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

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Basic information

Entry
Database: PDB / ID: 5evz
TitleCrystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with ADP and inorganic phosphate
Components78 kDa glucose-regulated protein
KeywordsCHAPERONE / ATPase domain / nucleotide-binding / endoplasmic reticulum
Function / homology
Function and homology information


regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response ...regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / negative regulation of IRE1-mediated unfolded protein response / PERK regulates gene expression / protein folding in endoplasmic reticulum / cerebellar Purkinje cell layer development / misfolded protein binding / post-translational protein targeting to membrane, translocation / Modulation of host responses by IFN-stimulated genes / ER overload response / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of PERK-mediated unfolded protein response / non-chaperonin molecular chaperone ATPase / : / protein serine/threonine kinase inhibitor activity / Regulation of HSF1-mediated heat shock response / negative regulation of protein-containing complex assembly / endoplasmic reticulum unfolded protein response / cellular response to glucose starvation / ERAD pathway / heat shock protein binding / substantia nigra development / protein folding chaperone / 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 / negative regulation of transforming growth factor beta receptor signaling pathway / ATP-dependent protein folding chaperone / unfolded protein binding / melanosome / Platelet degranulation / protein-folding chaperone binding / ribosome binding / protein refolding / midbody / positive regulation of cell migration / cadherin binding / endoplasmic reticulum lumen / protein domain specific binding / focal adhesion / intracellular membrane-bounded organelle / calcium ion binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular exosome / ATP binding / nucleus / membrane / 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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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 20, 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

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)89,8058
Polymers88,7122
Non-polymers1,0936
Water9,620534
1
A: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9034
Polymers44,3561
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9034
Polymers44,3561
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.550, 74.802, 89.220
Angle α, β, γ (deg.)90.000, 98.600, 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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
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: 1.82→50 Å / Num. obs: 64199 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.077 / Χ2: 2.236 / Net I/av σ(I): 36.923 / Net I/σ(I): 13.4 / Num. measured all: 317997
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.82-1.854.60.45731911.28399.9
1.85-1.894.90.42731531.30899.8
1.89-1.924.90.35132061.36199.9
1.92-1.964.90.29332231.47100
1.96-24.90.24731531.62499.9
2-2.0550.22132131.672100
2.05-2.150.19231811.842100
2.1-2.1650.17432191.88100
2.16-2.2250.15732091.965100
2.22-2.2950.14331732.11100
2.29-2.3750.13232202.218100
2.37-2.4750.12432052.322100
2.47-2.5850.11332212.402100
2.58-2.7250.09932072.636100
2.72-2.895.10.08732122.683100
2.89-3.1150.07532142.989100
3.11-3.4350.07132463.537100
3.43-3.924.90.0632043.63899.9
3.92-4.9450.04932512.982100
4.94-504.90.04332982.56699.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.537
Highest resolutionLowest resolution
Rotation44.27 Å2.02 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EXW

5exw


Resolution: 1.85→44.31 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2061 / WRfactor Rwork: 0.1665 / FOM work R set: 0.8796 / SU B: 5.075 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1398 / SU Rfree: 0.1292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 3120 5.1 %RANDOM
Rwork0.1654 ---
obs0.1674 58565 99.83 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 95.62 Å2 / Biso mean: 32.051 Å2 / Biso min: 8.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å2-1.12 Å2
2---0.45 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.85→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5920 0 66 534 6520
Biso mean--19.88 31.7 -
Num. residues----763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196093
X-RAY DIFFRACTIONr_bond_other_d0.0010.025907
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9778230
X-RAY DIFFRACTIONr_angle_other_deg0.727313612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2275764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57424.964278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.873151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1891538
X-RAY DIFFRACTIONr_chiral_restr0.0710.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026890
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021330
X-RAY DIFFRACTIONr_mcbond_it1.1571.5033059
X-RAY DIFFRACTIONr_mcbond_other1.1521.5033058
X-RAY DIFFRACTIONr_mcangle_it1.6562.2483822
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 228 -
Rwork0.191 4290 -
all-4518 -
obs--99.71 %
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)
11.29720.04560.06042.55310.33911.26460.03810.18320.018-0.3605-0.0599-0.054-0.04060.0420.02180.05460.01580.01160.02940.00610.006927.24050.9007-8.2891
21.49820.09550.38653.205-0.30521.9766-0.0521-0.07590.01270.0676-0.0316-0.2567-0.08750.25080.08370.02160.0040.00350.05220.01660.033913.2907-11.4243-38.9145
31.02-0.39350.21924.00850.51360.9855-0.0363-0.1184-0.06760.36920.0527-0.35120.04910.1636-0.01640.047-0.0009-0.01540.0720.01620.068335.04644.817611.2882
40.74451.02890.13194.3535-0.29661.7103-0.02040.20280.0944-0.73950.03140.2575-0.0179-0.0307-0.0110.20880.0454-0.04520.10140.00750.08312.6424-15.8359-56.7998
52.348-0.2956-0.49331.5046-0.191.74640.03630.07650.0462-0.1866-0.03180.2858-0.1382-0.392-0.00450.05840.0325-0.04140.0988-0.020.08397.56843.541-2.1949
63.8735-0.00760.41441.0601-0.60692.9507-0.1339-0.6245-0.23470.28370.22350.1134-0.0661-0.5256-0.08970.10620.07160.04620.20350.040.0739-3.3584-13.8236-26.8069
72.3992-0.14961.47355.94420.35083.27570.1888-0.4411-0.35490.96540.1119-0.74870.4706-0.0421-0.30070.2368-0.0098-0.14230.17150.04380.23617.5794-13.661419.9234
81.9336-2.8253.28678.3713-7.479810.2704-0.3926-0.15360.0227-0.19040.7280.269-0.4913-0.8225-0.33540.25670.003-0.02260.24230.04130.1141-15.05323.2068-48.4381
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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