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- PDB-7n1r: A novel and unique ATP hydrolysis to AMP by a human Hsp70 BiP -

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Basic information

Entry
Database: PDB / ID: 7n1r
TitleA novel and unique ATP hydrolysis to AMP by a human Hsp70 BiP
ComponentsEndoplasmic reticulum chaperone BiP
KeywordsCHAPERONE / protein-ligand complex
Function / homology
Function and homology information


regulation of protein folding in endoplasmic reticulum / regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / cerebellum structural organization / maintenance of protein localization in endoplasmic reticulum / negative regulation of IRE1-mediated unfolded protein response / IRE1alpha activates chaperones / cerebellar Purkinje cell layer development ...regulation of protein folding in endoplasmic reticulum / regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / cerebellum structural organization / maintenance of protein localization in endoplasmic reticulum / negative regulation of IRE1-mediated unfolded protein response / IRE1alpha activates chaperones / cerebellar Purkinje cell layer development / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / PERK regulates gene expression / protein folding in endoplasmic reticulum / misfolded protein binding / post-translational protein targeting to membrane, translocation / ERAD pathway / ER overload response / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / endoplasmic reticulum-Golgi intermediate compartment / Regulation of HSF1-mediated heat shock response / cellular response to glucose starvation / negative regulation of protein-containing complex assembly / : / endoplasmic reticulum unfolded protein response / protein folding chaperone / heat shock protein binding / substantia nigra development / cellular response to interleukin-4 / response to endoplasmic reticulum stress / positive regulation of protein ubiquitination / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / melanosome / unfolded protein binding / ribosome binding / Platelet degranulation / midbody / protein-folding chaperone binding / protein refolding / positive regulation of cell migration / cadherin binding / protein domain specific binding / endoplasmic reticulum lumen / focal adhesion / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / endoplasmic reticulum / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Endoplasmic reticulum targeting sequence. / 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, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
Model detailsA crystal structure of BiP in the complex with AMP after the hydrolysis of ATP included in the ...A crystal structure of BiP in the complex with AMP after the hydrolysis of ATP included in the crystallization buffer by BiP.
AuthorsYang, J. / Musayev, F. / Liu, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098592 United States
CitationJournal: Protein Sci. / Year: 2022
Title: A novel and unique ATP hydrolysis to AMP by a human Hsp70 Binding immunoglobin protein (BiP).
Authors: Li, H. / Musayev, F.N. / Yang, J. / Su, J. / Liu, Q. / Wang, W. / Fang, X. / Zhou, L. / Liu, Q.
History
DepositionMay 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmic reticulum chaperone BiP
B: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,96835
Polymers134,4762
Non-polymers3,49233
Water19,2401068
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A: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,03618
Polymers67,2381
Non-polymers1,79817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,93217
Polymers67,2381
Non-polymers1,69416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.988, 76.388, 79.917
Angle α, β, γ (deg.)84.880, 62.490, 63.140
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Endoplasmic reticulum chaperone BiP / 78 kDa glucose-regulated protein / GRP-78 / Binding-immunoglobulin protein / BiP / Heat shock ...78 kDa glucose-regulated protein / GRP-78 / Binding-immunoglobulin protein / BiP / Heat shock protein 70 family protein 5 / HSP70 family protein 5 / Heat shock protein family A member 5 / Immunoglobulin heavy chain-binding protein


Mass: 67237.977 Da / Num. of mol.: 2 / Fragment: UNP residue 25-633 / Mutation: L3,4 modification (TASDNQP to VGG)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P11021, non-chaperonin molecular chaperone ATPase

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Non-polymers , 7 types, 1101 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1068 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4.5
Details: 18-22% PEG1000, 0.1 M phosphate citrate, pH 4.5, 0.2 M lithium sulfate, 2% w/v dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 83507 / % possible obs: 97.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 35.976 Å2 / CC1/2: 0.985 / R split: 0.067 / Rrim(I) all: 0.095 / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 3 / Num. unique obs: 5328 / CC1/2: 0.76 / CC star: 0.929 / Rpim(I) all: 0.369 / Rrim(I) all: 0.519 / Χ2: 2.004 / % possible all: 84.11

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6ASY

6asy


Resolution: 2.03→45.31 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.673 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 4408 5 %RANDOM
Rwork0.1743 ---
obs0.1768 83507 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 198.85 Å2 / Biso mean: 31.885 Å2 / Biso min: 3.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å21.74 Å2-0.7 Å2
2--0.5 Å2-1 Å2
3---0.54 Å2
Refinement stepCycle: final / Resolution: 2.03→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9418 0 203 1068 10689
Biso mean--41.84 31.56 -
Num. residues----1212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0149868
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179096
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.68713353
X-RAY DIFFRACTIONr_angle_other_deg0.8961.65521391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83851246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94424.049494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51151812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3631552
X-RAY DIFFRACTIONr_chiral_restr0.0690.21331
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210971
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021635
LS refinement shellResolution: 2.03→2.083 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 304 -
Rwork0.238 5328 -
all-5632 -
obs--84.11 %

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