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- PDB-4kzw: Structure of the carbohydrate-recognition domain of the C-type le... -

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Basic information

Entry
Database: PDB / ID: 4kzw
TitleStructure of the carbohydrate-recognition domain of the C-type lectin mincle
ComponentsC-TYPE LECTIN MINCLE
KeywordsCarbohydrate-binding protein / C-type lectin / carbohydrate recognition domain
Function / homology
Function and homology information


Dectin-2 family / T cell differentiation involved in immune response / glycolipid binding / antifungal innate immune response / Fc-gamma receptor signaling pathway / pattern recognition receptor activity / positive regulation of cytokine production / phagocytic vesicle membrane / carbohydrate binding / defense response to bacterium ...Dectin-2 family / T cell differentiation involved in immune response / glycolipid binding / antifungal innate immune response / Fc-gamma receptor signaling pathway / pattern recognition receptor activity / positive regulation of cytokine production / phagocytic vesicle membrane / carbohydrate binding / defense response to bacterium / external side of plasma membrane / metal ion binding
Similarity search - Function
CD209-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 ...CD209-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
CITRATE ANION / C-type lectin domain family 4 member E
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsFeinberg, H. / Jegouzo, S.A.F. / Rowntree, T.J.W. / Guan, Y. / Brash, M.A. / Taylor, M.E. / Weis, W.I. / Drickamer, K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Mechanism for Recognition of an Unusual Mycobacterial Glycolipid by the Macrophage Receptor Mincle.
Authors: Feinberg, H. / Jegouzo, S.A. / Rowntree, T.J. / Guan, Y. / Brash, M.A. / Taylor, M.E. / Weis, W.I. / Drickamer, K.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-TYPE LECTIN MINCLE
B: C-TYPE LECTIN MINCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8548
Polymers31,4812
Non-polymers3726
Water2,774154
1
A: C-TYPE LECTIN MINCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0335
Polymers15,7411
Non-polymers2924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C-TYPE LECTIN MINCLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8213
Polymers15,7411
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.29, 64.29, 127.16
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein C-TYPE LECTIN MINCLE


Mass: 15740.721 Da / Num. of mol.: 2
Fragment: CARBOHYDRATE RECOGNITION DOMAIN (UNP RESIDUES 79-208)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CLEC4E / Plasmid: pT5T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E1BHM0
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE SEQUENCE MATCHES NCBI SEQUENCE XM_592701.4, AND THE CONFLICT AT RESIDUE 174 ...AUTHORS STATE THAT THE SEQUENCE MATCHES NCBI SEQUENCE XM_592701.4, AND THE CONFLICT AT RESIDUE 174 IS A KNOWN POLYMORPHISM.

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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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein: 3.5 mg/ml mincle, 2.5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl. Reservoir: 20% polyethylene glycol 4,000, 20% 2-propanol and 0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, ...Details: Protein: 3.5 mg/ml mincle, 2.5 mM CaCl2, 10 mM Tris-Cl, pH 8.0, 25 mM NaCl. Reservoir: 20% polyethylene glycol 4,000, 20% 2-propanol and 0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.85→33.72 Å / Num. obs: 24890 / % possible obs: 98.2 % / Redundancy: 10.4 % / Rsym value: 0.038 / Net I/σ(I): 33.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.9510.60.421.93842836360.4297.8
1.95-2.0710.50.2273.43619934320.22798.3
2.07-2.2110.10.15453208831680.15496.8
2.21-2.3910.90.1017.63287730290.10198.8
2.39-2.6210.60.06212.32944627770.06299.1
2.62-2.9310.20.04516.62556124950.04597.5
2.93-3.3810.70.03219.92405022410.03299.6
3.38-4.149.80.028231819918550.02897.8
4.14-5.8510.20.02424.81508214790.02499.8
5.85-33.725100.01928.577667780.01995.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→33.72 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8395 / SU ML: 0.22 / σ(F): 0 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1245 5 %
Rwork0.179 --
obs0.182 24888 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.71 Å2 / Biso mean: 48.2 Å2 / Biso min: 21.02 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 18 154 2355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012307
X-RAY DIFFRACTIONf_angle_d1.0273090
X-RAY DIFFRACTIONf_chiral_restr0.074313
X-RAY DIFFRACTIONf_plane_restr0.005400
X-RAY DIFFRACTIONf_dihedral_angle_d12.931824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.92430.29231390.24392611275098
1.9243-2.01180.24251400.21012624276498
2.0118-2.11790.28421320.20252611274398
2.1179-2.25050.26771390.20492570270996
2.2505-2.42430.26891390.20222643278299
2.4243-2.66810.25641390.19692674281399
2.6681-3.0540.25441300.20852607273797
3.054-3.84680.21631430.167926762819100
3.8468-33.73020.18071440.14632627277197
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)
16.37782.81261.43593.9001-0.98512.0191-0.2904-0.78650.74941.4956-0.3119-1.8586-1.03620.40990.42830.5696-0.06-0.11040.4379-0.07840.51098.566558.124260.0939
25.9448-0.12-0.40439.18262.39080.6860.1373-0.5134-0.06170.7156-0.2471-0.2903-0.29140.00770.1280.41-0.0232-0.04650.2072-0.01740.16643.851747.969657.6166
36.7289-0.09435.28238.17721.58024.5044-0.4922-1.266-0.41060.20280.27850.2531-0.1636-0.08030.10240.39840.04780.0760.4530.09550.3084-2.265844.293564.0704
44.2161-3.86531.75055.6695-3.42532.2906-0.5312-1.13610.27140.9070.48060.1343-1.4016-0.1734-0.14290.48080.04760.0370.2464-0.09280.3003-3.579655.800160.5441
54.94660.9928-2.93845.9224.47766.27730.1444-0.28650.69620.2698-0.15210.2095-1.2620.2186-0.09970.5415-0.0464-0.05070.1484-0.05340.29520.139960.373149.8812
67.77430.7907-3.43694.5707-0.88247.60490.11980.1755-0.294-0.14960.0971.180.3637-0.7499-0.0860.28040.0055-0.0590.19980.04350.5036-8.017247.883553.275
76.7558-4.0904-4.0317.1961-0.71695.05560.1586-0.60840.25430.46260.01511.34460.3396-0.4822-0.12540.4490.07460.10840.3296-0.10570.7081-13.176756.652959.7038
81.9633-1.8596-3.15827.0330.01878.0619-0.01440.67860.369-0.7903-0.02071.3048-0.4865-0.9506-0.09880.36290.0757-0.28360.16360.08290.736-12.346454.997647.2404
98.17236.4009-0.95445.33030.93898.4269-0.24580.2229-0.50250.17970.64081.52750.5847-1.7131-0.16210.3816-0.1016-0.05630.40760.19360.9421-14.413243.515451.7609
108.21833.8577-3.33458.5212.15886.38150.15690.43260.7257-0.94910.14880.8082-0.1283-0.3596-0.28010.44110.0316-0.09430.19670.02170.323-4.772455.513942.7772
112.02173.734-0.07768.4137-2.32545.14350.16660.0398-0.9757-0.00060.27541.05680.4508-0.4043-0.43480.3531-0.0478-0.03910.2503-0.0440.4928-6.199843.070852.0159
128.67096.26436.77946.90095.69865.7045-0.0358-0.8140.4082-0.59810.0041-0.2479-0.93550.8871-0.01840.5807-0.1260.04120.5374-0.14940.33384.930858.143966.0672
136.521-5.97293.99477.0458-1.9774.2659-0.4307-0.55840.9489-0.1436-0.1198-1.65840.14451.4437-0.41810.3572-0.14940.31041.53720.17460.481520.782336.428462.1881
144.566-0.46451.41274.6396-1.61444.71360.00070.3418-0.3013-0.4320.1432-0.09030.15291.1456-0.13430.25240.0470.00820.4331-0.06110.219511.18830.115765.8825
153.7609-4.3042.37484.9301-2.83084.59170.7215-0.0231-2.4104-0.42980.3540.22942.0369-0.8838-0.87180.9505-0.0733-0.27920.37990.04260.84941.935714.991663.0844
162.8529-1.10653.47070.9127-0.66285.68410.98430.024-1.7813-0.21480.27880.23812.21250.451-0.41990.95860.3199-0.27480.4994-0.08320.74958.677416.596467.722
177.5635-0.83533.88094.9526-1.44738.00460.4218-0.3692-0.7167-0.14690.34060.47270.8495-0.4052-0.71030.26410.0482-0.02710.32640.08940.32496.111124.823472.6601
183.0341.2429-3.42450.5134-1.35493.7491-0.26191.9332-0.1796-1.0041-0.2196-0.498-0.17441.2920.24410.5656-0.07950.20981.39780.06640.325719.196832.61655.7807
191.99992.7562-2.84414.49541.51715.26921.845-1.9805-1.44921.145-0.3157-0.92141.1423-0.2594-1.25421.1584-0.7127-0.2490.9639-0.15590.5818-11.483341.967144.0049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 79:88 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 89:99 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 100:110 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 111:119 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 120:129 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 130:149 )A0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 150:159 )A0
8X-RAY DIFFRACTION8CHAIN A AND (RESID 160:169 )A0
9X-RAY DIFFRACTION9CHAIN A AND (RESID 170:181 )A0
10X-RAY DIFFRACTION10CHAIN A AND (RESID 182:190 )A0
11X-RAY DIFFRACTION11CHAIN A AND (RESID 191:202 )A0
12X-RAY DIFFRACTION12CHAIN A AND (RESID 203:211 )A0
13X-RAY DIFFRACTION13CHAIN B AND (RESID 79:88 )B0
14X-RAY DIFFRACTION14CHAIN B AND (RESID 89:139 )B0
15X-RAY DIFFRACTION15CHAIN B AND (RESID 140:149 )B0
16X-RAY DIFFRACTION16CHAIN B AND (RESID 150:176 )B0
17X-RAY DIFFRACTION17CHAIN B AND (RESID 177:202 )B0
18X-RAY DIFFRACTION18CHAIN B AND (RESID 203:211 )B0
19X-RAY DIFFRACTION19CHAIN A AND RESID 301A301

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