[English] 日本語
Yorodumi
- PDB-5hcb: Globular Domain of the Entamoeba histolytica calreticulin in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hcb
TitleGlobular Domain of the Entamoeba histolytica calreticulin in complex with glucose
ComponentsCalreticulin
KeywordsSUGAR BINDING PROTEIN / chaperone / legume lectin domain / fusion protein
Function / homology
Function and homology information


symbiont-mediated suppression of host complement activation / complement component C1q complex binding / host cell surface binding / uropod / phagocytic cup / positive regulation of phagocytosis / protein export from nucleus / carbohydrate binding / endoplasmic reticulum lumen / cell surface ...symbiont-mediated suppression of host complement activation / complement component C1q complex binding / host cell surface binding / uropod / phagocytic cup / positive regulation of phagocytosis / protein export from nucleus / carbohydrate binding / endoplasmic reticulum lumen / cell surface / endoplasmic reticulum / metal ion binding / cytosol
Similarity search - Function
Calreticulin / 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 ...Calreticulin / 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 speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMoreau, C.P. / Cioci, G. / Ianello, M. / Laffly, E. / Chouquet, A. / Ferreira, A. / Thielens, N.M. / Gaboriaud, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR 09-PIRI-0021 France
CitationJournal: IUCrJ / Year: 2016
Title: Structures of parasite calreticulins provide insights into their flexibility and dual carbohydrate/peptide-binding properties.
Authors: Moreau, C. / Cioci, G. / Iannello, M. / Laffly, E. / Chouquet, A. / Ferreira, A. / Thielens, N.M. / Gaboriaud, C.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calreticulin
B: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,57011
Polymers62,9422
Non-polymers6279
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-111 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.320, 149.320, 117.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

21A-508-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Calreticulin /


Mass: 31471.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote)
Plasmid: pJexpress411 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2VN92

-
Non-polymers , 5 types, 26 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 5.18 Å3/Da / Density % sol: 76.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.7 M ammonium sulfate, 0.1 M Tri-Sodium citrate pH 5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.9→47.2 Å / Num. obs: 29847 / % possible obs: 99.5 % / Redundancy: 8.82 % / Rsym value: 0.103 / Net I/σ(I): 16.08
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 9.08 % / Mean I/σ(I) obs: 1.82 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
Cootmodel building
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.2 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 1492 5 %
Rwork0.189 --
obs0.1906 29835 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4270 0 30 17 4317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134403
X-RAY DIFFRACTIONf_angle_d1.8135933
X-RAY DIFFRACTIONf_dihedral_angle_d18.4162662
X-RAY DIFFRACTIONf_chiral_restr0.159614
X-RAY DIFFRACTIONf_plane_restr0.01772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-2.99370.34271310.30072489X-RAY DIFFRACTION98
2.9937-3.10060.37181330.30232530X-RAY DIFFRACTION100
3.1006-3.22470.33261340.2762541X-RAY DIFFRACTION100
3.2247-3.37150.27241340.23322550X-RAY DIFFRACTION100
3.3715-3.54920.25061340.21382547X-RAY DIFFRACTION100
3.5492-3.77140.26091350.19362559X-RAY DIFFRACTION100
3.7714-4.06250.22731350.17692570X-RAY DIFFRACTION100
4.0625-4.4710.17251350.15572574X-RAY DIFFRACTION100
4.471-5.11730.1771370.14532601X-RAY DIFFRACTION100
5.1173-6.44470.20271380.17022614X-RAY DIFFRACTION100
6.4447-47.22540.18731460.18872768X-RAY DIFFRACTION100
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)
12.58640.68680.73724.86430.4744.4770.0093-0.8877-0.16130.2496-0.31730.2682-0.30410.23240.25810.4022-0.1038-0.06350.8830.20450.7876-175.9021-23.1539136.5335
29.3628-3.1336-0.63011.95561.03230.76510.3274-0.98790.78380.0337-0.1915-0.49890.21350.5504-0.22280.7221-0.0261-0.16271.15630.11690.857-156.0793-17.6703138.1513
33.7422-0.7719-0.94373.9631-0.00333.2405-0.0323-1.4759-0.33530.7448-0.14640.65320.1022-0.10280.28370.5447-0.1002-0.05231.24170.22850.7803-181.9883-29.9969143.6996
45.29650.83320.99315.05362.76794.8203-0.0872-0.7454-0.5424-0.1550.2605-0.5330.25941.0166-0.2050.43660.08030.14630.90690.22610.5221-128.8087-29.2829127.7702
54.62650.73971.21235.95643.17227.208-0.144-0.5321-0.4650.02930.00170.13190.26290.08680.14990.34560.02610.07280.6650.2630.5437-140.5341-32.1618125.2737
62.2885-0.51160.64653.5832-0.04033.8364-0.1391-1.1114-0.67480.30460.23760.50820.3203-0.2224-0.04080.54760.00750.06761.10330.51630.784-147.7448-35.553134.0657
74.0096-1.29481.01071.16390.52121.09890.1371-1.0935-1.02830.13430.18540.7080.349-0.1739-0.25210.6627-0.12720.01961.01280.52351.0737-160.8837-34.2781128.8881
84.2812-0.8810.83812.9521-0.09242.68150.018-1.2825-1.07710.42880.2812-0.01220.49640.0898-0.27620.60230.03560.11530.99380.42820.7292-136.4111-36.8531133.8437
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 182 )
2X-RAY DIFFRACTION2chain 'A' and (resid 183 through 307 )
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 359 )
4X-RAY DIFFRACTION4chain 'B' and (resid 14 through 72 )
5X-RAY DIFFRACTION5chain 'B' and (resid 73 through 134 )
6X-RAY DIFFRACTION6chain 'B' and (resid 135 through 182 )
7X-RAY DIFFRACTION7chain 'B' and (resid 183 through 294 )
8X-RAY DIFFRACTION8chain 'B' and (resid 295 through 359 )

+
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