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- PDB-6nhk: Mortalin nucleotide binding domain in the ADP-bound state -

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Basic information

Entry
Database: PDB / ID: 6nhk
TitleMortalin nucleotide binding domain in the ADP-bound state
ComponentsStress-70 protein, mitochondrial
KeywordsCHAPERONE / Hsp70 / Mitochondrial
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Stress-70 protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.777 Å
AuthorsPage, R.C. / Moseng, M.A. / Nix, J.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R35 GM128595 United States
National Science Foundation (NSF, United States)MCB 15-52113 United States
CitationJournal: J.Phys.Chem.B / Year: 2019
Title: Biophysical Consequences of EVEN-PLUS Syndrome Mutations for the Function of Mortalin.
Authors: Moseng, M.A. / Nix, J.C. / Page, R.C.
History
DepositionDec 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
B: Stress-70 protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6739
Polymers82,4882
Non-polymers1,1857
Water1448
1
A: Stress-70 protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8825
Polymers41,2441
Non-polymers6394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Stress-70 protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7904
Polymers41,2441
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.263, 60.102, 91.699
Angle α, β, γ (deg.)90.00, 97.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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: 41243.926 Da / Num. of mol.: 2 / Mutation: I363L
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) / Strain (production host): Rosetta 2(DE3) / References: UniProt: P38646

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Non-polymers , 5 types, 15 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.17 M Ammonium Acetate, 0.085 M Sodium Citrate:HCl pH 5.6, 25.5% (w/v) PEG 4000, 15% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.777→56.87 Å / Num. obs: 24320 / % possible obs: 99.08 % / Redundancy: 3.7 % / Biso Wilson estimate: 73.51 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.61
Reflection shellResolution: 2.777→2.877 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2310 / CC1/2: 0.54 / % possible all: 94

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ATU

3atu


Resolution: 2.777→56.868 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.2
RfactorNum. reflection% reflection
Rfree0.2958 1989 8.19 %
Rwork0.2555 --
obs0.2588 24273 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.777→56.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 0 72 8 5370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035434
X-RAY DIFFRACTIONf_angle_d0.6077424
X-RAY DIFFRACTIONf_dihedral_angle_d12.631849
X-RAY DIFFRACTIONf_chiral_restr0.045888
X-RAY DIFFRACTIONf_plane_restr0.005983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7775-2.84690.45241290.40711479X-RAY DIFFRACTION92
2.8469-2.92390.43791410.39261573X-RAY DIFFRACTION99
2.9239-3.00990.42441430.36841590X-RAY DIFFRACTION100
3.0099-3.10710.39911420.35781570X-RAY DIFFRACTION99
3.1071-3.21810.43331420.33791604X-RAY DIFFRACTION100
3.2181-3.34690.30861400.31031582X-RAY DIFFRACTION100
3.3469-3.49920.36881410.30411585X-RAY DIFFRACTION100
3.4992-3.68370.36981430.29161592X-RAY DIFFRACTION100
3.6837-3.91440.3051430.28221595X-RAY DIFFRACTION100
3.9144-4.21660.28271450.25311617X-RAY DIFFRACTION100
4.2166-4.64080.27621430.23381602X-RAY DIFFRACTION100
4.6408-5.31190.27761440.23251603X-RAY DIFFRACTION100
5.3119-6.69070.27171460.24181631X-RAY DIFFRACTION100
6.6907-56.87960.20321470.17151661X-RAY DIFFRACTION99

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