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- PDB-4r9j: L-ficolin complexed to glucosamine-6-sulfate -

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Basic information

Entry
Database: PDB / ID: 4r9j
TitleL-ficolin complexed to glucosamine-6-sulfate
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 ...: / 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
2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose / ACETATE ION / Ficolin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 5, 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: Atomic model / Data collection ...Atomic model / Data collection / 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_struct_special_symmetry / struct_asym / struct_conn / struct_site / 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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _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 / _pdbx_struct_special_symmetry.label_asym_id / _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
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
G: Ficolin-2
A: Ficolin-2
B: Ficolin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,08920
Polymers73,8343
Non-polymers2,25517
Water4,216234
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)25,2907
Polymers24,6111
Non-polymers6796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Ficolin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2886
Polymers24,6111
Non-polymers6775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: Ficolin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5117
Polymers24,6111
Non-polymers9006
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.170, 97.170, 139.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11G-486-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21A
12G
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010G72 - 288
2010A72 - 288
1020G72 - 288
2020B72 - 288
1030A72 - 288
2030B72 - 288

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules GAB

#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: 24611.273 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

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Sugars , 3 types, 5 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-3LJ / 2-amino-2-deoxy-6-O-sulfo-alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 259.234 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO8S
IdentifierTypeProgram
DGlcpN[6S]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
6-sulfo-a-D-glucopyranose-osamineCOMMON NAMEGMML 1.0
a-D-GlcpN6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 246 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7
Details: Protien 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. Cryoprotection was ...Details: Protien 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. Cryoprotection was achieved by adding PEG 400 to the drop just before flash-cooling the crystal in liquid nitrogen, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 45239 / Num. obs: 45165 / % possible obs: 99.83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.1-2.151100
2.15-2.211100
2.21-2.281100
2.28-2.351100
2.35-2.421100
2.42-2.511100
2.51-2.61100
2.6-2.711100
2.71-2.831100
2.83-2.971100
2.97-3.131100
3.13-3.321100
3.32-3.551100
3.55-3.831100
3.83-4.2199.9
4.2-4.71100
4.7-5.421100
5.42-6.641100
6.64-9.41100
9.4-20187.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.96 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.154 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20336 2259 5 %RANDOM
Rwork0.17238 ---
obs0.17394 42907 99.83 %-
all-42907 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.116 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.02 Å20 Å2
2---0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5205 0 138 234 5577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195598
X-RAY DIFFRACTIONr_bond_other_d0.0090.024922
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.9357589
X-RAY DIFFRACTIONr_angle_other_deg1.5353.00311243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.055666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.59623.686293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47215842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.561537
X-RAY DIFFRACTIONr_chiral_restr0.2010.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026491
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021468
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_it1.7561.5872669
X-RAY DIFFRACTIONr_mcbond_other1.7461.5852664
X-RAY DIFFRACTIONr_mcangle_it2.6712.3583318
X-RAY DIFFRACTIONr_mcangle_other3.0592.8523319
X-RAY DIFFRACTIONr_scbond_it2.2821.8452929
X-RAY DIFFRACTIONr_scbond_other2.6012.1892920
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9563.2024250
X-RAY DIFFRACTIONr_long_range_B_refined5.10415.5476338
X-RAY DIFFRACTIONr_long_range_B_other5.08515.5056264
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)
11G123080.12
12A123080.12
21G124290.11
22B124290.11
31A127100.1
32B127100.1
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 164 -
Rwork0.187 3119 -
obs--99.94 %
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)
10.2240.109-0.10430.3607-0.16250.3819-0.0004-0.02640.02370.06060.02490.0741-0.0209-0.0466-0.02450.03530.02060.00130.02980.00090.028656.72-10.985-9.141
21.37810.0451-0.01160.3384-0.1560.3187-0.0144-0.0879-0.20370.01050.043-0.01280.02330.0383-0.02860.02470.01880.00360.03030.00680.036146.948-16.534-5.933
30.1901-0.2253-0.00160.60260.01210.23730.03230.02110.0487-0.00950.013-0.0268-0.07170.0305-0.04530.04160.00960.02790.03220.01570.033956.986-21.605-5.646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A72 - 288
2X-RAY DIFFRACTION1A301 - 306
3X-RAY DIFFRACTION2B72 - 288
4X-RAY DIFFRACTION2B301 - 305
5X-RAY DIFFRACTION3G72 - 288
6X-RAY DIFFRACTION3G301 - 308

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