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- PDB-4kbo: Crystal structure of the human Mortalin (GRP75) ATPase domain in ... -

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Basic information

Entry
Database: PDB / ID: 4kbo
TitleCrystal structure of the human Mortalin (GRP75) ATPase domain in the apo form
ComponentsStress-70 protein, mitochondrial
KeywordsSIGNALING PROTEIN / ATPase / ATP Binding
Function / homology
Function and homology information


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 / inner mitochondrial membrane organization / Cristae formation / Mitochondrial protein import / iron-sulfur cluster assembly ...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 / inner mitochondrial membrane organization / Cristae formation / Mitochondrial protein import / iron-sulfur cluster assembly / mitochondrial nucleoid / chaperone cofactor-dependent protein refolding / Regulation of HSF1-mediated heat shock response / protein folding chaperone / Mitochondrial protein degradation / heat shock protein binding / protein export from nucleus / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / erythrocyte differentiation / ATP-dependent protein folding chaperone / intracellular protein transport / regulation of erythrocyte differentiation / unfolded protein binding / protein refolding / mitochondrial inner membrane / mitochondrial matrix / focal adhesion / ubiquitin protein ligase binding / nucleolus / negative regulation of apoptotic process / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / ATP binding / nucleus / cytoplasm
Similarity search - Function
Chaperone DnaK / Defensin A-like - #30 / Defensin A-like / 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 70 family / Hsp70 protein ...Chaperone DnaK / Defensin A-like - #30 / Defensin A-like / 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 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Stress-70 protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAmick, J. / Page, R.C. / Nix, J.C. / Misra, S.
CitationJournal: Protein Sci. / Year: 2014
Title: Crystal structure of the nucleotide-binding domain of mortalin, the mitochondrial Hsp70 chaperone.
Authors: Amick, J. / Schlanger, S.E. / Wachnowsky, C. / Moseng, M.A. / Emerson, C.C. / Dare, M. / Luo, W.I. / Ithychanda, S.S. / Nix, J.C. / Cowan, J.A. / Page, R.C. / Misra, S.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2May 7, 2014Group: Other
Revision 1.3May 21, 2014Group: Database references
Revision 1.4Jun 4, 2014Group: Database references
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stress-70 protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4392
Polymers41,4161
Non-polymers231
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.197, 67.812, 120.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 41416.062 Da / Num. of mol.: 1 / Fragment: NUCLEOTIDE BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRP75, HSPA9, HSPA9B / Plasmid: pGST//2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P38646
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350, 0.2M di-ammonium tartrate, 0.02M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1
DetectorType: NOIR-1 / Detector: CCD / Date: Jan 14, 2013
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→60.384 Å / Num. all: 10669 / Num. obs: 10669 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 96.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
SCALAdata scaling
PHENIX(1.8.1_1168)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E88

2e88


Resolution: 2.8→60.38 Å / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 500 5 %RANDOM
Rwork0.2184 ---
obs0.2214 10008 91.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→60.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 1 7 2787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132817
X-RAY DIFFRACTIONf_angle_d0.863823
X-RAY DIFFRACTIONf_dihedral_angle_d13.4711023
X-RAY DIFFRACTIONf_chiral_restr0.059450
X-RAY DIFFRACTIONf_plane_restr0.004508
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.8-3.08180.3321100.29872164216485
3.0818-3.52770.31711260.24732346234693
3.5277-4.44430.23411280.19472443244395
4.4443-60.39850.25161360.18952555255594

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