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- PDB-2j0h: L-ficolin complexed to acetyl-choline -

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Basic information

Entry
Database: PDB / ID: 2j0h
TitleL-ficolin complexed to acetyl-choline
ComponentsFICOLIN-2
KeywordsLECTIN / GLYCOPROTEIN / FICRINOGEN-LIKE / INNATE IMMUNITY / PATTERN RECOGNITION PROTEIN / COLLAGEN / IMMUNOLOGY / LECTIN- LIKE
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
ACETYLCHOLINE / Ficolin-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGarlatti, V. / Gaboriaud, C.
CitationJournal: Embo J. / Year: 2007
Title: Structural Insights Into the Innate Immune Recognition Specificities of L- and H-Ficolins.
Authors: Garlatti, V. / Belloy, N. / Martin, L. / Lacroix, M. / Matsushita, M. / Endo, Y. / Fujita, T. / Fontecilla-Camps, J.C. / Arlaud, G.J. / Thielens, N.M. / Gaboriaud, C.
History
DepositionAug 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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.occupancy / _atom_site.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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FICOLIN-2
B: FICOLIN-2
C: FICOLIN-2
D: FICOLIN-2
E: FICOLIN-2
F: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,35819
Polymers148,3766
Non-polymers1,98213
Water1,62190
1
A: FICOLIN-2
B: FICOLIN-2
C: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,33310
Polymers74,1883
Non-polymers1,1457
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: FICOLIN-2
E: FICOLIN-2
F: FICOLIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0259
Polymers74,1883
Non-polymers8376
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.060, 97.060, 140.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12C
22B
32E
42F

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRLEULEUAA79 - 849 - 14
211THRTHRLEULEUBB79 - 849 - 14
311THRTHRLEULEUCC79 - 849 - 14
411THRTHRLEULEUDD79 - 849 - 14
511THRTHRLEULEUEE79 - 849 - 14
611THRTHRLEULEUFF79 - 849 - 14
121GLYGLYILEILEAA87 - 9617 - 26
221GLYGLYILEILEBB87 - 9617 - 26
321GLYGLYILEILECC87 - 9617 - 26
421GLYGLYILEILEDD87 - 9617 - 26
521GLYGLYILEILEEE87 - 9617 - 26
621GLYGLYILEILEFF87 - 9617 - 26
131VALVALGLNGLNAA106 - 12136 - 51
231VALVALGLNGLNBB106 - 12136 - 51
331VALVALGLNGLNCC106 - 12136 - 51
431VALVALGLNGLNDD106 - 12136 - 51
531VALVALGLNGLNEE106 - 12136 - 51
631VALVALGLNGLNFF106 - 12136 - 51
141ARGARGALAALAAA123 - 15753 - 87
241ARGARGALAALABB123 - 15753 - 87
341ARGARGALAALACC123 - 15753 - 87
441ARGARGALAALADD123 - 15753 - 87
541ARGARGALAALAEE123 - 15753 - 87
641ARGARGALAALAFF123 - 15753 - 87
151SERSERALAALAAA184 - 191114 - 121
251SERSERALAALABB184 - 191114 - 121
351SERSERALAALACC184 - 191114 - 121
451SERSERALAALADD184 - 191114 - 121
551SERSERALAALAEE184 - 191114 - 121
651SERSERALAALAFF184 - 191114 - 121
161SERSERGLYGLYAA248 - 271178 - 201
261SERSERGLYGLYBB248 - 271178 - 201
361SERSERGLYGLYCC248 - 271178 - 201
461SERSERGLYGLYDD248 - 271178 - 201
561SERSERGLYGLYEE248 - 271178 - 201
661SERSERGLYGLYFF248 - 271178 - 201
171GLYGLYARGARGAA273 - 286203 - 216
271GLYGLYARGARGBB273 - 286203 - 216
371GLYGLYARGARGCC273 - 286203 - 216
471GLYGLYARGARGDD273 - 286203 - 216
571GLYGLYARGARGEE273 - 286203 - 216
671GLYGLYARGARGFF273 - 286203 - 216
112ASPASPASNASNCC224 - 231154 - 161
212ASPASPASNASNBB224 - 231154 - 161
312ASPASPASNASNEE224 - 231154 - 161
412ASPASPASNASNFF224 - 231154 - 161

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
FICOLIN-2 / COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2 / FICOLIN-B / FICOLIN B / SERUM LECTIN P35 / EBP-37 ...COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2 / FICOLIN-B / FICOLIN B / SERUM LECTIN P35 / EBP-37 / HUCOLIN / L-FICOLIN


Mass: 24729.318 Da / Num. of mol.: 6 / Fragment: C-TERMINAL BINDING DOMAIN, RESIDUES 96-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLASMA / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q15485

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Sugars , 2 types, 2 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
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / 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 , 3 types, 101 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-ACH / ACETYLCHOLINE


Mass: 146.207 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C7H16NO2 / Comment: neurotransmitter*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.57 Å3/Da / Density % sol: 51.74 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97951
DetectorDate: Sep 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.85→19.96 Å / Num. obs: 32678 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JC9

1jc9


Resolution: 2.85→15 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.855 / SU B: 17.639 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1655 5 %RANDOM
Rwork0.21 ---
obs0.213 31443 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20.56 Å20 Å2
2--1.12 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10343 0 123 90 10556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02110735
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.92114555
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63451291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86123.682573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.221151612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9721569
X-RAY DIFFRACTIONr_chiral_restr0.0990.21452
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028511
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.35271
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3360.57046
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.5801
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.342
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2980.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.90226450
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.524310088
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.10934970
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.66444467
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A452tight positional00.05
12B452tight positional00.05
13C452tight positional00.05
14D452tight positional00.05
15E452tight positional00.05
16F452tight positional00.05
21C32tight positional0.010.05
22B32tight positional0.010.05
23E32tight positional0.020.05
24F32tight positional0.010.05
11A433medium positional0.130.5
12B433medium positional0.120.5
13C433medium positional0.10.5
14D433medium positional0.140.5
15E433medium positional0.120.5
16F433medium positional0.110.5
21C27medium positional0.130.5
22B27medium positional0.090.5
23E27medium positional0.140.5
24F27medium positional0.120.5
11A452tight thermal0.010.5
12B452tight thermal0.010.5
13C452tight thermal00.5
14D452tight thermal0.010.5
15E452tight thermal0.010.5
16F452tight thermal00.5
21C32tight thermal0.010.5
22B32tight thermal0.010.5
23E32tight thermal0.010.5
24F32tight thermal0.010.5
11A433medium thermal0.082
12B433medium thermal0.062
13C433medium thermal0.062
14D433medium thermal0.072
15E433medium thermal0.062
16F433medium thermal0.062
21C27medium thermal0.072
22B27medium thermal0.072
23E27medium thermal0.062
24F27medium thermal0.062
LS refinement shellResolution: 2.85→2.95 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.392 128
Rwork0.306 2428

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