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- PDB-6ghv: Structure of a DC-SIGN CRD in complex with high affinity glycomimetic. -

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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 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 / symbiont entry into host cell / immune response / 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. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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.

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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

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Phasing

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

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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 %

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