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- PDB-4yli: CL-K1 trimer -

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Basic information

Entry
Database: PDB / ID: 4yli
TitleCL-K1 trimer
ComponentsCollectin-11
KeywordsSUGAR BINDING PROTEIN / C-type carbohydrate-recognition domain / collectin / C-type lectin
Function / homology
Function and homology information


calcium-dependent carbohydrate binding / Lectin pathway of complement activation / fucose binding / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / oligosaccharide binding / developmental process / collagen trimer / antimicrobial humoral response ...calcium-dependent carbohydrate binding / Lectin pathway of complement activation / fucose binding / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / oligosaccharide binding / developmental process / collagen trimer / antimicrobial humoral response / serine-type endopeptidase complex / complement activation / Scavenging by Class A Receptors / execution phase of apoptosis / Initial triggering of complement / D-mannose binding / external side of plasma membrane / calcium ion binding / proteolysis / DNA binding / extracellular space / extracellular region / identical protein binding
Similarity search - Function
: / Collectin, C-type lectin-like domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 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. ...: / Collectin, C-type lectin-like domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsWallis, R. / Girija, U.V. / Gingras, A.R. / Moody, P.C.E. / Marshall, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1000191/1 United Kingdom
CitationJournal: Bmc Biol. / Year: 2015
Title: Molecular basis of sugar recognition by collectin-K1 and the effects of mutations associated with 3MC syndrome.
Authors: Girija, U.V. / Furze, C.M. / Gingras, A.R. / Yoshizaki, T. / Ohtani, K. / Marshall, J.E. / Wallis, A.K. / Schwaeble, W.J. / El-Mezgueldi, M. / Mitchell, D.A. / Moody, P.C. / Wakamiya, N. / Wallis, R.
History
DepositionMar 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: 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
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_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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collectin-11
B: Collectin-11
C: Collectin-11
D: Collectin-11
E: Collectin-11
F: Collectin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,83538
Polymers103,8816
Non-polymers1,95432
Water88349
1
A: Collectin-11
B: Collectin-11
C: Collectin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,98120
Polymers51,9403
Non-polymers1,04117
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-155 kcal/mol
Surface area23510 Å2
MethodPISA
2
D: Collectin-11
E: Collectin-11
F: Collectin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,85418
Polymers51,9403
Non-polymers91315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-138 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.990, 107.590, 77.820
Angle α, β, γ (deg.)90.000, 91.490, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA116 - 306
211chain BB116 - 306
311chain CC117 - 306
411chain DD116 - 306
511chain EE122 - 306
611chain FF116 - 306

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Components

#1: Protein
Collectin-11 / Collectin kidney protein 1 / CL-K1


Mass: 17313.422 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COLEC11, UNQ596/PRO1182 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BWP8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES pH 7.0 10% v/v ethanol and 4 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.45→48.21 Å / Num. obs: 42224 / % possible obs: 95.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 10.09
Reflection shellResolution: 2.45→2.538 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.03 / Num. unique all: 3791 / % possible all: 87.15

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B08

1b08


Resolution: 2.45→48.208 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 2140 5.07 %
Rwork0.1869 40051 -
obs0.1887 42191 95.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.23 Å2 / Biso mean: 74.4579 Å2 / Biso min: 33.18 Å2
Refinement stepCycle: final / Resolution: 2.45→48.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7162 0 105 49 7316
Biso mean--76.41 60.68 -
Num. residues----919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037379
X-RAY DIFFRACTIONf_angle_d0.6169876
X-RAY DIFFRACTIONf_chiral_restr0.0251032
X-RAY DIFFRACTIONf_plane_restr0.0021297
X-RAY DIFFRACTIONf_dihedral_angle_d10.9912741
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4352X-RAY DIFFRACTION6.974TORSIONAL
12B4352X-RAY DIFFRACTION6.974TORSIONAL
13C4352X-RAY DIFFRACTION6.974TORSIONAL
14D4352X-RAY DIFFRACTION6.974TORSIONAL
15E4352X-RAY DIFFRACTION6.974TORSIONAL
16F4352X-RAY DIFFRACTION6.974TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.5070.3361320.28312336246884
2.507-2.56970.33281450.27092650279596
2.5697-2.63920.32711440.26032739288398
2.6392-2.71680.31641460.25342753289998
2.7168-2.80450.32591110.23372746285798
2.8045-2.90470.3021510.23162711286298
2.9047-3.0210.26241490.23222746289598
3.021-3.15850.27291290.2352757288698
3.1585-3.3250.27971520.22812703285597
3.325-3.53320.23891330.21792616274993
3.5332-3.80590.24311320.18572464259688
3.8059-4.18870.21121610.1722741290298
4.1887-4.79440.1741640.14352755291999
4.7944-6.03850.19451560.1632709286596
6.0385-48.21690.14821350.14422625276092
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)
17.04297.13065.32339.06077.15625.1437-0.32880.37771.2574-0.8886-0.04991.1672-1.18870.06140.38220.8585-0.1021-0.1020.637-0.19641.133241.9216-8.969212.0892
25.8219-1.28370.59855.8336-3.74334.8753-0.4978-0.61050.68840.866-0.08551.188-0.4601-0.04760.47610.6215-0.15390.12430.5712-0.2460.641634.3488-34.789515.353
34.93223.7886-2.46178.8121-2.85962.61340.5258-0.67390.46510.9419-0.30510.3065-0.41570.202-0.21930.7021-0.26970.17790.6884-0.24060.62931.7907-46.333121.2437
46.98595.34794.19933.88462.90413.0879-0.0503-0.33120.50310.9331-0.20360.40020.09360.0490.16390.7201-0.1738-0.0310.608-0.15510.691446.827-16.162519.0946
56.026-1.3494-2.0264.6784-0.00328.7385-0.06090.24620.06760.2978-0.50230.01240.13650.07370.46530.3752-0.09740.02870.4735-0.15590.492745.6967-33.5758-1.4154
64.216-0.3107-0.51236.78873.42924.24880.07950.10760.0821-0.1485-0.49660.0413-0.06120.02960.42480.3451-0.00080.01260.4437-0.00470.354649.6796-39.9404-11.9495
78.51917.79625.26768.51447.03628.4876-0.17210.0390.5334-0.91640.3322-0.2401-0.79830.95070.07240.8192-0.1318-0.05070.7446-0.21020.810250.8066-12.96358.2646
89.2094-2.18875.23381.0053-0.55047.3664-0.2127-1.00551.06340.19530.09060.1085-0.4733-0.9190.09740.5829-0.0086-0.1010.6343-0.21830.845517.3138-21.373-1.9719
96.5623-5.24425.29455.5726-5.39994.3473-0.3729-0.7923-1.17340.07230.8923-0.18160.5995-1.3778-0.07460.84920.1857-0.02710.60020.13270.852211.4946-50.200347.4939
105.06013.11320.88822.2902-0.06994.12290.36910.22910.5762-0.31840.0531-0.18670.10620.4869-0.51070.48190.10110.13130.48150.10770.684813.4652-26.389534.7801
113.2423.1631-0.47128.4018-2.03815.42850.1559-0.05070.00950.2768-0.0942-0.2045-0.04570.3304-0.02720.49520.10340.15710.53490.1090.539817.8674-21.34833.3173
123.7271.9203-1.64248.7649-3.05533.27260.0604-0.0698-0.06710.3258-0.0418-0.0105-0.19290.53640.02110.49210.01480.1470.57370.08130.470320.2401-13.482828.7276
139.57291.38851.74981.97892.05492.44310.30950.0895-0.97921.19740.29710.61740.70150.6988-0.52760.90130.1846-0.01550.55010.00620.6547.9138-42.210253.2847
144.54850.32864.74415.61853.20837.1346-0.19490.2344-0.55030.44340.43190.09980.3055-0.6414-0.02040.5994-0.00980.01110.6120.08920.6294-2.3155-38.013533.4455
154.7408-0.49745.54976.53472.10797.34910.29210.0396-0.67040.0422-0.24340.54340.70040.3094-0.26230.5853-0.0257-0.08430.66120.10790.6276-4.8745-40.451527.6935
167.41031.58644.64237.0212.70715.22360.20630.8373-0.517-0.127-0.17230.49370.6373-0.1571-0.05180.5852-0.0481-0.09330.8258-0.02270.6586-9.7851-40.09619.4821
178.9491-8.03566.73016.923-6.56285.05230.5056-0.04310.4814-1.0785-0.6593-1.75920.83220.5920.48680.77260.18220.03660.69430.10560.889619.7861-42.430950.9337
185.235-3.0048-1.7087.49030.65584.2990.0811-0.04780.48820.0694-0.257-1.0610.61990.24520.10750.52250.11570.08140.44250.06490.3849-0.2558-25.057748.4291
197.6285-0.29760.41428.51082.85627.110.0384-0.11940.2841-0.4319-0.0039-0.8684-0.17770.0384-0.04180.34390.11270.05020.37460.05160.4382-5.345-22.241352.0722
203.3866-4.2825-0.69467.24292.3212.6854-0.1252-0.2190.29840.3140.05820.35290.2486-0.2938-0.14080.45140.08530.01940.44960.12660.4355-14.8987-18.44955.4074
214.6279-3.413-1.97915.17181.00745.76330.5216-0.10290.8649-0.325-0.1166-0.6363-0.2086-0.2791-0.38250.50810.08830.0920.45110.05950.547-11.4671-14.473152.8616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 116 through 141 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 162 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 269 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 116 through 142 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 143 through 162 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 163 through 269 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 117 through 141 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 142 through 269 )C0
9X-RAY DIFFRACTION9chain 'D' and (resid 116 through 141 )D0
10X-RAY DIFFRACTION10chain 'D' and (resid 142 through 162 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 163 through 195 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 196 through 270 )D0
13X-RAY DIFFRACTION13chain 'E' and (resid 122 through 141 )E0
14X-RAY DIFFRACTION14chain 'E' and (resid 142 through 162 )E0
15X-RAY DIFFRACTION15chain 'E' and (resid 163 through 196 )E0
16X-RAY DIFFRACTION16chain 'E' and (resid 197 through 270 )E0
17X-RAY DIFFRACTION17chain 'F' and (resid 116 through 141 )F0
18X-RAY DIFFRACTION18chain 'F' and (resid 142 through 162 )F0
19X-RAY DIFFRACTION19chain 'F' and (resid 163 through 196 )F0
20X-RAY DIFFRACTION20chain 'F' and (resid 197 through 222 )F0
21X-RAY DIFFRACTION21chain 'F' and (resid 223 through 269 )F0

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