[English] 日本語
Yorodumi
- PDB-7nl6: Crystal Structure of DC-SIGN in complex with a triazole-based gly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nl6
TitleCrystal Structure of DC-SIGN in complex with a triazole-based glycomimetic ligand
ComponentsDC-SIGN, CRD domain
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology
Function and homology information


B cell adhesion / cell-cell recognition / intracellular transport of virus / peptide antigen transport / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / regulation of T cell proliferation ...B cell adhesion / cell-cell recognition / intracellular transport of virus / peptide antigen transport / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / regulation of T cell proliferation / RSV-host interactions / D-mannose binding / antigen processing and presentation / positive regulation of T cell proliferation / CD209 (DC-SIGN) signaling / viral genome replication / endocytosis / peptide antigen binding / host cell / virus receptor activity / carbohydrate binding / adaptive immune response / intracellular signal transduction / immune response / symbiont entry into host cell / external side of plasma membrane / innate immune response / virion attachment to host cell / cell surface / extracellular region / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / CD209-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
NITRATE ION / Chem-UH8 / CD209 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJakob, R.P. / Cramer, J. / Lakkaichi, A. / Aliu, B. / Cattaneo, I. / Klein, S. / Jiang, X. / Rabbani, S. / Schwardt, O. / Ernst, B. / Maier, T.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Sweet Drugs for Bad Bugs: A Glycomimetic Strategy against the DC-SIGN-Mediated Dissemination of SARS-CoV-2.
Authors: Cramer, J. / Lakkaichi, A. / Aliu, B. / Jakob, R.P. / Klein, S. / Cattaneo, I. / Jiang, X. / Rabbani, S. / Schwardt, O. / Zimmer, G. / Ciancaglini, M. / Abreu Mota, T. / Maier, T. / Ernst, B.
History
DepositionFeb 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DC-SIGN, CRD domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5546
Polymers20,0491
Non-polymers5055
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-24 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.473, 59.473, 73.939
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-664-

HOH

21A-678-

HOH

31A-690-

HOH

41A-698-

HOH

51A-700-

HOH

-
Components

#1: Protein DC-SIGN, CRD domain / C-type lectin domain family 4 member L / Dendritic cell-specific ICAM-3-grabbing non-integrin 1 / ...C-type lectin domain family 4 member L / Dendritic cell-specific ICAM-3-grabbing non-integrin 1 / DC-SIGN / DC-SIGN1 / CD209 antigen


Mass: 20049.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD209, CLEC4L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NNX6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-UH8 / Methyl 2-deoxy-2-(4-(pyridine-3-yl))-1,2,3-triazol-1-yl)-alpha-D-mannopyranoside / (2~{R},3~{S},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-methoxy-5-(4-pyridin-3-yl-1,2,3-triazol-1-yl)oxane-3,4-diol


Mass: 322.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20.5% PEG 3350 and 0.05M NH4NO3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.2→42.262 Å / Num. obs: 8051 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.295 / Rpim(I) all: 0.084 / Net I/σ(I): 6.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.75 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 795 / CC1/2: 0.468 / Rpim(I) all: 0.49 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SL4

1sl4


Resolution: 2.2→42.262 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 381 4.73 %
Rwork0.1942 7666 -
obs0.1958 8047 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.09 Å2 / Biso mean: 32.8902 Å2 / Biso min: 16.72 Å2
Refinement stepCycle: final / Resolution: 2.2→42.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1070 0 48 102 1220
Biso mean--29.77 35.57 -
Num. residues----132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2005-2.51890.29581430.25042476
2.5189-3.17330.26221090.20822544
3.1733-42.2620.18761290.17142646
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)
14.0616-0.76811.50623.45160.45554.4131-0.075-0.07440.39990.0422-0.01580.13240.0931-0.14910.08190.1768-0.0072-0.00350.18330.0260.265814.7581-30.92853.2862
21.50390.79770.26581.90030.52551.61340.0496-0.15650.05280.0973-0.09180.1481-0.0233-0.0710.05240.1856-0.00480.00540.216-0.00290.240613.7401-23.211119.5692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 253 through 270 )A253 - 270
2X-RAY DIFFRACTION2chain 'A' and (resid 271 through 384 )A271 - 384

+
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