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- PDB-6jjj: Trimeric structure of Kupffer cell C-type lectin receptor Clec4f -

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Basic information

Entry
Database: PDB / ID: 6jjj
TitleTrimeric structure of Kupffer cell C-type lectin receptor Clec4f
ComponentsC-type lectin domain family 4 member F
KeywordsSUGAR BINDING PROTEIN / C-type lectin receptor / Clec4f / Kupffer cell receptor
Function / homology
Function and homology information


NK T cell activation / glycolipid binding / galactose binding / endocytosis / membrane => GO:0016020 / 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 F
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.792 Å
AuthorsWen, Y. / Ouyang, Z. / Felix, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaNO.31870132 and NO.81741088 China
CitationJournal: Febs Lett. / Year: 2020
Title: Trimeric structure of the mouse Kupffer cell C-type lectin receptor Clec4f.
Authors: Ouyang, Z. / Felix, J. / Zhou, J. / Pei, Y. / Ma, B. / Hwang, P.M. / Lemieux, M.J. / Gutsche, I. / Zheng, F. / Wen, Y.
History
DepositionFeb 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-type lectin domain family 4 member F
B: C-type lectin domain family 4 member F
C: C-type lectin domain family 4 member F
D: C-type lectin domain family 4 member F
E: C-type lectin domain family 4 member F
F: C-type lectin domain family 4 member F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,79218
Polymers110,3116
Non-polymers48112
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-130 kcal/mol
Surface area46170 Å2
Unit cell
Length a, b, c (Å)75.150, 75.190, 61.200
Angle α, β, γ (deg.)90.01, 90.04, 120.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
C-type lectin domain family 4 member F / C-type lectin superfamily member 13 / C-type lectin 13 / Kupffer cell receptor


Mass: 18385.174 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clec4f, Clecsf13, Kclr / Production host: Escherichia coli (E. coli) / References: UniProt: P70194
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Potassium thiocyanate, 30% Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.79→32.6 Å / Num. obs: 27730 / % possible obs: 93.82 % / Redundancy: 3.4 % / Net I/σ(I): 7.93
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KQG

3kqg


Resolution: 2.792→32.559 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 37.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2925 2593 9.6 %
Rwork0.2502 --
obs0.2544 27010 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.792→32.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7370 0 12 6 7388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037610
X-RAY DIFFRACTIONf_angle_d0.6910332
X-RAY DIFFRACTIONf_dihedral_angle_d13.0714354
X-RAY DIFFRACTIONf_chiral_restr0.037984
X-RAY DIFFRACTIONf_plane_restr0.0051354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7922-2.8430.54451110.47871124X-RAY DIFFRACTION80
2.843-2.89760.36441580.44331307X-RAY DIFFRACTION98
2.8976-2.95670.54471690.39291282X-RAY DIFFRACTION97
2.9567-3.0210.37231430.39471355X-RAY DIFFRACTION97
3.021-3.09120.34831350.35261310X-RAY DIFFRACTION97
3.0912-3.16850.3971250.3521301X-RAY DIFFRACTION96
3.1685-3.2540.33771570.31731402X-RAY DIFFRACTION97
3.254-3.34970.33031370.29871332X-RAY DIFFRACTION98
3.3497-3.45770.38371290.29011315X-RAY DIFFRACTION97
3.4577-3.58110.33091500.26341372X-RAY DIFFRACTION97
3.5811-3.72430.3076890.2965724X-RAY DIFFRACTION54
3.7243-3.89360.31041380.25341348X-RAY DIFFRACTION99
3.8936-4.09850.35821350.2421319X-RAY DIFFRACTION98
4.0985-4.35470.23351480.24591361X-RAY DIFFRACTION97
4.3547-4.690.2611510.20791304X-RAY DIFFRACTION97
4.69-5.16030.25451020.2141307X-RAY DIFFRACTION96
5.1603-5.90320.27311410.22121309X-RAY DIFFRACTION96
5.9032-7.42280.33581510.25131361X-RAY DIFFRACTION97
7.4228-32.56160.22931240.21851284X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 151.427 Å / Origin y: 82.1814 Å / Origin z: -36.1647 Å
111213212223313233
T0.956 Å20.0216 Å2-0.0017 Å2-0.9408 Å2-0.008 Å2--0.6105 Å2
L0.4767 °20.0714 °2-0.0128 °2-0.4848 °2-0.04 °2--0.1945 °2
S-0.0048 Å °-0.069 Å °0.0293 Å °0.1185 Å °-0.04 Å °0.0015 Å °-0.009 Å °-0.0019 Å °0.0391 Å °
Refinement TLS groupSelection details: all

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