[English] 日本語
Yorodumi
- PDB-7qe4: B-trefoil lectin from Salpingoeca rosetta in complex with GalNAc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qe4
TitleB-trefoil lectin from Salpingoeca rosetta in complex with GalNAc
ComponentsSarol-1
KeywordsSUGAR BINDING PROTEIN / lectin / GalNAc / b-trefoil / pore forming lectin
Function / homologyRicin B-like lectins / 2-acetamido-2-deoxy-alpha-D-galactopyranose / 2-acetamido-2-deoxy-beta-D-galactopyranose / Uncharacterized protein
Function and homology information
Biological speciesSalpingoeca rosetta (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNotova, S. / Varrot, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission814029European Union
CitationJournal: Commun Biol / Year: 2022
Title: The choanoflagellate pore-forming lectin SaroL-1 punches holes in cancer cells by targeting the tumor-related glycosphingolipid Gb3.
Authors: Notova, S. / Bonnardel, F. / Rosato, F. / Siukstaite, L. / Schwaiger, J. / Lim, J.H. / Bovin, N. / Varrot, A. / Ogawa, Y. / Romer, W. / Lisacek, F. / Imberty, A.
History
DepositionDec 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Sarol-1
BBB: Sarol-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,71213
Polymers77,8612
Non-polymers1,85111
Water17,601977
1
AAA: Sarol-1
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 39.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)39,8516
Polymers38,9301
Non-polymers9205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Sarol-1
hetero molecules


  • defined by author
  • 39.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)39,8617
Polymers38,9301
Non-polymers9316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.158, 59.254, 209.612
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 5 - 326 / Label seq-ID: 26 - 347

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein Sarol-1


Mass: 38930.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salpingoeca rosetta (eukaryote) / Gene: PTSG_08235 / Plasmid: pET28aTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2UID9

-
Sugars , 2 types, 8 molecules

#2: Sugar
ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 980 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 977 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.5 % / Description: rock
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M MOPSO, Bis-Tris pH 6.5, 100 mM AA Morpheus I, 25 % PEG SMEAR MEDIUM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.980107 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980107 Å / Relative weight: 1
ReflectionResolution: 1.7→45.19 Å / Num. obs: 79471 / % possible obs: 100 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.041 / Rrim(I) all: 0.089 / Net I/σ(I): 14.6
Reflection shell

Num. unique obs: 79471 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all
9-45.197.10.0390.9970.0210.045
1.7-1.738.30.6160.890.3390.705

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
XDSdata reduction
Aimless1.12.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QE3

7qe3


Resolution: 1.7→44.28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.06 / SU ML: 0.068 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.103
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2061 3914 4.931 %
Rwork0.1688 75465 -
all0.171 --
obs-79379 99.963 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.143 Å2
Baniso -1Baniso -2Baniso -3
1-1.285 Å20 Å20 Å2
2---0.214 Å20 Å2
3----1.071 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5007 0 123 977 6107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135404
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154939
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.6627386
X-RAY DIFFRACTIONr_angle_other_deg1.3691.58111435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24721.418275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9815851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0541535
X-RAY DIFFRACTIONr_chiral_restr0.0640.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026151
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021213
X-RAY DIFFRACTIONr_nbd_refined0.1930.2750
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.24414
X-RAY DIFFRACTIONr_nbtor_refined0.1590.22491
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2614
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0980.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1220.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2260.218
X-RAY DIFFRACTIONr_nbd_other0.1880.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.278
X-RAY DIFFRACTIONr_mcbond_it1.1831.8292662
X-RAY DIFFRACTIONr_mcbond_other1.1771.8292661
X-RAY DIFFRACTIONr_mcangle_it1.7662.743348
X-RAY DIFFRACTIONr_mcangle_other1.7662.7413349
X-RAY DIFFRACTIONr_scbond_it1.8232.0232742
X-RAY DIFFRACTIONr_scbond_other1.8232.0232743
X-RAY DIFFRACTIONr_scangle_it2.8262.9584032
X-RAY DIFFRACTIONr_scangle_other2.8252.9584033
X-RAY DIFFRACTIONr_lrange_it4.50522.7485796
X-RAY DIFFRACTIONr_lrange_other4.20421.6915553
X-RAY DIFFRACTIONr_ncsr_local_group_10.1280.059737
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.127920.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.127920.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.282910.2395560X-RAY DIFFRACTION99.9658
1.744-1.7920.2692710.2135362X-RAY DIFFRACTION100
1.792-1.8440.2232430.1945235X-RAY DIFFRACTION99.9818
1.844-1.9010.2172760.1775042X-RAY DIFFRACTION99.9624
1.901-1.9630.2182960.1694912X-RAY DIFFRACTION99.9808
1.963-2.0320.1932430.1624761X-RAY DIFFRACTION100
2.032-2.1090.1952330.1594618X-RAY DIFFRACTION100
2.109-2.1950.2142440.1634441X-RAY DIFFRACTION99.9573
2.195-2.2920.2052170.1594284X-RAY DIFFRACTION100
2.292-2.4040.2132050.1624050X-RAY DIFFRACTION99.9765
2.404-2.5340.2052180.1633879X-RAY DIFFRACTION100
2.534-2.6880.222040.1723698X-RAY DIFFRACTION99.9488
2.688-2.8730.1721840.1553469X-RAY DIFFRACTION100
2.873-3.1040.2071580.1663252X-RAY DIFFRACTION99.9707
3.104-3.40.1961670.1623006X-RAY DIFFRACTION100
3.4-3.8010.1791150.1632748X-RAY DIFFRACTION99.8953
3.801-4.3890.1831010.152470X-RAY DIFFRACTION99.9611
4.389-5.3740.1911140.1492072X-RAY DIFFRACTION99.9543
5.374-7.5980.227880.2051639X-RAY DIFFRACTION100

+
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