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- PDB-6eoc: Crystal structure of AMPylated GRP78 in apo form (Crystal form 2) -

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Basic information

Entry
Database: PDB / ID: 6eoc
TitleCrystal structure of AMPylated GRP78 in apo form (Crystal form 2)
Components78 kDa glucose-regulated protein
KeywordsCHAPERONE / GRP78 / BIP / AMPylation / apo
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
CITRATE ANION / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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 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 1.2Jan 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6933
Polymers57,4081
Non-polymers2852
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, the protein sample was shown as monomeric by size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-18 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.088, 75.408, 98.308
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: SO4, CITRATE / Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: I79_019946 / Production host: Escherichia coli (E. coli) / References: UniProt: G3I8R9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 5% PEG1000, 0.1M Na2HPO4-Citrate, ph4.2, 0.2M LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / 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: 1.67→75.41 Å / Num. obs: 59490 / % possible obs: 98.3 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.051 / Rrim(I) all: 0.096 / Net I/σ(I): 12
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2986 / CC1/2: 0.888 / Rpim(I) all: 0.464 / Rrim(I) all: 0.861 / % possible all: 100

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Processing

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

5o4p


Resolution: 1.67→59.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.498 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24923 3010 5.1 %RANDOM
Rwork0.21121 ---
obs0.21305 56476 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.139 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å2-0 Å2
2--0.2 Å20 Å2
3---1.64 Å2
Refinement stepCycle: 1 / Resolution: 1.67→59.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 18 284 4269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194057
X-RAY DIFFRACTIONr_bond_other_d0.0010.023828
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.9745497
X-RAY DIFFRACTIONr_angle_other_deg0.86738901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2415520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0725.393178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62715714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2551522
X-RAY DIFFRACTIONr_chiral_restr0.0680.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02752
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_it0.8732.2672080
X-RAY DIFFRACTIONr_mcbond_other0.8722.2662079
X-RAY DIFFRACTIONr_mcangle_it1.5323.3932600
X-RAY DIFFRACTIONr_mcangle_other1.5323.3952601
X-RAY DIFFRACTIONr_scbond_it1.0032.4251977
X-RAY DIFFRACTIONr_scbond_other1.0022.4251975
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6793.5642897
X-RAY DIFFRACTIONr_long_range_B_refined2.98726.8134239
X-RAY DIFFRACTIONr_long_range_B_other2.98726.8154240
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.668→1.711 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 225 -
Rwork0.296 4188 -
obs--100 %

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