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- PDB-3rg0: Structural and functional relationships between the lectin and ar... -

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Basic information

Entry
Database: PDB / ID: 3rg0
TitleStructural and functional relationships between the lectin and arm domains of calreticulin
ComponentsCalreticulin
KeywordsCHAPERONE / beta-sandwich / monoglucosylated proteins binding / carbohydrate binding / calcium binding / endoplasmic reticulum
Function / homology
Function and homology information


Calnexin/calreticulin cycle / Scavenging by Class A Receptors / cytolytic granule / positive regulation of dendritic cell chemotaxis / cortical granule / negative regulation of trophoblast cell migration / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / cellular response to electrical stimulus / endoplasmic reticulum quality control compartment ...Calnexin/calreticulin cycle / Scavenging by Class A Receptors / cytolytic granule / positive regulation of dendritic cell chemotaxis / cortical granule / negative regulation of trophoblast cell migration / negative regulation of retinoic acid receptor signaling pathway / complement component C1q complex binding / cellular response to electrical stimulus / endoplasmic reticulum quality control compartment / regulation of meiotic nuclear division / response to glycoside / sarcoplasmic reticulum lumen / hormone binding / nuclear export signal receptor activity / negative regulation of intracellular steroid hormone receptor signaling pathway / : / molecular sequestering activity / cardiac muscle cell differentiation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / cortical actin cytoskeleton organization / nuclear androgen receptor binding / cellular response to organic substance / response to testosterone / cellular response to lithium ion / smooth endoplasmic reticulum / protein localization to nucleus / negative regulation of neuron differentiation / phagocytic vesicle / positive regulation of cell cycle / positive regulation of phagocytosis / : / positive regulation of substrate adhesion-dependent cell spreading / protein export from nucleus / positive regulation of endothelial cell migration / acrosomal vesicle / sarcoplasmic reticulum / peptide binding / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / cellular response to virus / positive regulation of non-canonical NF-kappaB signal transduction / cellular senescence / unfolded protein binding / integrin binding / protein folding / response to estradiol / nuclear envelope / spermatogenesis / carbohydrate binding / collagen-containing extracellular matrix / negative regulation of translation / protein stabilization / ribosome / response to xenobiotic stimulus / iron ion binding / external side of plasma membrane / endoplasmic reticulum lumen / 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 / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / protein-containing complex / extracellular space / 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. / Helix hairpin bin / Endoplasmic reticulum targeting sequence. ...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. / Helix hairpin bin / Endoplasmic reticulum targeting sequence. / Jelly Rolls - #200 / Helix Hairpins / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsKozlov, G. / Pocanschi, C.L. / Brockmeier, U. / Williams, D.B. / Gehring, K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Functional Relationships between the Lectin and Arm Domains of Calreticulin.
Authors: Pocanschi, C.L. / Kozlov, G. / Brockmeier, U. / Brockmeier, A. / Williams, D.B. / Gehring, K.
History
DepositionApr 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1812
Polymers38,1411
Non-polymers401
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.062, 71.701, 108.386
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


Mass: 38140.992 Da / Num. of mol.: 1
Fragment: lectin domain with partially truncated arm domain, UNP residues 18-238 and 273-284
Mutation: C163S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Calr / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P14211
#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.: 26 / 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: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25% PEG 1500, 0.1 M MIB buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9779 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 20, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 10651 / Num. obs: 10321 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.55→2.59 Å / % possible all: 77.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O0V

3o0v


Resolution: 2.57→43.23 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.895 / SU B: 29.235 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 1.01 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28558 516 4.8 %RANDOM
Rwork0.23416 ---
obs0.23663 10321 96.42 %-
all-10651 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.581 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20 Å20 Å2
2--0.23 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.57→43.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 1 26 2359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222394
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9373239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.055290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29325.528123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76115399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.126156
X-RAY DIFFRACTIONr_chiral_restr0.070.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021866
X-RAY DIFFRACTIONr_nbd_refined0.1750.2887
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.276
X-RAY DIFFRACTIONr_metal_ion_refined0.1460.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.26
X-RAY DIFFRACTIONr_mcbond_it0.2121.51484
X-RAY DIFFRACTIONr_mcangle_it0.37722324
X-RAY DIFFRACTIONr_scbond_it0.37531048
X-RAY DIFFRACTIONr_scangle_it0.6264.5915
LS refinement shellResolution: 2.569→2.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 26 -
Rwork0.371 574 -
obs--73.89 %
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)
11.1841-0.11740.24963.5652-0.92161.95810.0141-0.1492-0.15730.08270.22560.49690.0899-0.3119-0.23970.1005-0.02840.01850.17360.10840.20134.75542.29825.4934
22.246-0.54430.58682.593-0.95812.7278-0.0326-0.18550.00330.26970.042-0.0982-0.03530.0746-0.00940.13460.0029-0.01240.14670.060.163420.40053.53959.674
31.4069-0.5671.18910.2285-0.47931.00510.2240.22980.0288-0.24280.1899-0.2253-0.35060.2341-0.41390.325-0.04530.00170.2347-0.0650.141746.25895.371732.0533
41.12780.37460.21021.30610.11191.26860.1072-0.399-0.2580.38650.0762-0.0120.2009-0.0094-0.18340.15120.01390.01360.1550.0830.043119.107-0.277816.4298
53.7669-3.11513.092411.5781-9.70211.0040.20620.40410.1508-0.9264-0.3394-0.24130.21280.36610.13320.310.0029-0.02270.10690.00470.050514.38852.7924-11.6595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 121
2X-RAY DIFFRACTION2A122 - 195
3X-RAY DIFFRACTION3A196 - 289
4X-RAY DIFFRACTION4A290 - 335
5X-RAY DIFFRACTION5A336 - 367

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