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- PDB-3o0x: Structural basis of carbohydrate recognition by calreticulin -

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Basic information

Entry
Database: PDB / ID: 3o0x
TitleStructural basis of carbohydrate recognition by calreticulin
ComponentsCalreticulin
KeywordsCHAPERONE / jelly roll fold / carbohydrate binding / calcium binding
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 / cellular response to electrical stimulus / endoplasmic reticulum quality control compartment / regulation of meiotic nuclear division ...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 / cellular response to electrical stimulus / endoplasmic reticulum quality control compartment / regulation of meiotic nuclear division / complement component C1q complex binding / response to glycoside / sarcoplasmic reticulum lumen / nuclear export signal receptor activity / negative regulation of intracellular steroid hormone receptor signaling pathway / hormone binding / cardiac muscle cell differentiation / molecular sequestering activity / 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 lithium ion / response to testosterone / protein localization to nucleus / negative regulation of neuron differentiation / smooth endoplasmic reticulum / positive regulation of cell cycle / ERAD pathway / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phagocytosis / protein export from nucleus / phagocytic vesicle / 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 / carbohydrate binding / spermatogenesis / collagen-containing extracellular matrix / protein stabilization / negative regulation of translation / ribosome / response to xenobiotic stimulus / iron ion binding / endoplasmic reticulum lumen / external side of plasma membrane / mRNA binding / ubiquitin protein ligase binding / calcium ion binding / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum membrane / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / protein-containing complex / extracellular space / extracellular region / membrane / cytosol
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
Calreticulin / Calreticulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKozlov, G. / Gehring, K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis of carbohydrate recognition by calreticulin.
Authors: Kozlov, G. / Pocanschi, C.L. / Rosenauer, A. / Bastos-Aristizabal, S. / Gorelik, A. / Williams, D.B. / Gehring, K.
History
DepositionJul 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_label_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calreticulin
B: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0136
Polymers62,6002
Non-polymers1,4134
Water6,738374
1
A: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0073
Polymers31,3001
Non-polymers7072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0073
Polymers31,3001
Non-polymers7072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.619, 43.225, 84.632
Angle α, β, γ (deg.)90.00, 96.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calreticulin


Mass: 31300.049 Da / Num. of mol.: 2 / Fragment: lectin domain / 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: Q3TVD2, UniProt: P14211*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-3DManpa1-2DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a1122h-1a_1-5][a2122h-1a_1-5]/1-1-1-2/a2-b1_b2-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(3+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% (w/v) PEG 2000 MME, 0.15 M KSCN, 0.1 M Tris, pH 8.0, 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: Mar 3, 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→42.08 Å / Num. all: 34470 / Num. obs: 34462 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.03 Å / % possible all: 99.9

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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 3o0w

3o0w


Resolution: 2.01→42.08 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.159 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24041 1807 5 %RANDOM
Rwork0.19052 ---
all0.2 34470 --
obs0.1931 34462 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.759 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å2-0.06 Å2
2--0.83 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.01→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4023 0 92 374 4489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224229
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9595720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07525.747221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84815708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.813158
X-RAY DIFFRACTIONr_chiral_restr0.080.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023212
X-RAY DIFFRACTIONr_nbd_refined0.1880.21789
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22838
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2349
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.211
X-RAY DIFFRACTIONr_mcbond_it0.5581.52561
X-RAY DIFFRACTIONr_mcangle_it0.89923966
X-RAY DIFFRACTIONr_scbond_it1.53631937
X-RAY DIFFRACTIONr_scangle_it2.3074.51752
LS refinement shellResolution: 2.007→2.059 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 120 -
Rwork0.209 2483 -
obs--96.91 %
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)
11.92990.3826-0.91051.0504-0.24391.4070.2111-0.04020.14210.0323-0.08910.0194-0.22140.1014-0.1220.0592-0.0268-0.00160.0006-0.01650.018311.48510.071937.9542
21.73470.3968-0.85411.3133-0.16321.5361-0.04640.1487-0.2627-0.1251-0.0541-0.07240.121-0.04250.10050.0187-0.0039-0.01370.0046-0.01980.038911.0022-5.705234.264
31.84960.0989-0.86271.0273-0.22691.53610.00920.0079-0.2475-0.119-0.0719-0.16060.07410.19230.06270.00750.0036-0.0170.0009-0.01050.038916.3681-0.882734.5669
416.6537-4.9212-10.65853.18890.824112.1632-0.0569-0.3495-0.19470.06340.02470.20090.1305-0.44920.03210.0512-0.1334-0.05970.1551-0.0128-0.05734.98022.731758.4378
51.47430.3879-0.89661.11030.14354.1917-0.11440.2058-0.0990.06930.03370.01890.5974-0.63620.08060.0657-0.12530.03030.1087-0.0278-0.006718.2768-0.9433-2.5549
60.69870.3045-0.54331.0443-0.08281.6908-0.02760.15570.00130.00950.03520.05570.1191-0.2933-0.00760.01360.00010.0070.0836-0.00570.005922.04516.4466-3.6677
71.14730.15050.09071.2716-0.24122.12460.03430.20580.2394-0.01890.03270.2062-0.3664-0.3828-0.0670.00180.0860.02710.06360.04140.02418.600317.7191-3.814
834.51381.089612.55513.0408-0.40928.14030.311-0.9043-0.67280.9857-0.0798-0.4664-0.06980.9004-0.23120.077-0.0436-0.12040.1324-0.0397-0.134132.16319.572718.8929
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 121
2X-RAY DIFFRACTION2A122 - 195
3X-RAY DIFFRACTION3A196 - 344
4X-RAY DIFFRACTION4A345 - 365
5X-RAY DIFFRACTION5B18 - 49
6X-RAY DIFFRACTION6B50 - 136
7X-RAY DIFFRACTION7B137 - 348
8X-RAY DIFFRACTION8B349 - 364

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