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- PDB-3vpp: Crystal Structure of the Human CLEC9A C-type Lectin-Like Domain -

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Basic information

Entry
Database: PDB / ID: 3vpp
TitleCrystal Structure of the Human CLEC9A C-type Lectin-Like Domain
ComponentsC-type lectin domain family 9 member A
KeywordsIMMUNE SYSTEM / Dendritic Cell / C-Type Lectin-Like domain / Membrane
Function / homology
Function and homology information


positive regulation of cytokine production => GO:0001819 / receptor-mediated endocytosis / carbohydrate binding / membrane => GO:0016020 / cell surface
Similarity search - Function
C-type lectin domain family 9 member A / Natural killer cell receptor-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 domain family 9 member A / Natural killer cell receptor-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 9 member A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.642 Å
AuthorsCzabotar, P.E. / Zhang, J.G. / Policheni, A.N. / Shortman, K. / Lahoud, M.H. / Colman, P.M.
CitationJournal: Immunity / Year: 2012
Title: The dendritic cell receptor Clec9A binds damaged cells via exposed actin filaments.
Authors: Zhang, J.G. / Czabotar, P.E. / Policheni, A.N. / Caminschi, I. / Wan, S.S. / Kitsoulis, S. / Tullett, K.M. / Robin, A.Y. / Brammananth, R. / van Delft, M.F. / Lu, J. / O'Reilly, L.A. / ...Authors: Zhang, J.G. / Czabotar, P.E. / Policheni, A.N. / Caminschi, I. / Wan, S.S. / Kitsoulis, S. / Tullett, K.M. / Robin, A.Y. / Brammananth, R. / van Delft, M.F. / Lu, J. / O'Reilly, L.A. / Josefsson, E.C. / Kile, B.T. / Chin, W.J. / Mintern, J.D. / Olshina, M.A. / Wong, W. / Baum, J. / Wright, M.D. / Huang, D.C. / Mohandas, N. / Coppel, R.L. / Colman, P.M. / Nicola, N.A. / Shortman, K. / Lahoud, M.H.
History
DepositionMar 7, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Apr 16, 2014Group: Experimental preparation
Revision 1.3Apr 28, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_conn_angle ...entity_src_gen / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_struct_conn_angle.ptnr1_auth_asym_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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 9 member A
B: C-type lectin domain family 9 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2004
Polymers30,1192
Non-polymers802
Water5,585310
1
A: C-type lectin domain family 9 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1002
Polymers15,0601
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C-type lectin domain family 9 member A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1002
Polymers15,0601
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.170, 53.824, 57.446
Angle α, β, γ (deg.)90.00, 109.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C-type lectin domain family 9 member A


Mass: 15059.679 Da / Num. of mol.: 2 / Fragment: C-Type Lectin-Like Domain, UNP RESIDUES 110-241 / Mutation: S225D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC9A, UNQ9341/PRO34046 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q6UXN8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 8000, 0.2M MgCl2, 0.1M Tris pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.64→20 Å / Num. all: 58250 / Num. obs: 56639 / % possible obs: 97.2 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 3.81 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.33
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.64-1.743.650.7652.18762193.5
1.74-1.863.840.4773.468541196.7
1.86-2.013.850.2755.617978197.3
2.01-2.23.850.1737.847369198
2.2-2.453.860.1239.976698197.8
2.45-2.833.840.09811.725960198.9
2.83-3.443.810.07914.745072199.1
3.44-4.83.740.06917.483962199.2
4.8-203.860.06717.842297198.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1FM5

1fm5


Resolution: 1.642→19.894 Å / SU ML: 0.21 / σ(F): 1.24 / Phase error: 23.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2843 5.02 %Random
Rwork0.1889 ---
all0.1908 59476 --
obs0.1908 56633 97.39 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.24 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.6189 Å2-0 Å2-5.6379 Å2
2---0.6171 Å20 Å2
3----5.0017 Å2
Refinement stepCycle: LAST / Resolution: 1.642→19.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 2 310 2272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072046
X-RAY DIFFRACTIONf_angle_d1.1222775
X-RAY DIFFRACTIONf_dihedral_angle_d13.523735
X-RAY DIFFRACTIONf_chiral_restr0.074283
X-RAY DIFFRACTIONf_plane_restr0.006350
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6423-1.67060.32641290.3144244688
1.6706-1.7010.33481410.3025263696
1.701-1.73370.3411400.2774269596
1.7337-1.7690.26651400.2428262897
1.769-1.80750.25251400.2179268397
1.8075-1.84950.2531400.207267797
1.8495-1.89570.23181430.195268598
1.8957-1.94690.24971410.1878266197
1.9469-2.00420.22331440.1744271197
2.0042-2.06880.2491410.187267097
2.0688-2.14260.23381430.1935272798
2.1426-2.22830.24981390.1746271598
2.2283-2.32960.21641410.1763269098
2.3296-2.45220.21291470.1819273398
2.4522-2.60550.22651420.1824272199
2.6055-2.80620.23821470.1884276099
2.8062-3.08770.19241450.1831270699
3.0877-3.53230.20191460.1655274599
3.5323-4.44210.19871480.15022749100
4.4421-19.89520.21271460.2042752100
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)
13.0010.9610.73072.06040.38061.28310.0178-0.0958-0.14790.10880.00430.22380.2835-0.4143-0.01590.1723-0.06660.03010.199-0.00490.1065-10.11266.40846.4593
22.36180.55560.96091.80080.02412.33220.16860.0106-0.24240.23940.0546-0.1090.4140.0707-0.18210.1670.0208-0.02390.0762-0.00930.1288-0.38973.64943.4783
32.9671-0.3854-0.35392.53251.47366.3656-0.0193-0.23310.51680.04230.0173-0.0099-0.25-0.27350.07610.10680.0062-0.00150.1664-0.00670.2106-13.509712.1992-4.3643
42.6717-0.97440.23943.80540.64522.0490.0394-0.03840.1336-0.0384-0.12750.0445-0.225-0.09890.00210.08290.0052-0.00920.0525-0.01590.0707-2.000714.8753-0.131
51.46420.3019-0.5610.1005-0.08490.23880.19380.4644-0.0195-0.11760.1685-0.50070.10360.5148-0.07470.1010.01990.05370.2749-0.05610.21877.56464.5071-11.3019
62.3377-0.6941.63232.4702-0.00663.071-0.04080.18590.10910.20340.0138-0.422-0.03960.1857-0.04880.09270.0075-0.02080.0794-0.00380.09721.09166.2644-10.5168
71.014-0.0058-0.04291.51970.24131.80760.05290.01210.0032-0.03770.0267-0.0430.09940.0743-0.04630.1031-0.0069-0.00080.0932-0.01760.0831-0.731711.397-0.2205
81.6785-0.1042-0.29760.83370.79422.9218-0.0891-0.13550.1874-0.208-0.13580.1804-0.5881-0.82380.11280.09780.1109-0.03410.2436-0.0660.152-23.2739-6.3141-24.3192
93.3287-2.93660.46375.08720.45372.4691-0.13180.24020.314-0.82370.07570.0407-0.6612-0.0751-0.00120.2632-0.0013-0.03080.11660.01930.1217-14.8371-3.8875-34.1382
100.59580.06311.3220.6676-1.08425.195-0.19740.01210.23360.165-0.1380.0267-0.66950.25170.07560.0970.00940.00230.1035-0.00360.1305-13.546-2.8623-22.0514
115.59651.79822.70173.44981.11634.3126-0.0676-0.1428-0.34230.11340.0158-0.03640.2663-0.66080.1380.1359-0.02260.05030.17260.0160.1171-17.7536-11.9101-14.2352
123.02341.4149-0.49844.8849-0.44832.76780.0746-0.1771-0.3460.1267-0.1029-0.04830.3312-0.3667-0.03230.0984-0.0329-0.00170.0966-0.00080.109-15.8479-16.8414-25.4358
130.5264-0.1653-0.43330.10140.10960.3608-0.06560.20830.2408-0.2471-0.0275-1.0358-0.38821.12510.07480.1264-0.09910.0680.37930.03380.35572.4656-4.2774-27.3636
141.1178-2.1914-0.16445.16950.26795.4035-0.14470.0554-0.01510.0491-0.0229-0.17-0.46110.32090.0850.0753-0.01530.00320.08160.00310.1334-3.5478-1.7029-23.0056
151.0571-0.1713-0.74732.03710.22368.94190.06770.3096-0.3184-0.39920.1484-0.20290.24290.3283-0.08460.16680.00240.0010.1902-0.04390.1291-1.2816-9.9527-20.822
161.6890.160.72781.58290.2321.6898-0.0241-0.0344-0.10160.03470.0182-0.0814-0.0752-0.0301-0.01480.06110.00450.0060.0805-0.01230.0764-11.9105-11.1972-26.4237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 111:133)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 134:153)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 154:166)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 167:179)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 180:188)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 189:209)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 210:237)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 111:133)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 134:144)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 145:153)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 154:166)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 167:176)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 177:184)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 185:193)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 194:209)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 210:237)

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