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- PDB-4qww: Crystal structure of the Fab410-BfAChE complex -

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Basic information

Entry
Database: PDB / ID: 4qww
TitleCrystal structure of the Fab410-BfAChE complex
Components
  • (Fab410 antibody ...) x 2
  • Acetylcholinesterase
KeywordsHYDROLASE/IMMUNE SYSTEM / a/b hydrolase fold / acetylcholinesterase / monoclonal antibody / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


acetylcholine catabolic process in synaptic cleft / acetylcholinesterase / acetylcholinesterase activity / synaptic cleft / toxin activity / plasma membrane
Similarity search - Function
Acetylcholinesterase, fish/snake / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family ...Acetylcholinesterase, fish/snake / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Acetylcholinesterase
Similarity search - Component
Biological speciesBungarus fasciatus (banded krait)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBourne, Y. / Renault, L. / Marchot, P.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of Snake Venom Acetylcholinesterase in Complex with Inhibitory Antibody Fragment Fab410 Bound at the Peripheral Site: EVIDENCE FOR OPEN AND CLOSED STATES OF A BACK DOOR CHANNEL.
Authors: Bourne, Y. / Renault, L. / Marchot, P.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Jun 28, 2017Group: Database references / Category: struct_ref_seq
Item: _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.db_align_beg / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _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: Acetylcholinesterase
B: Acetylcholinesterase
C: Fab410 antibody light chain
D: Fab410 antibody heavy chain
E: Fab410 antibody light chain
F: Fab410 antibody heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,19313
Polymers217,9126
Non-polymers4,2817
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.592, 251.336, 73.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 60321.832 Da / Num. of mol.: 2 / Fragment: UNP residues 32-566 / Source method: isolated from a natural source / Source: (natural) Bungarus fasciatus (banded krait) / References: UniProt: Q92035, acetylcholinesterase

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Antibody , 2 types, 4 molecules CEDF

#2: Antibody Fab410 antibody light chain


Mass: 23286.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Fab410 antibody heavy chain


Mass: 25347.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Sugars , 3 types, 5 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


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 , 2 types, 230 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 3.34 Å3/Da / Density % sol: 63.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 7.0-12.5% PEG8000, 0.2 M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 4, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→78 Å / Num. obs: 81126 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 68.36 Å2 / Rsym value: 0.105 / Net I/σ(I): 10.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER2.11.5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1J06 & 1IQW

1j06

1iqw


Resolution: 2.7→39.53 Å / Cor.coef. Fo:Fc: 0.9339 / Cor.coef. Fo:Fc free: 0.9076 / SU R Cruickshank DPI: 0.481 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.467 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 4060 5.01 %RANDOM
Rwork0.1989 ---
obs0.2009 81030 99.9 %-
Displacement parametersBiso mean: 60.76 Å2
Baniso -1Baniso -2Baniso -3
1--12.5277 Å20 Å20 Å2
2--8.3565 Å20 Å2
3---4.1712 Å2
Refine analyzeLuzzati coordinate error obs: 0.446 Å
Refinement stepCycle: LAST / Resolution: 2.7→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14968 0 286 228 15482
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115762HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.221541HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5217SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes341HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2279HARMONIC5
X-RAY DIFFRACTIONt_it15762HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion19.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2073SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17497SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2899 279 4.79 %
Rwork0.2255 5549 -
all0.2284 5828 -
obs--99.9 %
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)
11.57121.0093-0.69912.1399-0.17542.1269-0.31730.36460.1847-0.54420.2270.11920.5442-0.41420.09030.304-0.152-0.0913-0.23860.0256-0.30415.5658-38.2139-41.6353
20.9917-0.3273-0.0642.8015-0.06582.093-0.2008-0.1359-0.1120.54420.09240.0926-0.4036-0.15730.10840.3040.02340.0302-0.3040.0043-0.30414.5199-76.55384.4392
30.783-0.28340.53142.0388-0.00041.80990.0321-0.0123-0.14010.1007-0.02910.52330.06040.0099-0.003-0.0589-0.01160.0472-0.1506-0.0510.075518.864-108.639-13.4954
42.0413-1.36440.65882.0604-0.24051.5476-0.13050.1648-0.3662-0.03540.01430.49210.0008-0.1780.1162-0.0716-0.06070.0328-0.1089-0.06640.175623.4936-138.82-27.8907
51.00680.4264-0.10212.1281-0.11452.1740.0651-0.10630.2040.01680.00560.5438-0.2219-0.1477-0.0707-0.15490.0421-0.0649-0.1465-0.04780.115219.5715-5.9225-23.8396
61.80940.601-0.1691.73540.70772.4134-0.2087-0.14460.3593-0.2294-0.09070.5442-0.4157-0.25720.29940.05660.152-0.152-0.2362-0.14540.069824.155223.753-9.0584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 535
2X-RAY DIFFRACTION2{ B|* }B4 - 535
3X-RAY DIFFRACTION3{ C|1 - C|109 D|1 - D|124 }C1 - 109
4X-RAY DIFFRACTION3{ C|1 - C|109 D|1 - D|124 }D1 - 124
5X-RAY DIFFRACTION4{ C|110 - C|212 D|125 - D|225 }C110 - 212
6X-RAY DIFFRACTION4{ C|110 - C|212 D|125 - D|225 }D125 - 225
7X-RAY DIFFRACTION5{ E|1 - E|109 F|1 - F|124 }E1 - 109
8X-RAY DIFFRACTION5{ E|1 - E|109 F|1 - F|124 }F1 - 124
9X-RAY DIFFRACTION6{ E|110 - E|211 F|125 - F|225 }E110 - 211
10X-RAY DIFFRACTION6{ E|110 - E|211 F|125 - F|225 }F125 - 225

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