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Basic information

Entry
Database: PDB / ID: 2xr6
TitleCrystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo trimannoside mimic.
ComponentsCD209 ANTIGEN
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE BINDING / MANNOSE
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 / 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 via plasma membrane cell adhesion molecules / 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 / symbiont entry into host cell / external side of plasma membrane / innate immune response / 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-07B / 2-AZIDOETHANOL / alpha-D-mannopyranose / CD209 antigen
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsThepaut, M. / Suitkeviciute, I. / Sattin, S. / Reina, J. / Bernardi, A. / Fieschi, F.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Unique Dc-Sign Clustering Activity of a Small Glycomimetic: A Lesson for Ligand Design.
Authors: Sutkeviciute, I. / Thepaut, M. / Sattin, S. / Berzi, A. / Mcgeagh, J. / Grudinin, S. / Weiser, J. / Le Roy, A. / Reina, J.J. / Rojo, J. / Clerici, M. / Bernardi, A. / Ebel, C. / Fieschi, F.
History
DepositionSep 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references / Non-polymer description
Revision 1.2Aug 27, 2014Group: Database references
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD209 ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,40911
Polymers19,5021
Non-polymers90610
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.330, 71.330, 52.666
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

21A-2084-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein CD209 ANTIGEN / DC-SIGN / DENDRITIC CELL-SPECIFIC ICAM-3-GRABBING NON-INTEGRIN 1 / DC-SIGN1 / C-TYPE LECTIN DOMAIN ...DC-SIGN / DENDRITIC CELL-SPECIFIC ICAM-3-GRABBING NON-INTEGRIN 1 / DC-SIGN1 / C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER L / CD209


Mass: 19502.465 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 250-404 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PASK-IBA7PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NNX6
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 174 molecules

#3: Chemical ChemComp-07B / dimethyl (1S,2S,4S,5S)-4,5-dihydroxycyclohexane-1,2-dicarboxylate


Mass: 232.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O6
#4: Chemical ChemComp-AE9 / 2-AZIDOETHANOL


Mass: 87.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5N3O
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 253 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 384 TO SER
Has protein modificationY
Nonpolymer detailsTHE PSEUDO TRIMANNOSIDE MIMIC COMPOSED OF RESIDUES A1385-A1388 IS DIMETHYL (1S,2S,4S,5S)-4-(1-ALPHA- ...THE PSEUDO TRIMANNOSIDE MIMIC COMPOSED OF RESIDUES A1385-A1388 IS DIMETHYL (1S,2S,4S,5S)-4-(1-ALPHA-D-MANNOPYRANOSYL)-5-[6-[1- (2-AZIDOETHYL)-ALPHA-D-MANNOPYRANOSYL]]-CYCLOHEXANE-1,2-DICARBOXYLAT
Sequence detailsC235S, C384S, RESIDUES MASWSHPQFEKIEGR COMING FROM EXPRESSION PLASMI COMING FROM EXPRESSION PLASMID ...C235S, C384S, RESIDUES MASWSHPQFEKIEGR COMING FROM EXPRESSION PLASMI COMING FROM EXPRESSION PLASMID WERE INSERTED AT THE N-TERMINUS

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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: 1.8 Å3/Da / Density % sol: 31 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: VAPOR DIFFUSION, HANGING DROP, 293K. 35% PEG 3350, 200MM NACL, 100MM CACODYLATE PH 6.5, CRYOPROTECTED IN PARATONE-N

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 9, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.35→50.44 Å / Num. obs: 30348 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.34 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.13
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.82 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IT6

2it6


Resolution: 1.35→50.44 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.16786 1536 5.1 %RANDOM
Rwork0.14704 ---
obs0.14808 28812 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.112 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.35→50.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 0 49 166 1266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221306
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.9431815
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1965177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03325.49371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90115214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.292155
X-RAY DIFFRACTIONr_chiral_restr0.1160.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211038
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2550.2682
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.2844
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2140
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5551.5735
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.64421206
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5693571
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8794.5585
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.08533
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.351→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 109 -
Rwork0.186 2103 -
obs--100 %

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