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- PDB-5f2r: Crystal structure of human GRP78 (70kDa heat shock protein 5 / BI... -

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Basic information

Entry
Database: PDB / ID: 5f2r
TitleCrystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with AMP-PCP
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 / cerebellar Purkinje cell layer development / protein folding in endoplasmic reticulum / misfolded protein binding / post-translational protein targeting to membrane, translocation / protein serine/threonine kinase inhibitor activity / Modulation of host responses by IFN-stimulated genes / ER overload response / IRE1-mediated unfolded protein response / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of PERK-mediated unfolded protein response / non-chaperonin molecular chaperone ATPase / : / 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 / 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 / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
DepositionDec 2, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)89,7716
Polymers88,7122
Non-polymers1,0594
Water3,981221
1
A: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8863
Polymers44,3561
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8863
Polymers44,3561
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.958, 74.549, 88.414
Angle α, β, γ (deg.)90.000, 98.150, 90.000
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: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 27 - 406 / Label seq-ID: 20 - 399

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

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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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
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: 2.11→50 Å / Num. obs: 40808 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.132 / Χ2: 1.946 / Net I/av σ(I): 20.873 / Net I/σ(I): 9.3 / Num. measured all: 163471
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.11-2.153.10.40919471.31595.9
2.15-2.193.40.37320091.36398.6
2.19-2.233.50.35620241.42898.4
2.23-2.273.50.33820171.45398.8
2.27-2.323.60.31120381.4599.2
2.32-2.383.70.320121.57899.1
2.38-2.443.80.28620101.51999.4
2.44-2.53.80.28920491.52399.5
2.5-2.5840.28620461.53199.7
2.58-2.664.10.25920411.63299.9
2.66-2.754.20.23720511.68999.8
2.75-2.864.20.22220301.77599.8
2.86-2.994.30.19520602.02799.6
2.99-3.154.30.15820272.12399.9
3.15-3.354.40.13520552.119100
3.35-3.614.40.11620752.30399.8
3.61-3.974.40.10420632.68499.8
3.97-4.544.40.09420522.88799.7
4.54-5.724.50.09720732.35199.9
5.72-504.30.08121292.95599.4

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Processing

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

5exw


Resolution: 2.15→44 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2248 / WRfactor Rwork: 0.1886 / FOM work R set: 0.8539 / SU B: 10.829 / SU ML: 0.149 / SU R Cruickshank DPI: 0.317 / SU Rfree: 0.2118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.317 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1940 5.1 %RANDOM
Rwork0.1987 ---
obs0.2005 36420 99.32 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 110.79 Å2 / Biso mean: 35.688 Å2 / Biso min: 13.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å2-0 Å2-1.29 Å2
2---1.08 Å20 Å2
3----0.28 Å2
Refinement stepCycle: final / Resolution: 2.15→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5900 0 64 221 6185
Biso mean--25.28 27.89 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196055
X-RAY DIFFRACTIONr_bond_other_d0.0040.025882
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9778179
X-RAY DIFFRACTIONr_angle_other_deg0.888313551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2995757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5724.928276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.865151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3921538
X-RAY DIFFRACTIONr_chiral_restr0.0750.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026833
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021319
X-RAY DIFFRACTIONr_mcbond_it1.3381.6713037
X-RAY DIFFRACTIONr_mcbond_other1.3381.6713036
X-RAY DIFFRACTIONr_mcangle_it2.0332.5023791
Refine LS restraints NCS

Ens-ID: 1 / Number: 23579 / 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: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 156 -
Rwork0.24 2627 -
all-2783 -
obs--97.99 %
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)
11.01850.0178-0.0982.80480.34261.1620.00670.14360.004-0.2865-0.0042-0.0282-0.03170.0785-0.00250.04310.01420.02690.05420.01930.042626.88730.9022-8.1425
21.1761-0.00560.72083.88350.08261.9291-0.0577-0.04960.03870.22090.0553-0.346-0.07990.15390.00240.06580.0268-0.01070.0761-0.00440.096712.824-11.5797-38.5878
31.35-1.2410.4763.5166-0.06371.0525-0.0569-0.1248-0.06260.29980.095-0.21390.07410.1626-0.03820.04920.00350.00670.110.00730.096834.71764.782111.261
41.51530.93290.00353.3129-1.0272.9972-0.03450.1940.1426-0.48160.0580.2864-0.0439-0.0536-0.02360.17740.0285-0.05150.12680.0010.12042.3646-15.9266-56.4589
52.6952-0.271-0.83761.3443-0.24972.0556-0.00540.03910.045-0.1882-0.00340.2082-0.1386-0.30020.00880.05820.0177-0.01630.0971-0.01630.10957.38663.6801-2.0429
64.1197-0.42860.00591.9632-0.68411.9939-0.1609-0.687-0.28830.50730.29530.1528-0.0001-0.4567-0.13440.24410.09330.04070.29590.04620.116-3.8016-14.2607-26.6804
75.3975-1.50483.10284.2556-0.46184.65860.0614-0.5731-0.29740.6620.1904-0.52290.4185-0.0684-0.25180.1940.0034-0.05420.17780.02830.219317.7105-13.684419.5748
82.6992-1.92753.41035.566-4.455410.6773-0.2136-0.13380.1152-0.29510.33940.008-0.3021-0.5243-0.12580.18250.03270.01930.25240.00410.1595-15.28173.1411-47.9111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 63
2X-RAY DIFFRACTION1A142 - 214
3X-RAY DIFFRACTION2B27 - 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 - 406
11X-RAY DIFFRACTION7A254 - 331
12X-RAY DIFFRACTION8B254 - 331

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