[English] 日本語
Yorodumi
- PDB-5m62: Structure of the Mus musclus Langerin carbohydrate recognition do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m62
TitleStructure of the Mus musclus Langerin carbohydrate recognition domain in complex with glucose
ComponentsC-type lectin domain family 4 member K
KeywordsIMMUNE SYSTEM / C-TYPE LECTIN / GLYCOPROTEIN / CARBOHYDRATE BINDING PROTEIN / CALCIUM BINDING / CRD Domain / LECTIN
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / carbohydrate binding / defense response to virus / external side of plasma membrane / plasma membrane
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) / C-type lectin-like/link domain superfamily ...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
beta-D-glucopyranose / alpha-D-glucopyranose / C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLoll, B. / Aretz, J. / Rademacher, C. / Wahl, M.C.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Bacterial Polysaccharide Specificity of the Pattern Recognition Receptor Langerin Is Highly Species-dependent.
Authors: Hanske, J. / Schulze, J. / Aretz, J. / McBride, R. / Loll, B. / Schmidt, H. / Knirel, Y. / Rabsch, W. / Wahl, M.C. / Paulson, J.C. / Rademacher, C.
History
DepositionOct 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 30, 2019Group: Data collection / Structure summary / Category: chem_comp / struct_keywords / Item: _chem_comp.type / _struct_keywords.text
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 domain family 4 member K
B: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,95717
Polymers35,0352
Non-polymers1,92215
Water4,972276
1
A: C-type lectin domain family 4 member K
hetero molecules

A: C-type lectin domain family 4 member K
hetero molecules

A: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,71830
Polymers52,5533
Non-polymers3,16527
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
2
B: C-type lectin domain family 4 member K
hetero molecules

B: C-type lectin domain family 4 member K
hetero molecules

B: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,15321
Polymers52,5533
Non-polymers2,60118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Unit cell
Length a, b, c (Å)144.420, 144.420, 144.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-618-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein C-type lectin domain family 4 member K / Langerin


Mass: 17517.512 Da / Num. of mol.: 2 / Fragment: Carbohydrate binding domain, UNP Residues 194-331 / Mutation: C118S
Source method: isolated from a genetically manipulated source
Details: N-terminal AG is a cloning artifact C-terminal Strep-tag First residue of sequence is ILE 194
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd207, Clec4k / Plasmid: puc19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VBX4

-
Sugars , 2 types, 3 molecules

#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 288 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES, pH 6.0, 30% (v/v) polyethylene glycol 600, 5% (w/v) polyethylene glycol 1000, and 10% (v/v) glycerol, 5% Glucose

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2016
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11L, -K, H20.5
ReflectionResolution: 1.7→50 Å / Num. obs: 54929 / % possible obs: 100 % / Redundancy: 40.4 % / Biso Wilson estimate: 29.1 Å2 / CC1/2: 1 / Rrim(I) all: 0.116 / Rsym value: 0.114 / Net I/σ(I): 28.2
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 41.1 % / Mean I/σ(I) obs: 3.2 / CC1/2: 0.85 / Rrim(I) all: 1.783 / Rsym value: 1.761 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K8Y

5k8y


Resolution: 1.7→45.67 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.7 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.014 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16436 2593 4.7 %RANDOM
Rwork0.14385 ---
obs0.14485 52330 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.054 Å2
Baniso -1Baniso -2Baniso -3
1--19.73 Å22.23 Å2-2.01 Å2
2--10.17 Å2-39.82 Å2
3---9.56 Å2
Refinement stepCycle: 1 / Resolution: 1.7→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 103 276 2603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192528
X-RAY DIFFRACTIONr_bond_other_d0.0020.022253
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9323425
X-RAY DIFFRACTIONr_angle_other_deg0.982.9985207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75522.903124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21615389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5911518
X-RAY DIFFRACTIONr_chiral_restr0.1950.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212872
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02666
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_it0.6652.0531156
X-RAY DIFFRACTIONr_mcbond_other0.6652.0521155
X-RAY DIFFRACTIONr_mcangle_it1.0653.0771466
X-RAY DIFFRACTIONr_mcangle_other1.0643.0791467
X-RAY DIFFRACTIONr_scbond_it0.8562.2481372
X-RAY DIFFRACTIONr_scbond_other0.8552.2481372
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3453.2951960
X-RAY DIFFRACTIONr_long_range_B_refined3.84424.8983047
X-RAY DIFFRACTIONr_long_range_B_other3.84424.8853046
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 171 -
Rwork0.354 3842 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5633-0.36450.3682.644-2.29422.69420.02340.10130.1202-0.0749-0.0616-0.04190.0093-0.03220.03810.05020.0221-0.00140.07140.01130.054-34.737533.9249-24.0651
20.10440.09810.18120.3669-0.15970.8636-0.00420.00690.0127-0.01440.0167-0.00580.0069-0.0723-0.01250.05530.0126-0.00640.0575-0.00250.0591-35.837326.7742-10.4219
30.7082.13930.148410.72172.10142.53950.01310.02120.04560.2252-0.10390.23850.0188-0.41830.09080.01030.0058-0.00140.1197-0.01670.093-50.004724.2491-7.1071
40.30470.2590.01790.2826-0.08771.13610.02170.0140.02670.05860.00350.01170.0936-0.0845-0.02520.07830.0052-0.00040.0529-0.00450.0466-37.536920.4319-8.5376
52.4514-0.5586-2.19090.77440.5722.6338-0.0407-0.0873-0.03330.08650.03450.1037-0.04740.02020.00620.06160.02630.00620.0565-0.00140.0533-33.855934.764624.0967
60.31970.1057-0.250.11670.16131.04380.00970.00750.00330.0056-0.00030.004-0.06770.0287-0.00940.05730.0085-0.00330.0556-0.00760.0596-26.739535.815810.4651
710.80472.96880.7282.6018-0.48770.4442-0.06830.09890.39620.04850.01510.0534-0.1817-0.01170.05320.17840.0255-0.01080.0068-0.00770.0804-24.114949.92337.4229
80.25880.2221-0.04910.4831-0.12881.05830.01630.03910.00280.0249-0.00810.0196-0.08380.0989-0.00830.05340.0042-0.00260.0743-0.00460.0502-20.418237.56598.5096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A192 - 213
2X-RAY DIFFRACTION2A214 - 271
3X-RAY DIFFRACTION3A272 - 282
4X-RAY DIFFRACTION4A283 - 327
5X-RAY DIFFRACTION5B192 - 213
6X-RAY DIFFRACTION6B214 - 271
7X-RAY DIFFRACTION7B272 - 282
8X-RAY DIFFRACTION8B283 - 327

+
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