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- PDB-3ldl: Crystal structure of human GRP78 (70kDa heat shock protein 5 / BI... -

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Basic information

Entry
Database: PDB / ID: 3ldl
TitleCrystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with ATP
Components78 kDa glucose-regulated protein
KeywordsCHAPERONE / GRP78 / HSP70 / HSC70 / HEAT SHOCK / PROTEIN FOLDING / ATP-BINDING / ADENOSINE / NUCLEOSIDE / NUCLEOTIDE-BINDING / STRESS RESPONSE / SMALL MOLECULE INHIBITOR / SELECTIVITY / Endoplasmic reticulum / Phosphoprotein
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 / negative regulation of IRE1-mediated unfolded protein response / cerebellar Purkinje cell layer development / endoplasmic reticulum chaperone complex / PERK regulates gene expression / protein folding in endoplasmic reticulum / misfolded protein binding / post-translational protein targeting to membrane, translocation / ER overload response / non-chaperonin molecular chaperone ATPase / endoplasmic reticulum-Golgi intermediate compartment / chaperone cofactor-dependent protein refolding / Regulation of HSF1-mediated heat shock response / negative regulation of protein-containing complex assembly / cellular response to interleukin-4 / cellular response to glucose starvation / endoplasmic reticulum unfolded protein response / ERAD pathway / heat shock protein binding / protein folding chaperone / substantia nigra development / 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 / unfolded protein binding / melanosome / Platelet degranulation / ribosome binding / protein-folding chaperone binding / midbody / protein refolding / positive regulation of cell migration / cadherin binding / protein domain specific binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / focal adhesion / 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 / ATP hydrolysis activity / 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
ADENOSINE-5'-TRIPHOSPHATE / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDokurno, P. / Surgenor, A.E. / Shaw, T. / Macias, A.T. / Massey, A.J. / Williamson, D.S.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Adenosine-Derived Inhibitors of 78 kDa Glucose Regulated Protein (Grp78) ATPase: Insights into Isoform Selectivity.
Authors: Macias, A.T. / Williamson, D.S. / Allen, N. / Borgognoni, J. / Clay, A. / Daniels, Z. / Dokurno, P. / Drysdale, M.J. / Francis, G.L. / Graham, C.J. / Howes, R. / Matassova, N. / Murray, J.B. ...Authors: Macias, A.T. / Williamson, D.S. / Allen, N. / Borgognoni, J. / Clay, A. / Daniels, Z. / Dokurno, P. / Drysdale, M.J. / Francis, G.L. / Graham, C.J. / Howes, R. / Matassova, N. / Murray, J.B. / Parsons, R. / Shaw, T. / Surgenor, A.E. / Terry, L. / Wang, Y. / Wood, M. / Massey, A.J.
History
DepositionJan 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)85,6385
Polymers84,6002
Non-polymers1,0393
Water8,125451
1
A: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8072
Polymers42,3001
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 78 kDa glucose-regulated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8313
Polymers42,3001
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.985, 74.326, 90.260
Angle α, β, γ (deg.)90.00, 98.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42299.852 Da / Num. of mol.: 2 / Fragment: ATPase domain (residues 26-407)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P11021
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris buffer, 25% Peg3350, 0.1M Na,K tartrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.973 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2007 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 30393 / Num. obs: 30393 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2879 / % possible all: 87.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3FZF

3fzf


Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9 / SU B: 8.914 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.678 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27852 1548 5.1 %RANDOM
Rwork0.19354 ---
obs0.19776 28636 92.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å2-1.13 Å2
2---1.63 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5892 0 63 451 6406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226048
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9778178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4624.964274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.466151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6671537
X-RAY DIFFRACTIONr_chiral_restr0.0960.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024507
X-RAY DIFFRACTIONr_nbd_refined0.2190.22925
X-RAY DIFFRACTIONr_nbtor_refined0.3010.24073
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2523
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.221
X-RAY DIFFRACTIONr_mcbond_it0.7111.53862
X-RAY DIFFRACTIONr_mcangle_it1.22826081
X-RAY DIFFRACTIONr_scbond_it1.73132425
X-RAY DIFFRACTIONr_scangle_it2.684.52097
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 128 -
Rwork0.246 1922 -
obs--87.76 %

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