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- PDB-2liq: Solution structure of CCL2 in complex with glycan -

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Basic information

Entry
Database: PDB / ID: 2liq
TitleSolution structure of CCL2 in complex with glycan
ComponentsCCL2 lectin
KeywordsSUGAR BINDING PROTEIN / carbohydrate recognition
Function / homology: / CCL2 lectin-like / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / carbohydrate binding / Mainly Beta / CCL2 lectin
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsSchubert, M. / Bleuler-Martinez, S. / Walti, M.A. / Egloff, P. / Aebi, M. / Kuenzler, M. / Allain, F.H.-T.
CitationJournal: Plos Pathog. / Year: 2012
Title: Plasticity of the beta-Trefoil Protein Fold in the Recognition and Control of Invertebrate Predators and Parasites by a Fungal Defence System
Authors: Schubert, M. / Bleuler-Martinez, S. / Butschi, A. / Walti, M.A. / Egloff, P. / Stutz, K. / Yan, S. / Wilson, I.B. / Hengartner, M.O. / Aebi, M. / Allain, F.H. / Kunzler, M.
History
DepositionAug 30, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: pdbx_database_related
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_nmr_software / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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 / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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
Revision 2.1Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.authors
Revision 2.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CCL2 lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1892
Polymers16,6041
Non-polymers5851
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein CCL2 lectin


Mass: 16604.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (fungus) / Gene: ccl2 / Production host: Escherichia coli (E. coli) / References: UniProt: B3GA02
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]methyl 2-acetamido-2- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 584.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAc[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_1*OC_2*NCC/3=O][a1221m-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 15N-HSQC
1312D NOESY
1413D 15N edited NOESY
1512D 15N F1-filtered,F2-filtered NOESY
1622D NOESY
1722D TOCSY
1822D 13C-HSQC (at natural abundance)
1922D 15N-HSQC (for H/D exchange)
11032D 13C-HSQC for aliphatic region
11132D 13C-HSQC for aromatic region
11233D 13Cedited-NOESY for aliphatic region
11332D 13Cedited NOESY for aromatic region
11433D HNCA
11533D HN(CA)CB
11633D HNCO
11742D 13C-HSQC for aliphatic region
11842D 13C-HSQC for aromatic region
11943D (H)CCH-COSY
12042D 13C F1-filtered TOCSY
12142D 13C F1-filtered NOESY
12242D 13C F1-filtered, F2-filtered NOESY
12343D 13C F1-edited, F3-filtered NOESY for aliphatic region
12443D 13C F1-edited, F3-filtered NOESY for aromatic region
12552D constant-time 13C-HSQC to unambiguously assign the stereochemical methyl groups of VAL and LEU

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 13C; U-100% 15N] CCL2, 1 mM SUGAR (3-MER), 50 mM potassium phosphate, 100 mM sodium chloride, ~41 mM [U-100% 2H] acetic acid, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution21 mM [U-100% 13C; U-100% 15N] CCL2, 1 mM SUGAR (3-MER), 50 mM potassium phosphate, 100 mM sodium chloride, ~41 mM [U-100% 2H] acetic acid, 100% D2Osample_2100% D2O
solution31 mM [U-100% 15N] CCL2, 1 mM SUGAR (3-MER), 50 mM potassium phosphate, 100 mM sodium chloride, ~41 mM [U-100% 2H] acetic acid, 90% H2O/10% D2Osample_390% H2O/10% D2O
solution41 mM [U-100% 15N] CCL2, 1 mM SUGAR (3-MER), 50 mM potassium phosphate, 100 mM sodium chloride, ~41 mM [U-100% 2H] acetic acid, 100% D2Osample_4100% D2O
solution51 mM [U-1% 13C; U-100% 15N] CCL2, 1 mM SUGAR (3-MER), 50 mM potassium phosphate, 100 mM sodium chloride, 41 mM [U-100% 2H] acetic acid 95%H2O/5% D2Osample_595% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCCL2-1[U-100% 13C; U-100% 15N]1
1 mMSUGAR (3-MER)-21
50 mMpotassium phosphate-31
100 mMsodium chloride-41
41 mMacetic acid-5[U-100% 2H]1
1 mMCCL2-6[U-100% 13C; U-100% 15N]2
1 mMSUGAR (3-MER)-72
50 mMpotassium phosphate-82
100 mMsodium chloride-92
41 mMacetic acid-10[U-100% 2H]2
1 mMCCL2-11[U-100% 15N]3
1 mMSUGAR (3-MER)-123
50 mMpotassium phosphate-133
100 mMsodium chloride-143
41 mMacetic acid-15[U-100% 2H]3
1 mMCCL2-16[U-100% 15N]4
1 mMSUGAR (3-MER)-174
50 mMpotassium phosphate-184
100 mMsodium chloride-194
41 mMacetic acid-20[U-100% 2H]4
1 mMCCL2[U-1% 13C; U-100% 15N]5
1 mMSUGAR (3-MER)natural abundance5
50 mMpotassium phosphatenatural abundance5
100 mMsodium chloridenatural abundance5
41 mMacetic acid[U-100% 2H]5
Sample conditionsIonic strength: 150 / pH: 4.7 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7503
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
CYANAHerrmann, Guntert and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 7
NMR constraintsNOE constraints total: 2054 / NOE intraresidue total count: 446 / NOE long range total count: 1119 / NOE sequential total count: 489 / Hydrogen bond constraints total count: 98 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 85 / Protein psi angle constraints total count: 91
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 300 / Conformers submitted total number: 20

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