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- PDB-4wco: Crystal structure of extracellular domain of human lectin-like tr... -

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Basic information

Entry
Database: PDB / ID: 4wco
TitleCrystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the ligand for natural killer receptor-P1A
ComponentsC-type lectin domain family 2 member D
KeywordsIMMUNE SYSTEM / receptor / ectodomain / immunology / lectin
Function / homology
Function and homology information


Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / carbohydrate binding / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
: / Natural killer cell receptor-like, C-type lectin-like domain / 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 ...: / Natural killer cell receptor-like, C-type lectin-like domain / 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
ACETATE ION / C-type lectin domain family 2 member D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsKita, S. / Matsubara, H. / Kasai, Y. / Tamaoki, T. / Okabe, Y. / Fukuhara, H. / Kamishikiryo, J. / Ose, T. / Kuroki, K. / Maenaka, K.
CitationJournal: Eur.J.Immunol. / Year: 2015
Title: Crystal structure of extracellular domain of human lectin-like transcript 1 (LLT1), the ligand for natural killer receptor-P1A
Authors: Kita, S. / Matsubara, H. / Kasai, Y. / Tamaoki, T. / Okabe, Y. / Fukuhara, H. / Kamishikiryo, J. / Krayukhina, E. / Uchiyama, S. / Ose, T. / Kuroki, K. / Maenaka, K.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Nov 8, 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 / refine_hist / struct_conn
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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_conn.ptnr2_symmetry
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 2 member D
B: C-type lectin domain family 2 member D
C: C-type lectin domain family 2 member D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,37914
Polymers42,6483
Non-polymers73111
Water48627
1
A: C-type lectin domain family 2 member D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3403
Polymers14,2161
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-type lectin domain family 2 member D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5085
Polymers14,2161
Non-polymers2924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: C-type lectin domain family 2 member D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5306
Polymers14,2161
Non-polymers3145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.379, 84.658, 53.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein C-type lectin domain family 2 member D / Lectin-like NK cell receptor / Lectin-like transcript 1 / LLT-1 / Osteoclast inhibitory lectin


Mass: 14215.843 Da / Num. of mol.: 3 / Fragment: UNP residues 71-191 / Mutation: H176C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC2D, CLAX, LLT1, OCIL / Plasmid: pET22 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9UHP7
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate, pH6.5, 0.2 M zinc acetate and 5% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→37.7 Å / Num. obs: 14128 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 12.7
Reflection shellResolution: 2.46→2.55 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.87 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HUP

3hup


Resolution: 2.46→37.65 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2572 708 5.01 %
Rwork0.2182 --
obs0.2202 14127 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 24 27 2881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032937
X-RAY DIFFRACTIONf_angle_d0.7763954
X-RAY DIFFRACTIONf_dihedral_angle_d13.4151040
X-RAY DIFFRACTIONf_chiral_restr0.033377
X-RAY DIFFRACTIONf_plane_restr0.003511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4583-2.64810.32521330.28492642X-RAY DIFFRACTION100
2.6481-2.91450.27261450.26222619X-RAY DIFFRACTION100
2.9145-3.3360.28021460.24292663X-RAY DIFFRACTION100
3.336-4.20210.24221360.1952681X-RAY DIFFRACTION100
4.2021-37.6540.23491480.19432814X-RAY DIFFRACTION100
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)
14.40172.415-1.12928.23392.03563.59420.0774-0.2499-0.08210.8806-0.41430.5001-0.0347-0.35440.29260.292-0.03850.030.3136-0.05950.3464-34.866625.825326.2465
25.28514.2446-0.80335.0539-2.8513.06370.3255-0.13920.74390.39580.08741.3613-1.0337-0.2098-0.23470.5701-0.1030.26220.3678-0.20980.8157-33.875738.189831.2631
35.2522-1.5373-2.21387.64271.98311.7101-0.3573-0.1869-0.16711.02210.15320.05610.8031-0.0060.2520.4707-0.02990.01330.3187-0.03440.3071-26.043324.061428.2206
44.26970.08574.01271.86470.82284.16440.2176-0.35190.01990.4713-0.16920.0254-0.07470.0439-0.14610.5776-0.18430.05930.37660.03380.2891-20.122232.47133.9442
56.48611.0012.94936.59640.50683.01230.14780.37690.13310.5979-0.1787-0.0684-0.37270.557-0.02760.4269-0.12010.04830.39410.00720.2221-21.668735.393126.5997
61.92091.20370.93394.4866-0.0745.46420.03710.04690.09080.2550.05920.40350.0236-0.0537-0.0810.19740.00070.010.23490.00040.2997-35.478213.140813.4316
79.0439-4.2737-3.5873.7562.88758.6431-0.74521.2854-0.55690.0977-0.26991.1580.5323-1.03480.91190.5033-0.1511-0.12740.54560.03990.4632-42.29737.1942-1.2644
82.59290.0499-3.6042.09430.2026.80310.11140.73080.1814-0.4338-0.16710.202-0.3858-0.5945-0.01330.23210.0385-0.04510.34220.0140.3134-35.26713.67232.6177
92.6141-1.16650.65142.9706-1.48144.79630.07370.08670.04860.0254-0.1475-0.45210.11220.20820.10910.19170.01810.00520.21760.00020.3411-10.37862.6531-4.0281
103.6319-0.26131.19194.3526-1.53952.745-0.5148-0.11310.7665-0.2841-0.1512-0.3527-1.0508-0.46610.39490.31570.0366-0.01390.3571-0.02850.5031-18.545115.9364-8.0791
114.5415-0.66981.564.9074-2.0869.0013-0.13450.27880.2014-0.6833-0.1413-0.3580.4157-0.38240.22030.31070.03240.08860.2216-0.04450.3085-15.14674.9111-11.786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 71 through 95 )
2X-RAY DIFFRACTION2chain 'A' and (resid 96 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 187 )
6X-RAY DIFFRACTION6chain 'B' and (resid 71 through 135 )
7X-RAY DIFFRACTION7chain 'B' and (resid 136 through 147 )
8X-RAY DIFFRACTION8chain 'B' and (resid 151 through 188 )
9X-RAY DIFFRACTION9chain 'C' and (resid 74 through 135 )
10X-RAY DIFFRACTION10chain 'C' and (resid 136 through 166 )
11X-RAY DIFFRACTION11chain 'C' and (resid 167 through 187 )

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