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- PDB-5ex5: Crystal structure of human GRP78 (70kDa heat shock protein 5 / BI... -

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Basic information

Entry
Database: PDB / ID: 5ex5
TitleCrystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with 7-deaza-ADP and inorganic phosphate
Components78 kDa glucose-regulated protein
KeywordsCHAPERONE / ATPase domain / nucleotide-binding / endoplasmic reticulum
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 / : / protein folding chaperone / endoplasmic reticulum unfolded protein response / 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 / Defensin A-like - #30 / Endoplasmic reticulum targeting sequence. / Defensin A-like / 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 / Defensin A-like - #30 / Endoplasmic reticulum targeting sequence. / Defensin A-like / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
7-deazaadenosine-5'-diphosphate / PHOSPHATE ION / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHughes, S.J. / Antoshchenko, T. / Song, J.H. / Pizarro, J. / Park, H.W.
CitationJournal: Plos One / Year: 2016
Title: Probing the ATP Site of GRP78 with Nucleotide Triphosphate Analogs.
Authors: Hughes, S.J. / Antoshchenko, T. / Chen, Y. / Lu, H. / Pizarro, J.C. / Park, H.W.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)89,8038
Polymers88,7122
Non-polymers1,0916
Water9,008500
1
A: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9024
Polymers44,3561
Non-polymers5453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9024
Polymers44,3561
Non-polymers5453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.270, 74.709, 88.722
Angle α, β, γ (deg.)90.000, 98.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 78 kDa glucose-regulated protein / GRP-78 / Endoplasmic reticulum lumenal Ca(2+)-binding protein grp78 / Heat shock 70 kDa protein 5 / ...GRP-78 / Endoplasmic reticulum lumenal Ca(2+)-binding protein grp78 / Heat shock 70 kDa protein 5 / Immunoglobulin heavy chain-binding protein / BiP


Mass: 44356.090 Da / Num. of mol.: 2 / Fragment: ATPase domain (UNP residues 26-407)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11021
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-7DD / 7-deazaadenosine-5'-diphosphate


Mass: 426.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N4O10P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24-26% PEG3350, 0.1 M Tris-HCl, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 1, 2015
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 55831 / Num. obs: 55831 / % possible obs: 99.1 % / Redundancy: 4.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.064 / Rrim(I) all: 0.134 / Rsym value: 0.117 / Net I/σ(I): 9.3 / Num. measured all: 234113
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRsym value% possible all
1.9-24.20.5023.33381480750.8380.0310.05699.1
6.01-404.10.05619753918290.9930.0350.06398.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EXW

5exw


Resolution: 1.9→37.87 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2119 / WRfactor Rwork: 0.1685 / FOM work R set: 0.884 / SU B: 6.001 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1628 / SU Rfree: 0.1443 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 2824 5.1 %RANDOM
Rwork0.1708 ---
obs0.1729 52967 98.9 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.38 Å2 / Biso mean: 25.438 Å2 / Biso min: 4.67 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å2-0 Å2-1.1 Å2
2---0.15 Å20 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 1.9→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 66 500 6474
Biso mean--14.66 25.59 -
Num. residues----761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196093
X-RAY DIFFRACTIONr_bond_other_d0.0010.025915
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9778231
X-RAY DIFFRACTIONr_angle_other_deg0.712313628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1725764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73424.892278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.354151104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6821539
X-RAY DIFFRACTIONr_chiral_restr0.0690.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026891
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021332
X-RAY DIFFRACTIONr_mcbond_it1.0910.9423056
X-RAY DIFFRACTIONr_mcbond_other1.090.9423055
X-RAY DIFFRACTIONr_mcangle_it1.6351.4063820
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 207 -
Rwork0.204 3851 -
all-4058 -
obs--99.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5105-0.1461-0.01352.8180.46791.36730.01930.17570.0281-0.3654-0.0333-0.0622-0.05120.04330.0140.04770.00510.00890.0230.00580.004527.15280.9498-8.2701
21.40810.19770.32732.9315-0.13431.6126-0.0851-0.0889-0.00080.10070.0063-0.2605-0.07760.16710.07870.05720.0367-0.01210.05970.00320.035713.0055-11.4105-38.7385
30.8188-0.83320.19224.8350.1411.1663-0.0558-0.116-0.02330.36110.0524-0.29290.0150.12690.00340.02840.0008-0.0160.07390.00830.060134.87344.836311.3048
41.02461.2965-0.17925.1513-1.4112.3879-0.03210.15330.108-0.48720.07040.2593-0.0297-0.1359-0.03830.13610.0285-0.0470.0966-0.00360.06242.5509-15.7965-56.5979
52.3382-0.3589-0.67131.4025-0.10522.18060.0330.07120.0688-0.1532-0.02640.2017-0.1402-0.346-0.00670.03380.0197-0.0250.073-0.0130.07757.50073.6043-2.1622
64.0768-0.2207-0.19691.265-0.44652.0746-0.1489-0.6097-0.2970.32770.22560.141-0.0182-0.3463-0.07680.16230.08670.03560.21290.03650.0701-3.5799-14.0047-26.7001
74.2489-0.74142.40164.1722-0.54624.42610.0826-0.5524-0.26790.56450.1316-0.46420.3446-0.0702-0.21420.1340.0033-0.05920.15950.02790.144517.7895-13.586719.6578
81.609-1.66972.08745.9686-5.05758.1728-0.1944-0.01680.0404-0.24190.4580.1787-0.3087-0.5582-0.26360.17860.04270.00980.23560.02410.1192-15.35773.2327-48.0971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 63
2X-RAY DIFFRACTION1A142 - 214
3X-RAY DIFFRACTION2B26 - 63
4X-RAY DIFFRACTION2B142 - 214
5X-RAY DIFFRACTION3A64 - 141
6X-RAY DIFFRACTION4B64 - 141
7X-RAY DIFFRACTION5A215 - 253
8X-RAY DIFFRACTION5A332 - 407
9X-RAY DIFFRACTION6B215 - 253
10X-RAY DIFFRACTION6B332 - 407
11X-RAY DIFFRACTION7A254 - 331
12X-RAY DIFFRACTION8B254 - 331

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