[English] 日本語
Yorodumi
- PDB-6ghv: Structure of a DC-SIGN CRD in complex with high affinity glycomimetic. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ghv
TitleStructure of a DC-SIGN CRD in complex with high affinity glycomimetic.
ComponentsCD209 antigen
KeywordsSUGAR BINDING PROTEIN / DC-SIGN / Inhibitor
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 / leukocyte cell-cell adhesion / pattern recognition receptor activity ...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 / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding / regulation of T cell proliferation / positive regulation of T cell proliferation / CD209 (DC-SIGN) signaling / viral genome replication / peptide antigen binding / endocytosis / host cell / virus receptor activity / carbohydrate binding / adaptive immune response / intracellular signal transduction / immune response / innate immune response / external side of plasma membrane / symbiont entry into host cell / virion attachment to host cell / cell surface / extracellular region / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) ...CD209-like, C-type lectin-like domain / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-EZ8 / CD209 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsThepaut, M. / Achilli, S. / Medve, L. / Bernardi, A. / Fieschi, F.
Funding support France, 1items
OrganizationGrant numberCountry
European CommissionITN 642870 France
CitationJournal: Chemistry / Year: 2019
Title: Enhancing Potency and Selectivity of a DC-SIGN Glycomimetic Ligand by Fragment-Based Design: Structural Basis.
Authors: Medve, L. / Achilli, S. / Guzman-Caldentey, J. / Thepaut, M. / Senaldi, L. / Le Roy, A. / Sattin, S. / Ebel, C. / Vives, C. / Martin-Santamaria, S. / Bernardi, A. / Fieschi, F.
History
DepositionMay 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: 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
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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CD209 antigen
B: CD209 antigen
C: CD209 antigen
D: CD209 antigen
E: CD209 antigen
F: CD209 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,18744
Polymers106,4796
Non-polymers5,70738
Water11,890660
1
A: CD209 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7218
Polymers17,7471
Non-polymers9757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CD209 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6867
Polymers17,7471
Non-polymers9396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CD209 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6867
Polymers17,7471
Non-polymers9396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CD209 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6867
Polymers17,7471
Non-polymers9396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: CD209 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7218
Polymers17,7471
Non-polymers9757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: CD209 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6867
Polymers17,7471
Non-polymers9396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.612, 57.507, 107.247
Angle α, β, γ (deg.)90.00, 118.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 17746.582 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD209, CLEC4L / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NNX6
#2: Chemical
ChemComp-EZ8 / [1-[(2~{S},3~{S},4~{R},5~{S},6~{R})-2-[(1~{S},2~{S},4~{S},5~{S})-2-(2-chloroethyloxy)-4,5-bis[[4-(hydroxymethyl)phenyl]methylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methylazanium


Mass: 748.243 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C35H48ClN6O10 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 200mM Mg(NO3)2, 100mM MES pH6. Protein sample: 150mM NaCl, 4mM CaCl2, 25mM Tris pH8, 2% DMSO, 3.25 mM ligand and 5.54mg/mL protein.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 65455 / % possible obs: 98.4 % / Redundancy: 3.087 % / Biso Wilson estimate: 34.771 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.12 / Χ2: 1.005 / Net I/σ(I): 8.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.22.8070.5452.0184270.7690.66897.9
2.2-2.43.1390.3973130280.8680.47898.7
2.4-2.93.2210.1986.14190530.9560.23899.3
2.9-3.53.0590.0911.54107210.9870.1198.5
3.5-4.52.8120.05616.7774460.9930.06997.2
4.5-63.3580.05418.9739090.9940.06598.1
6-83.3170.05618.6216490.9930.06697.1
8-113.2150.04422.177500.9970.05295.4
11-153.0840.03923.832870.9960.04795.7
15-202.9550.03624.521100.9960.04491.7
20-262.5650.04122.17460.9940.0593.9
26-352.30.04223.49200.9870.05687
35-451.6670.03320.1890.9950.04690
40-45

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.583
Highest resolutionLowest resolution
Rotation92.67 Å3.5 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDS20180126data reduction
XSCALE20180126data scaling
MOLREP11.6.02phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K9I

1k9i


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.856 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.175 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23357 3261 5 %RANDOM
Rwork0.17592 ---
obs0.17879 62185 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.681 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20.55 Å2
2---2.31 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 344 660 7448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.027139
X-RAY DIFFRACTIONr_bond_other_d0.0080.025793
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.9329737
X-RAY DIFFRACTIONr_angle_other_deg1.1133.01913637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7585829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87725.466386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.447151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0491524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2938
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027977
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021579
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5383.2513214
X-RAY DIFFRACTIONr_mcbond_other2.5343.2493213
X-RAY DIFFRACTIONr_mcangle_it3.7274.8474017
X-RAY DIFFRACTIONr_mcangle_other3.7274.8494018
X-RAY DIFFRACTIONr_scbond_it2.9013.4773925
X-RAY DIFFRACTIONr_scbond_other2.9013.4763926
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3795.1045701
X-RAY DIFFRACTIONr_long_range_B_refined6.11437.3758791
X-RAY DIFFRACTIONr_long_range_B_other6.05937.1598707
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 235 -
Rwork0.296 4508 -
obs--97.81 %

+
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