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- PDB-3pos: Crystal structure of the globular domain of human calreticulin -

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Basic information

Entry
Database: PDB / ID: 3pos
TitleCrystal structure of the globular domain of human calreticulin
ComponentsCalreticulin
KeywordsCHAPERONE / legume lectin fold / CNX/CRT family / multi-functional / Carbohydrate binding / Peptide Binding / multi-compartmental
Function / homology
Function and homology information


Calnexin/calreticulin cycle / response to biphenyl / cytolytic granule / positive regulation of dendritic cell chemotaxis / ATF6 (ATF6-alpha) activates chaperone genes / nuclear receptor-mediated glucocorticoid signaling pathway / Assembly of Viral Components at the Budding Site / cortical granule / negative regulation of trophoblast cell migration / complement component C1q complex binding ...Calnexin/calreticulin cycle / response to biphenyl / cytolytic granule / positive regulation of dendritic cell chemotaxis / ATF6 (ATF6-alpha) activates chaperone genes / nuclear receptor-mediated glucocorticoid signaling pathway / Assembly of Viral Components at the Budding Site / cortical granule / negative regulation of trophoblast cell migration / complement component C1q complex binding / response to peptide / cellular response to electrical stimulus / regulation of meiotic nuclear division / sequestering of calcium ion / negative regulation of retinoic acid receptor signaling pathway / endoplasmic reticulum quality control compartment / protein folding in endoplasmic reticulum / sarcoplasmic reticulum lumen / hormone binding / negative regulation of intracellular steroid hormone receptor signaling pathway / nuclear export signal receptor activity / cardiac muscle cell differentiation / response to glycoside / cortical actin cytoskeleton organization / Scavenging by Class A Receptors / nuclear androgen receptor binding / Scavenging by Class F Receptors / cellular response to lithium ion / response to testosterone / molecular sequestering activity / negative regulation of neuron differentiation / protein localization to nucleus / smooth endoplasmic reticulum / positive regulation of cell cycle / positive regulation of phagocytosis / ERAD pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / endocytic vesicle lumen / positive regulation of substrate adhesion-dependent cell spreading / peptide binding / protein folding chaperone / positive regulation of endothelial cell migration / protein export from nucleus / acrosomal vesicle / protein maturation / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to virus / intracellular calcium ion homeostasis / phagocytic vesicle membrane / cellular senescence / integrin binding / unfolded protein binding / nuclear envelope / protein folding / response to estradiol / protein-folding chaperone binding / ER-Phagosome pathway / carbohydrate binding / spermatogenesis / regulation of apoptotic process / postsynapse / negative regulation of translation / protein stabilization / ribosome / iron ion binding / response to xenobiotic stimulus / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / positive regulation of cell population proliferation / calcium ion binding / ubiquitin protein ligase binding / positive regulation of gene expression / endoplasmic reticulum membrane / regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / Jelly Rolls - #200 ...Calreticulin / Calreticulin family repeated motif signature. / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsChouquet, A. / Paidassi, H. / Ling, W.-L. / Frachet, P. / Houen, G. / Arlaud, G.J. / Gaboriaud, C.
CitationJournal: Plos One / Year: 2011
Title: X-ray structure of the human calreticulin globular domain reveals a Peptide-binding area and suggests a multi-molecular mechanism
Authors: Chouquet, A. / Paidassi, H. / Ling, W.L. / Frachet, P. / Houen, G. / Arlaud, G.J. / Gaboriaud, C.
History
DepositionNov 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Assembly

Deposited unit
A: Calreticulin
B: Calreticulin
C: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5596
Polymers90,4393
Non-polymers1203
Water13,313739
1
A: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1862
Polymers30,1461
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1862
Polymers30,1461
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1862
Polymers30,1461
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.230, 91.100, 194.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calreticulin / CRP55 / Calregulin / Endoplasmic reticulum resident protein 60 / ERp60 / HACBP / grp60


Mass: 30146.271 Da / Num. of mol.: 3
Fragment: Globular domain, UNP residues 18-204 and 302-368 linked with GSG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALR, CRTC / Plasmid: pHFX-CRT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P27797
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 277.1 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 4000, 0.1M sodium acetate, 0.1M Tris, pH 8.5-9, VAPOR DIFFUSION, HANGING DROP, temperature 277.1K
PH range: 8.5 - 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 88382 / Num. obs: 88382 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 18.81
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 13 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6434 / % possible all: 83

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER2.8.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→19.94 Å / Cor.coef. Fo:Fc: 0.9545 / Cor.coef. Fo:Fc free: 0.9386 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 4379 4.96 %RANDOM
Rwork0.1698 ---
all0.1715 88317 --
obs0.1715 88317 --
Displacement parametersBiso mean: 18.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.0875 Å20 Å20 Å2
2--1.6765 Å20 Å2
3----1.589 Å2
Refine analyzeLuzzati coordinate error obs: 0.171 Å
Refinement stepCycle: LAST / Resolution: 1.65→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 3 739 6798
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2174SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes202HARMONIC2
X-RAY DIFFRACTIONt_gen_planes890HARMONIC5
X-RAY DIFFRACTIONt_it6258HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion769SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7781SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6258HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8447HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion4.11
X-RAY DIFFRACTIONt_other_torsion17.74
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2221 270 4.86 %
Rwork0.2098 5286 -
all0.2105 5556 -

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