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- PDB-6eob: Crystal structure of AMPylated GRP78 in apo form (Crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 6eob
TitleCrystal structure of AMPylated GRP78 in apo form (Crystal form 1)
Components78 kDa glucose-regulated protein
KeywordsCHAPERONE / AMPylation / GRP78 / Bip
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 / melanosome / endoplasmic reticulum lumen / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm ...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 / 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 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 70kD, C-terminal domain superfamily ...Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / 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 / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYan, Y. / Preissler, S. / Ron, D. / Read, R.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust200848/Z/16/Z United Kingdom
Wellcome Trust082961/Z/07/Z United Kingdom
British Heart FoundationPG/12/41/29679 United Kingdom
CitationJournal: Elife / Year: 2017
Title: AMPylation targets the rate-limiting step of BiP's ATPase cycle for its functional inactivation.
Authors: Preissler, S. / Rohland, L. / Yan, Y. / Chen, R. / Read, R.J. / Ron, D.
History
DepositionOct 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Nov 7, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Jan 17, 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: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5032
Polymers57,4081
Non-polymers951
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, shown as a monomer by size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-8 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.650, 69.070, 122.230
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 78 kDa glucose-regulated protein


Mass: 57407.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PO4 / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: I79_019946 / Production host: Escherichia coli (E. coli) / References: UniProt: G3I8R9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG1000, 0.1M NaKHPO4, PH6.2, 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2→61.12 Å / Num. obs: 37758 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.094 / Net I/σ(I): 8.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2743 / CC1/2: 0.522 / Rpim(I) all: 0.782 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O4P

5o4p


Resolution: 2→61.12 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.91 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27955 1871 5 %RANDOM
Rwork0.23814 ---
obs0.24014 35827 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.668 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å2-0 Å2
2---3.16 Å20 Å2
3---2.85 Å2
Refinement stepCycle: 1 / Resolution: 2→61.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 5 44 3988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194010
X-RAY DIFFRACTIONr_bond_other_d0.0010.023774
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9715439
X-RAY DIFFRACTIONr_angle_other_deg0.86738762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3355521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48625.407172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17615692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0931521
X-RAY DIFFRACTIONr_chiral_restr0.0650.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4812.3332084
X-RAY DIFFRACTIONr_mcbond_other0.4812.3322083
X-RAY DIFFRACTIONr_mcangle_it0.8693.4982605
X-RAY DIFFRACTIONr_mcangle_other0.8693.4992606
X-RAY DIFFRACTIONr_scbond_it0.4182.3831926
X-RAY DIFFRACTIONr_scbond_other0.4132.3821923
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7453.5412828
X-RAY DIFFRACTIONr_long_range_B_refined1.79327.374076
X-RAY DIFFRACTIONr_long_range_B_other1.79227.3594072
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 126 -
Rwork0.355 2607 -
obs--99.82 %
Refinement TLS params.Method: refined / Origin x: -20.5294 Å / Origin y: 5.2377 Å / Origin z: -14.2555 Å
111213212223313233
T0.0064 Å2-0.0149 Å2-0.0034 Å2-0.0993 Å20.001 Å2--0.1292 Å2
L0.5251 °2-0.2974 °20.0032 °2-1.4489 °20.1098 °2--0.5647 °2
S0.0254 Å °0.0533 Å °0.0156 Å °-0.0376 Å °-0.0213 Å °-0.0608 Å °-0.0396 Å °0.0615 Å °-0.0041 Å °

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