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

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Basic information

Entry
Database: PDB / ID: 3pow
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 / cytolytic granule / Assembly of Viral Components at the Budding Site / cortical granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / cellular response to electrical stimulus ...Calnexin/calreticulin cycle / cytolytic granule / Assembly of Viral Components at the Budding Site / cortical granule / positive regulation of dendritic cell chemotaxis / negative regulation of trophoblast cell migration / ATF6 (ATF6-alpha) activates chaperone genes / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / cellular response to electrical stimulus / intracellular glucocorticoid receptor signaling pathway / endoplasmic reticulum quality control compartment / sequestering of calcium ion / regulation of meiotic nuclear division / response to glycoside / sarcoplasmic reticulum lumen / protein folding in endoplasmic reticulum / hormone binding / nuclear export signal receptor activity / negative regulation of intracellular steroid hormone receptor signaling pathway / cardiac muscle cell differentiation / molecular sequestering activity / Scavenging by Class A Receptors / protein maturation by protein folding / Scavenging by Class F Receptors / cortical actin cytoskeleton organization / nuclear androgen receptor binding / response to testosterone / cellular response to lithium ion / smooth endoplasmic reticulum / protein localization to nucleus / negative regulation of neuron differentiation / positive regulation of cell cycle / positive regulation of phagocytosis / : / positive regulation of substrate adhesion-dependent cell spreading / protein folding chaperone / endocytic vesicle lumen / protein export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of endothelial cell migration / acrosomal vesicle / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / intracellular calcium ion homeostasis / cellular response to virus / positive regulation of non-canonical NF-kappaB signal transduction / phagocytic vesicle membrane / unfolded protein binding / cellular senescence / integrin binding / protein folding / response to estradiol / nuclear envelope / ER-Phagosome pathway / protein-folding chaperone binding / spermatogenesis / carbohydrate binding / collagen-containing extracellular matrix / regulation of apoptotic process / negative regulation of translation / protein stabilization / ribosome / response to xenobiotic stimulus / iron ion binding / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / mRNA binding / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / calcium ion binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / DNA binding / extracellular space / RNA binding / extracellular exosome / zinc ion binding / extracellular region / membrane / nucleus / 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: 1.55 Å
AuthorsGaboriaud, 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 1.3Nov 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_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_seq_id / _struct_conn.ptnr1_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: calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1862
Polymers30,1461
Non-polymers401
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.890, 70.390, 91.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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.: 1
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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 277.1 K / Method: vapor diffusion / pH: 6
Details: 30% PEG 4000, 0.2M ammonium acetate, 10mM magnesium acetate, and either 0.05M MES (pH 5.7 or 6.0), or 0.05M HEPES (pH 7.0), VAPOR DIFFUSION, temperature 277.1K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2010
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionNumber: 6705 / D res high: 1.54 Å / Num. obs: 6705 / % possible obs: 2.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)ID
1.541.648471.51
1.641.7511022.31
1.751.8910402.31
1.892.077851.91
2.072.3174421
2.312.667812.41
2.663.256772.41
3.254.5543021
4.55202992.41
ReflectionResolution: 1.54→20 Å / Num. all: 39833 / Num. obs: 39833 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 20.093 Å2 / Rsym value: 0.07
Reflection shell
Resolution (Å)Highest resolution (Å)Num. measured obsNum. possibleNum. unique obs% possible all
1.54-1.64847555088471.5
1.64-1.7511024718411022.3
1.75-1.8910404545810402.3
1.89-2.07785417367851.9
2.07-2.31744371647442
2.31-2.66781329927812.4
2.66-3.25677282466772.4
3.25-4.55430218524302
4.55299125442992.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3POS

3pos


Resolution: 1.55→10 Å / Cor.coef. Fo:Fc: 0.9472 / Cor.coef. Fo:Fc free: 0.9465 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 2009 5.04 %RANDOM
Rwork0.1762 ---
all0.1769 39833 --
obs0.1769 39833 --
Displacement parametersBiso max: 78.04 Å2 / Biso mean: 16.0774 Å2 / Biso min: 5.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.6946 Å20 Å20 Å2
2--0.4492 Å20 Å2
3---2.2454 Å2
Refine analyzeLuzzati coordinate error obs: 0.187 Å
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 1 334 2362
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d732SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes298HARMONIC5
X-RAY DIFFRACTIONt_it2085HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion256SEMIHARMONIC5
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_contact2497SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2085HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2813HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion4.42
X-RAY DIFFRACTIONt_other_torsion16.33
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2004 150 4.98 %
Rwork0.1833 2864 -
all0.1841 3014 -
Refinement TLS params.Method: refined / Origin x: 2.1858 Å / Origin y: 10.1515 Å / Origin z: 15.0518 Å
111213212223313233
T-0.0257 Å2-0.0005 Å20.0079 Å2--0.0436 Å20.0068 Å2---0.0181 Å2
L0.3666 °2-0.0684 °2-0.1035 °2-0.4362 °20.0827 °2--0.7258 °2
S-0.0184 Å °-0.0322 Å °0.0004 Å °0.0495 Å °-0.0019 Å °0.0089 Å °0.0399 Å °0.0497 Å °0.0203 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A 16 - A 202, A 304 - A 367, A 900 - A 900A16 - 202
2X-RAY DIFFRACTION1A 16 - A 202, A 304 - A 367, A 900 - A 900A304 - 367
3X-RAY DIFFRACTION1A 16 - A 202, A 304 - A 367, A 900 - A 900A900

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