[English] 日本語
Yorodumi
- PDB-1sl6: Crystal Structure of a fragment of DC-SIGNR (containg the carbohy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sl6
TitleCrystal Structure of a fragment of DC-SIGNR (containg the carbohydrate recognition domain and two repeats of the neck) complexed with Lewis-x.
ComponentsC-type lectin DC-SIGNR
KeywordsSUGAR BINDING PROTEIN / DC-SIGNR / C-TYPE LECTIN
Function / homology
Function and homology information


cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / virion binding / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding ...cell-cell recognition / intracellular transport of virus / peptide antigen transport / ICAM-3 receptor activity / virion binding / leukocyte cell-cell adhesion / pattern recognition receptor activity / antigen processing and presentation / RSV-host interactions / D-mannose binding / receptor-mediated endocytosis of virus by host cell / viral genome replication / peptide antigen binding / calcium-dependent protein binding / signaling receptor activity / host cell / virus receptor activity / carbohydrate binding / adaptive immune response / receptor-mediated virion attachment to host cell / intracellular signal transduction / immune response / symbiont entry into host cell / external side of plasma membrane / innate immune response / virion attachment to host cell / 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
Lewis X antigen, alpha anomer / : / C-type lectin domain family 4 member M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGuo, Y. / Feinberg, H. / Conroy, E. / Mitchell, D.A. / Alvarez, R. / Blixt, O. / Taylor, M.E. / Weis, W.I. / Drickamer, K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis for distinct ligand-binding and targeting properties of the receptors DC-SIGN and DC-SIGNR
Authors: Guo, Y. / Feinberg, H. / Conroy, E. / Mitchell, D.A. / Alvarez, R. / Blixt, O. / Taylor, M.E. / Weis, W.I. / Drickamer, K.
History
DepositionMar 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_asym_id / _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.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C-type lectin DC-SIGNR
B: C-type lectin DC-SIGNR
C: C-type lectin DC-SIGNR
D: C-type lectin DC-SIGNR
E: C-type lectin DC-SIGNR
F: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,56636
Polymers128,4276
Non-polymers4,13930
Water4,252236
1
A: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: C-type lectin DC-SIGNR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0946
Polymers21,4051
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.750, 153.750, 128.702
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein
C-type lectin DC-SIGNR


Mass: 21404.506 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: A fragment containing the CRD domain and two repeats from the neck domain
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): BL21/DE3 / Production host: Escherichia coli (E. coli) / References: GenBank: 12084795, UniProt: Q9H2X3*PLUS
#2: Polysaccharide
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Lewis X antigen / alpha anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis X antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.69 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 300, 0.2M NaCl, 0.1 Hepes pH=7.5. Protein solution: 10 mg/ml protein, 5mM CaCl2, 10 mM oligosaccharide., VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å
DetectorType: ADSC / Detector: CCD / Date: Jul 3, 2003
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 83241 / Num. obs: 80306 / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.054
Reflection shellResolution: 2.25→2.33 Å / Rsym value: 0.322 / % possible all: 84.5

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→41.96 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3723247.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 6102 8.4 %RANDOM
Rwork0.219 ---
obs0.219 73013 87.6 %-
all-80292 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.8621 Å2 / ksol: 0.348332 e/Å3
Displacement parametersBiso mean: 54.2 Å2
Baniso -1Baniso -2Baniso -3
1--13.33 Å2-4.11 Å20 Å2
2---13.33 Å20 Å2
3---26.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.25→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8256 0 240 236 8732
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.292.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 790 8.4 %
Rwork0.299 8666 -
obs--68.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM_NCARBOHYDRATE.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION5WATER.TOP

+
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