[English] 日本語
Yorodumi
- PDB-3p7f: Structure of the human Langerin carbohydrate recognition domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p7f
TitleStructure of the human Langerin carbohydrate recognition domain
ComponentsC-type lectin domain family 4 member K
KeywordsIMMUNE SYSTEM / C-type lectin / membrane protein / glycoprotein / Langerin / DC-SIGN / Carbohydrate binding protein / Calcium binding / sugar binding / Langerhans cells / CD207
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / D-mannose binding / endocytic vesicle / clathrin-coated endocytic vesicle membrane / signaling receptor activity / early endosome membrane / 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
C-type lectin domain family 4 member K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSkerra, A. / Schiefner, A.
CitationJournal: Mol.Immunol. / Year: 2008
Title: The carbohydrate recognition domain of Langerin reveals high structural similarity with the one of DC-SIGN but an additional, calcium-independent sugar-binding site.
Authors: Chatwell, L. / Holla, A. / Kaufer, B.B. / Skerra, A.
History
DepositionOct 12, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionNov 3, 2010ID: 3BBS
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / struct_ref_seq_dif / struct_site
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.ptnr2_auth_asym_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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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


Theoretical massNumber of molelcules
Total (without water)67,3838
Polymers67,2234
Non-polymers1604
Water1,964109
1
A: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8462
Polymers16,8061
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8462
Polymers16,8061
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: C-type lectin domain family 4 member K
hetero molecules


  • defined by author
  • 16.8 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)16,8462
Polymers16,8061
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: C-type lectin domain family 4 member K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8462
Polymers16,8061
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.760, 79.760, 90.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

-
Components

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


Mass: 16805.736 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP Residues 193-328)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD207, CLEC4K, Leucocyte cDNA / Plasmid: pLA1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: Q9UJ71
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: Protein: 10mg/ml Langerin in 10 mM Tris/HCl pH 7.5; Reservoir: 0.1 M Na-cacodylate, 13 %(w/v) PEG4000, 0.1 M MgCl2, 5mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 22, 2006
RadiationMonochromator: Osmic confocal Max-Flux Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 19624 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2159 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P7G

3p7g


Resolution: 2.5→28.2 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / SU B: 21.295 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.979 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24288 991 5.1 %RANDOM
Rwork0.18655 ---
obs0.18938 18632 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.053 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4273 0 4 109 4386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224455
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.9096077
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29324.22218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5715663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0611512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213532
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4031.52618
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8222.54222
X-RAY DIFFRACTIONr_scbond_it1.7493.51837
X-RAY DIFFRACTIONr_scangle_it2.908101855
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 99 -
Rwork0.237 1341 -
obs--99.86 %
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)
12.9885-0.9243-0.73813.1068-0.01084.04360.00030.0529-0.0796-0.0586-0.04360.08410.0707-0.07870.04320.04650.0112-0.06080.0914-0.02760.08957.017415.9775-33.8065
23.21920.5020.17942.8154-0.56992.7482-0.07160.09150.3303-0.2872-0.03760.2253-0.268-0.14220.10920.11440.0653-0.07790.087-0.0360.13854.787325.8897-33.9789
314.380816.04597.884517.94589.24769.43661.23860.2311-2.57881.60730.2464-2.8651.28861.7783-1.4850.60430.2886-0.23490.9472-0.10020.492627.36254.6427-29.621
43.4211-0.57011.67123.3811-1.40183.08710.110.20590.3746-0.1778-0.1178-0.1789-0.30520.19110.00780.107-0.00390.05260.09710.03090.099832.721429.4943-32.4
55.34570.61280.26483.49351.49030.70.21130.2224-0.55260.0125-0.2340.05870.1439-0.08650.02270.30730.0402-0.01950.07520.00590.095228.473413.9707-32.8286
62.19960.64060.19522.9626-0.44193.22040.05410.1603-0.1141-0.2034-0.053-0.29660.19460.3237-0.0010.0541-0.02040.02320.14040.01130.062136.645121.0547-31.8773
74.71861.484-0.79962.6921-1.43393.0878-0.056-0.136-0.27080.07320.0147-0.16950.42280.03090.04130.10260.0043-0.03030.02230.02890.082630.542313.0401-6.3511
85.6903-0.87660.71982.83261.65191.5758-0.1329-0.11150.71010.1206-0.0089-0.0761-0.2844-0.08010.14180.3440.0258-0.04420.0787-0.01070.140132.232526.8129-4.5719
94.7363-1.3266-0.40190.64-0.42494.1137-0.01270.1945-0.3321-0.25880.07140.29350.5228-0.3388-0.05870.313-0.0574-0.1920.13340.07260.205127.200210.9797-8.7827
1020.3796-0.5773-0.609613.7660.935411.3907-0.00460.0730.8824-0.2363-0.09270.1698-0.8969-0.60330.09730.2176-0.04710.07540.1401-0.06970.12478.350533.9532-2.4336
113.5209-0.99570.2693.91080.36514.37840.1141-0.0158-0.03310.0391-0.21940.20860.0018-0.18040.10530.0583-0.05070.04250.0831-0.0170.08915.847121.4806-8.1842
122.96940.0392-0.06013.50730.58044.8860.0945-0.109-0.27640.3559-0.23350.22650.4215-0.40510.13890.109-0.03640.07150.1719-0.03340.15012.147716.8305-6.1852
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A198 - 263
2X-RAY DIFFRACTION2A264 - 321
3X-RAY DIFFRACTION3A322 - 331
4X-RAY DIFFRACTION4B196 - 256
5X-RAY DIFFRACTION5B257 - 284
6X-RAY DIFFRACTION6B285 - 325
7X-RAY DIFFRACTION7C198 - 241
8X-RAY DIFFRACTION8C242 - 312
9X-RAY DIFFRACTION9C313 - 331
10X-RAY DIFFRACTION10D196 - 207
11X-RAY DIFFRACTION11D208 - 276
12X-RAY DIFFRACTION12D277 - 325

+
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://pdbjlvh1.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