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- PDB-4r9t: L-ficolin complexed to sulphates -

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Basic information

Entry
Database: PDB / ID: 4r9t
TitleL-ficolin complexed to sulphates
ComponentsFicolin-2
KeywordsSUGAR BINDING PROTEIN / FIBRINOGEN-LIKE domain / INNATE IMMUNITY / PATTERN RECOGNITION PROTEIN / LECTIN / IMMUNOLOGY / LECTIN-LIKE / plasma / extracellular
Function / homology
Function and homology information


mannan binding / recognition of apoptotic cell / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / opsonization / complement activation, lectin pathway / carbohydrate derivative binding / collagen trimer ...mannan binding / recognition of apoptotic cell / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / opsonization / complement activation, lectin pathway / carbohydrate derivative binding / collagen trimer / serine-type endopeptidase complex / proteoglycan binding / Initial triggering of complement / antigen binding / calcium-dependent protein binding / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / blood microparticle / defense response to Gram-positive bacterium / external side of plasma membrane / signaling receptor binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Ficolin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLaffly, E. / Lacroix, M. / Martin, L. / Vassal-Stermann, E. / Thielens, N. / Gaboriaud, C.
CitationJournal: Febs Lett. / Year: 2014
Title: Human ficolin-2 recognition versatility extended: An update on the binding of ficolin-2 to sulfated/phosphated carbohydrates.
Authors: Laffly, E. / Lacroix, M. / Martin, L. / Vassal-Stermann, E. / Thielens, N.M. / Gaboriaud, C.
History
DepositionSep 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ficolin-2
A: Ficolin-2
C: Ficolin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,22313
Polymers74,1763
Non-polymers1,04710
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ficolin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8623
Polymers24,7251
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Ficolin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4416
Polymers24,7251
Non-polymers7165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Ficolin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9214
Polymers24,7251
Non-polymers1953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.110, 96.110, 141.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13A
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B72 - 287
2010A72 - 287
1020B75 - 287
2020C75 - 287
1030A75 - 287
2030C75 - 287

NCS ensembles :
ID
1
2
3

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Components

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Protein / Sugars , 2 types, 4 molecules BAC

#1: Protein Ficolin-2 / 37 kDa elastin-binding protein / Collagen/fibrinogen domain-containing protein 2 / EBP-37 / Ficolin- ...37 kDa elastin-binding protein / Collagen/fibrinogen domain-containing protein 2 / EBP-37 / Ficolin-B / Ficolin-beta / Hucolin / L-ficolin / Serum lectin p35


Mass: 24725.373 Da / Num. of mol.: 3 / Fragment: SUGAR BINDING DOMAIN (UNP RESIDUES 97-313)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCN2, FCNL / Production host: unidentified Baculovirus / References: UniProt: Q15485
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 70 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein solution: 5.7 mg/ml in 145 mM NaCl, 50 mM triethanolamine-HCl, pH 7.4. Reservoir solution composed of 15% (w/v) PEG 8000, 200 mM Ca acetate and 0.1 M HEPES. Ligand soaking. ...Details: Protein solution: 5.7 mg/ml in 145 mM NaCl, 50 mM triethanolamine-HCl, pH 7.4. Reservoir solution composed of 15% (w/v) PEG 8000, 200 mM Ca acetate and 0.1 M HEPES. Ligand soaking. Cryoprotection was achieved by adding PEG 400 to the drop just before flash-cooling the crystal in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.25→48.05 Å / Num. all: 36420 / Num. obs: 36406 / % possible obs: 99.96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.25-2.31100
2.3-2.351100
2.35-2.41100
2.4-2.51100
2.5-31100
3-3.51100
3.5-41100
4-61100
6-101100
10-20197

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.05 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 11.069 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21782 1821 5 %RANDOM
Rwork0.18787 ---
obs0.18939 34600 99.96 %-
all-36423 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.719 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.03 Å20 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5195 0 59 61 5315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195425
X-RAY DIFFRACTIONr_bond_other_d0.0070.024767
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.9217345
X-RAY DIFFRACTIONr_angle_other_deg1.3063.00310886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97623.759290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48915822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.121535
X-RAY DIFFRACTIONr_chiral_restr0.1170.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026332
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021439
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8092.3952612
X-RAY DIFFRACTIONr_mcbond_other2.7852.3932608
X-RAY DIFFRACTIONr_mcangle_it4.3573.5683245
X-RAY DIFFRACTIONr_mcangle_other4.253.7243246
X-RAY DIFFRACTIONr_scbond_it3.4172.7112813
X-RAY DIFFRACTIONr_scbond_other3.4212.8312789
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4444.1174060
X-RAY DIFFRACTIONr_long_range_B_refined7.7520.2826052
X-RAY DIFFRACTIONr_long_range_B_other7.75320.2796044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B118730.12
12A118730.12
21B122210.09
22C122210.09
31A120250.11
32C120250.11
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 133 -
Rwork0.223 2528 -
obs--100 %
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)
10.28150.16970.07030.67040.03030.49040.03010.0005-0.0612-0.00240.0812-0.06180.1485-0.0034-0.11130.1705-0.0662-0.04630.17780.0230.0383-39.86321.166-17.924
20.7539-2.3236-1.09959.66593.07661.66170.07320.25530.11090.3802-0.0739-1.0351-0.0834-0.43020.00070.2580.0384-0.12980.3308-0.11150.2351-49.84116.126-17.469
30.2693-0.0168-0.08940.7413-0.69531.17330.00450.0682-0.0011-0.11090.09110.20790.0979-0.0781-0.09560.1643-0.0253-0.00620.13860.01430.0869-40.16110.69-14.339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B71 - 288
2X-RAY DIFFRACTION1B301 - 306
3X-RAY DIFFRACTION2A72 - 288
4X-RAY DIFFRACTION2A302
5X-RAY DIFFRACTION3C75 - 288
6X-RAY DIFFRACTION3C301 - 303

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