[English] 日本語
Yorodumi
- PDB-2xr5: Crystal structure of the complex of the carbohydrate recognition ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xr5
TitleCrystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.
ComponentsCD209 ANTIGEN
KeywordsSUGAR BINDING PROTEIN
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 / ETHANOLAMINE / alpha-D-mannopyranose / CD209 antigen
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsThepaut, M. / Suitkeviciute, I. / Sattin, S. / Reina, J. / Bernardi, A. / Fieschi, F.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Structure of a Glycomimetic Ligand in the Carbohydrate Recognition Domain of C-Type Lectin Dc-Sign. Structural Requirements for Selectivity and Ligand Design.
Authors: Thepaut, M. / Guzzi, C. / Sutkeviciute, I. / Sattin, S. / Ribeiro-Viana, R. / Varga, N. / Chabrol, E. / Rojo, J. / Bernardi, A. / Angulo, J. / Nieto, P.M. / Fieschi, F.
History
DepositionSep 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jan 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 1.3Mar 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 1.4Jul 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_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_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_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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 6, 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: CD209 ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,73210
Polymers19,0321
Non-polymers7009
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)71.450, 71.450, 52.670
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-2009-

HOH

21A-2070-

HOH

31A-2133-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 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 / MDC-SIGN1A TYPE I


Mass: 19031.984 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 254-404
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.: 1
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

-
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-ETA / ETHANOLAMINE


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NO
#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

-
Details

Has protein modificationY
Nonpolymer detailsTHE PSEUDO DIMANNOSIDE MIMIC COMPOSED OF RESIDUES A1384-A1386 IS DIMETHYL (1S,2S,4S,5S)-4-(1-ALPHA- ...THE PSEUDO DIMANNOSIDE MIMIC COMPOSED OF RESIDUES A1384-A1386 IS DIMETHYL (1S,2S,4S,5S)-4-(1-ALPHA-D-MANNOPYRANOSYL)-5-(2- AMINO-1-ETHYLOXY)-CYCLOHEXANE-1,2-DICARBOXYLATE
Sequence detailsSEQUENCE NUMBERING CORRESPONDS TO ISOFORM 1 (MDC-SIGN1A TYPE I). THE SIXTEEN RESIDUES INSERTED AT ...SEQUENCE NUMBERING CORRESPONDS TO ISOFORM 1 (MDC-SIGN1A TYPE I). THE SIXTEEN RESIDUES INSERTED AT THE N-TERMINUS (MASWSHPQFEKIEGRM) COME FROM THE EXPRESSION PLASMID.

-
Experimental details

-
Experiment

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

-
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. 20% PEG 3350, 200 MM NACL, 100 MM CACODYLATE PH 6.5, CRYOPROTECTED IN PARATONE-N.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9809
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2008 / Details: MIRRORS
RadiationMonochromator: CHANNEL-CUT SILICON MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9809 Å / Relative weight: 1
ReflectionResolution: 1.42→42.41 Å / Num. obs: 25925 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 25.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 28.67
Reflection shellResolution: 1.42→1.46 Å / Redundancy: 7.22 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 5.56 / % possible all: 92.4

-
Processing

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

2it6


Resolution: 1.42→42.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.843 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.17113 1297 5 %RANDOM
Rwork0.14838 ---
obs0.14954 24628 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.125 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.42→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 0 36 166 1266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211291
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9151779
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8655176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11825.41772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67615208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.542155
X-RAY DIFFRACTIONr_chiral_restr0.1140.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2690.2621
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2843
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4971.5738
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.65921194
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5543553
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9784.5561
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.424→1.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 88 -
Rwork0.175 1672 -
obs--100 %

+
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