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- PDB-3iuc: Crystal structure of the human 70kDa heat shock protein 5 (BiP/GR... -

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Basic information

Entry
Database: PDB / ID: 3iuc
TitleCrystal structure of the human 70kDa heat shock protein 5 (BiP/GRP78) ATPase domain in complex with ADP
ComponentsHeat shock 70kDa protein 5 (Glucose-regulated protein, 78kDa)
KeywordsCHAPERONE / helix / Structural Genomics / Structural Genomics Consortium / SGC / ATP-binding / Nucleotide-binding / Stress response
Function / homology
Function and homology information


stress response to metal ion / : / ATF6-mediated unfolded protein response / response to methamphetamine hydrochloride / cellular response to xenobiotic stimulus => GO:0071466 / 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 ...stress response to metal ion / : / ATF6-mediated unfolded protein response / response to methamphetamine hydrochloride / cellular response to xenobiotic stimulus => GO:0071466 / 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-mediated unfolded protein response / PERK regulates gene expression / protein folding in endoplasmic reticulum / luteolysis / misfolded protein binding / post-translational protein targeting to membrane, translocation / ERAD pathway / cellular response to antibiotic / ER overload response / IRE1-mediated unfolded protein response / non-chaperonin molecular chaperone ATPase / smooth endoplasmic reticulum / chaperone cofactor-dependent protein refolding / response to unfolded protein / endoplasmic reticulum-Golgi intermediate compartment / Regulation of HSF1-mediated heat shock response / cellular response to unfolded protein / cellular response to glucose starvation / cellular response to manganese ion / negative regulation of protein-containing complex assembly / : / endoplasmic reticulum unfolded protein response / protein folding chaperone / cellular response to cAMP / heat shock protein binding / substantia nigra development / cellular response to calcium ion / cellular response to interleukin-4 / response to endoplasmic reticulum stress / cellular response to nerve growth factor stimulus / response to cocaine / 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 / cellular response to gamma radiation / positive regulation of neuron projection development / neuron differentiation / melanosome / unfolded protein binding / ribosome binding / Platelet degranulation / midbody / protein-folding chaperone binding / protein refolding / neuron apoptotic process / 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
ADENOSINE-5'-DIPHOSPHATE / Endoplasmic reticulum chaperone BiP / Endoplasmic reticulum chaperone BiP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWisniewska, M. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Wisniewska, M. / Karlberg, T. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Kotyenova, T. / Kotzch, A. / Kraulis, P. / Markova, N. / Moche, M. / Nielsen, T.K. / Nordlund, P. / Nyman, T. / Persson, C. / Roos, A. / Schutz, P. / Siponen, M.I. / Svensson, L. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2010
Title: Crystal structures of the ATPase domains of four human Hsp70 isoforms: HSPA1L/Hsp70-hom, HSPA2/Hsp70-2, HSPA6/Hsp70B', and HSPA5/BiP/GRP78
Authors: Wisniewska, M. / Karlberg, T. / Lehtio, L. / Johansson, I. / Kotenyova, T. / Moche, M. / Schuler, H.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: Heat shock 70kDa protein 5 (Glucose-regulated protein, 78kDa)
C: Heat shock 70kDa protein 5 (Glucose-regulated protein, 78kDa)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4238
Polymers90,4082
Non-polymers1,0156
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Heat shock 70kDa protein 5 (Glucose-regulated protein, 78kDa)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7114
Polymers45,2041
Non-polymers5073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heat shock 70kDa protein 5 (Glucose-regulated protein, 78kDa)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7114
Polymers45,2041
Non-polymers5073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.212, 51.795, 94.994
Angle α, β, γ (deg.)98.85, 94.88, 117.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Heat shock 70kDa protein 5 (Glucose-regulated protein, 78kDa) / 70kDa heat shock protein 5 (BiP) / Heat shock 70kDa protein 5 (Glucose-regulated protein / 78kDa) / ...70kDa heat shock protein 5 (BiP) / Heat shock 70kDa protein 5 (Glucose-regulated protein / 78kDa) / isoform CRA_a


Mass: 45203.953 Da / Num. of mol.: 2 / Fragment: ATPase domain, UNP residue 26-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: B0QZ61, UniProt: P11021*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% PEG 6000, 0.2M CaCl2, 0.1M NaAcetate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.13→35 Å / Num. all: 44366 / Num. obs: 41864 / % possible obs: 94.4 % / Redundancy: 3.86 % / Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0035refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I33

3i33


Resolution: 2.4→29.12 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.865 / SU B: 9.166 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.659 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26981 1506 5 %RANDOM
Rwork0.18965 ---
obs0.19365 28620 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.648 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0 Å20.01 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5912 0 58 399 6369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226062
X-RAY DIFFRACTIONr_bond_other_d0.0010.024105
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9758196
X-RAY DIFFRACTIONr_angle_other_deg0.925310050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.045764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97225.036274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79151071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4411535
X-RAY DIFFRACTIONr_chiral_restr0.0870.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026746
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021177
X-RAY DIFFRACTIONr_mcbond_it0.691.53793
X-RAY DIFFRACTIONr_mcbond_other0.141.51571
X-RAY DIFFRACTIONr_mcangle_it1.31226110
X-RAY DIFFRACTIONr_scbond_it2.15132269
X-RAY DIFFRACTIONr_scangle_it3.6424.52086
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 112 -
Rwork0.224 2127 -
obs--100 %

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