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- PDB-5o4p: Crystal structure of AMPylated GRP78 -

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Basic information

Entry
Database: PDB / ID: 5o4p
TitleCrystal structure of AMPylated GRP78
Components78 kDa glucose-regulated protein
KeywordsATP BINDING PROTEIN / Bip/GRP78 / AMPylation
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 70 family ...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 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 / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsYan, Y. / Chen, R. / Ron, D. / Read, R.
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
DepositionMay 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Feb 7, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,58616
Polymers114,9902
Non-polymers1,59614
Water12,232679
1
A: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9756
Polymers57,4951
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,61110
Polymers57,4951
Non-polymers1,1169
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.330, 118.650, 83.150
Angle α, β, γ (deg.)90.00, 96.89, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 28 - 548 / Label seq-ID: 2 - 522

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 78 kDa glucose-regulated protein


Mass: 57494.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Gene: I79_019946 / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: G3I8R9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.5M Lithium Sulfate, 0.1M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.86→67.76 Å / Num. obs: 104104 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.6
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 109534 / CC1/2: 0.533 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IUC

3iuc


Resolution: 1.86→67.76 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.427 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 5399 4.9 %RANDOM
Rwork0.19438 ---
obs0.19526 104104 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.866 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20.01 Å2
2--1.37 Å20 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.86→67.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7983 0 70 679 8732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198182
X-RAY DIFFRACTIONr_bond_other_d0.0010.027702
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.97811083
X-RAY DIFFRACTIONr_angle_other_deg0.873317915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4251043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11625.402361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.566151448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7421545
X-RAY DIFFRACTIONr_chiral_restr0.0710.21293
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219070
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021511
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_it1.0762.3784172
X-RAY DIFFRACTIONr_mcbond_other1.0752.3774171
X-RAY DIFFRACTIONr_mcangle_it1.83.5595215
X-RAY DIFFRACTIONr_mcangle_other1.83.565216
X-RAY DIFFRACTIONr_scbond_it1.5222.6644010
X-RAY DIFFRACTIONr_scbond_other1.5062.6253955
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4613.8325785
X-RAY DIFFRACTIONr_long_range_B_refined4.02528.538779
X-RAY DIFFRACTIONr_long_range_B_other3.81928.2278614
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 32408 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 417 -
Rwork0.295 7660 -
obs--98.99 %

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