[English] 日本語
Yorodumi
- PDB-3o0w: Structural basis of carbohydrate recognition by calreticulin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o0w
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 / complement component C1q complex binding / : / 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 / : / endoplasmic reticulum quality control compartment / cellular response to electrical stimulus / 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 / 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 / : / response to testosterone / cellular response to lithium ion / : / ERAD pathway / protein localization to nucleus / negative regulation of neuron differentiation / smooth endoplasmic reticulum / positive regulation of cell cycle / positive regulation of phagocytosis / positive regulation of substrate adhesion-dependent cell spreading / phagocytic vesicle / 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 / negative regulation of DNA-templated transcription / mRNA binding / 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. / 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 / SAD / Resolution: 1.95 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 / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0073
Polymers31,3001
Non-polymers7072
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.727, 43.769, 133.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Calreticulin /


Mass: 31300.049 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: 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.: 1
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.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25.5% (w/v) PEG 2000 MME, 0.15 M KSCN, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
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: 1.95→41.59 Å / Num. all: 17985 / Num. obs: 17355 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.95→1.98 Å / % possible all: 80.2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→41.59 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.106 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25055 951 5.2 %RANDOM
Rwork0.19657 ---
all0.2 17985 --
obs0.19928 17355 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.709 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.71 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 46 177 2217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222091
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9582827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.325.648108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7915347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.318154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021586
X-RAY DIFFRACTIONr_nbd_refined0.1920.2878
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21411
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2186
X-RAY DIFFRACTIONr_metal_ion_refined0.0490.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.27
X-RAY DIFFRACTIONr_mcbond_it0.81.51263
X-RAY DIFFRACTIONr_mcangle_it1.01121963
X-RAY DIFFRACTIONr_scbond_it1.553956
X-RAY DIFFRACTIONr_scangle_it2.3964.5864
LS refinement shellResolution: 1.948→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 65 -
Rwork0.208 1012 -
obs--78.27 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more