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- PDB-3o0v: Crystal structure of the calreticulin lectin domain -

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Basic information

Entry
Database: PDB / ID: 3o0v
TitleCrystal structure of the calreticulin lectin domain
ComponentsCalreticulin
KeywordsCHAPERONE / jelly roll fold / carbohydrate binding / calcium binding
Function / homology
Function and homology information


Calnexin/calreticulin cycle / Scavenging by Class A Receptors / response to biphenyl / cytolytic granule / positive regulation of dendritic cell chemotaxis / cortical granule / negative regulation of trophoblast cell migration / cellular response to electrical stimulus / complement component C1q complex binding / response to peptide ...Calnexin/calreticulin cycle / Scavenging by Class A Receptors / response to biphenyl / cytolytic granule / positive regulation of dendritic cell chemotaxis / cortical granule / negative regulation of trophoblast cell migration / cellular response to electrical stimulus / complement component C1q complex binding / response to peptide / regulation of meiotic nuclear division / negative regulation of retinoic acid receptor signaling pathway / endoplasmic reticulum quality control compartment / sarcoplasmic reticulum lumen / response to glycoside / hormone binding / negative regulation of intracellular steroid hormone receptor signaling pathway / nuclear export signal receptor 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 lithium ion / response to testosterone / molecular sequestering activity / negative regulation of neuron differentiation / protein localization to nucleus / smooth endoplasmic reticulum / positive regulation of phagocytosis / phagocytic vesicle / positive regulation of cell cycle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / protein folding chaperone / peptide binding / protein export from nucleus / acrosomal vesicle / 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 / cellular senescence / integrin binding / unfolded protein binding / nuclear envelope / response to estradiol / carbohydrate binding / : / spermatogenesis / postsynapse / negative regulation of translation / protein stabilization / ribosome / iron ion binding / endoplasmic reticulum lumen / response to xenobiotic stimulus / external side of plasma membrane / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / 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: 2.3 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 1.3Sep 6, 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_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.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_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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)31,1532
Polymers31,1121
Non-polymers401
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.111, 75.320, 79.587
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


Mass: 31112.467 Da / Num. of mol.: 1 / 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 29% (w/v) PEG 2000 MME, 0.2 M KSCN, 10 mM taurine, and 0.1 M Tris, pH 8.5, 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 4, 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: 2.3→39.79 Å / Num. all: 11586 / Num. obs: 11400 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.34 Å / % possible all: 100

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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: 2.3→39.79 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.882 / SU B: 15.253 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27469 572 4.8 %RANDOM
Rwork0.21359 ---
all0.22 ---
obs0.21633 11377 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.957 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--1.26 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 1 56 2075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222067
X-RAY DIFFRACTIONr_angle_refined_deg0.9421.9332787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0495249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90925.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43315353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.731154
X-RAY DIFFRACTIONr_chiral_restr0.0640.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021602
X-RAY DIFFRACTIONr_nbd_refined0.1820.2788
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21361
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2116
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.27
X-RAY DIFFRACTIONr_mcbond_it0.2881.51285
X-RAY DIFFRACTIONr_mcangle_it0.46421985
X-RAY DIFFRACTIONr_scbond_it0.6013916
X-RAY DIFFRACTIONr_scangle_it0.9564.5802
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 45 -
Rwork0.255 797 -
obs--99.29 %
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)
11.0434-0.7377-1.01692.35822.15423.08560.00540.0992-0.17630.0432-0.15370.39860.2369-0.23630.14830.0149-0.0793-0.01890.1178-0.0450.0628-23.29492.5956-12.6351
21.2942-0.0087-0.08651.66330.32691.7447-0.03470.1671-0.0956-0.0215-0.01810.23940.1025-0.07730.05290.0316-0.01510.00410.1079-0.01640.0392-16.83597.8046-9.3448
31.92320.1174-1.27322.43040.53911.8731-0.0556-0.0188-0.60090.7292-0.09980.24960.7187-0.12040.15540.2064-0.05850.0735-0.0016-0.02020.0182-15.279-2.1758-1.8536
41.5264-0.1597-0.23341.91440.72711.5499-0.08980.0017-0.26170.18360.1812-0.26610.41450.2924-0.09150.07990.0619-0.01070.06-0.03410-4.43531.6035-7.5514
52.5447-2.1466-0.117910.56510.96842.8766-0.00160.40140.2038-0.4104-0.036-0.101-0.34720.07450.03760.0535-0.0314-0.00890.17250.0383-0.0651-10.418714.9349-20.1007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 48
2X-RAY DIFFRACTION2A49 - 114
3X-RAY DIFFRACTION3A115 - 137
4X-RAY DIFFRACTION4A138 - 330
5X-RAY DIFFRACTION5A331 - 363

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