
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
Citation
Journal: 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.
#1: Journal: 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, 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)118,0695
Polymers117,5373
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: 23520.863 Da / Num. of mol.: 2
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 wild-type GrpE1
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: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175318 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 137.62 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00337311
ELECTRON MICROSCOPYf_angle_d0.49279865
ELECTRON MICROSCOPYf_chiral_restr0.04081141
ELECTRON MICROSCOPYf_plane_restr0.00291281
ELECTRON MICROSCOPYf_dihedral_angle_d3.4308989

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