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- PDB-7a4v: Crystal structure of lid-truncated ADP-bound BiP in an oligomeric... -

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Basic information

Entry
Database: PDB / ID: 7a4v
TitleCrystal structure of lid-truncated ADP-bound BiP in an oligomeric state
ComponentsEndoplasmic reticulum chaperone BiP
KeywordsCHAPERONE / ER / Endoplasmic reticulum / Hsp70 / GRP78
Function / homology
Function and homology information


negative regulation of IRE1-mediated unfolded protein response / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / negative regulation of protein-containing complex assembly / ATP-dependent protein folding chaperone / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process ...negative regulation of IRE1-mediated unfolded protein response / post-translational protein targeting to membrane, translocation / non-chaperonin molecular chaperone ATPase / negative regulation of protein-containing complex assembly / ATP-dependent protein folding chaperone / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol
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-5'-DIPHOSPHATE / : / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsPerera, L.A. / Ron, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust200848/Z/16/Z United Kingdom
CitationJournal: Elife / Year: 2020
Title: Calcium depletion challenges endoplasmic reticulum proteostasis by destabilising BiP-substrate complexes.
Authors: Preissler, S. / Rato, C. / Yan, Y. / Perera, L.A. / Czako, A. / Ron, D.
History
DepositionAug 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1945
Polymers57,5431
Non-polymers6504
Water5,693316
1
A: Endoplasmic reticulum chaperone BiP
hetero molecules

A: Endoplasmic reticulum chaperone BiP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,38710
Polymers115,0862
Non-polymers1,3018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
Unit cell
Length a, b, c (Å)50.179, 51.249, 118.801
Angle α, β, γ (deg.)90.000, 99.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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: 57543.043 Da / Num. of mol.: 1 / Mutation: T229A, V461F
Source method: isolated from a genetically manipulated source
Details: Ser27 is the remnants of an expression tag / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: HSPA5, GRP78, I79_019946 / Production host: Escherichia coli M15 (bacteria)
References: UniProt: G3I8R9, non-chaperonin molecular chaperone ATPase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.619433 Å3/Da / Density % sol: 53.07245 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M potassium citrate tribasic monohydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.94→29.27 Å / Num. obs: 43705 / % possible obs: 99.1 % / Redundancy: 3.3 % / CC1/2: 0.999 / Net I/σ(I): 13.7
Reflection shellResolution: 1.94→1.99 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2937 / CC1/2: 0.717 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HAB

6hab


Resolution: 1.94→29.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.117 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 2186 5 %RANDOM
Rwork0.1839 ---
obs0.186 41507 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.97 Å2 / Biso mean: 34.398 Å2 / Biso min: 17.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å2-0.44 Å2
2---1.35 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.94→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 40 316 4293
Biso mean--44.88 42.64 -
Num. residues----521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134082
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173898
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.655535
X-RAY DIFFRACTIONr_angle_other_deg1.2331.5858977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62223.834193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61815691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5861520
X-RAY DIFFRACTIONr_chiral_restr0.0560.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02867
LS refinement shellResolution: 1.944→1.995 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 138 -
Rwork0.272 2926 -
all-3064 -
obs--94.68 %

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