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- PDB-8d9z: Crystal structure of Cobra alpha-neurotoxin in complex with Centi... -

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Basic information

Entry
Database: PDB / ID: 8d9z
TitleCrystal structure of Cobra alpha-neurotoxin in complex with Centi-LNX-D09 antibody
Components
  • (Centi-LNX-D09 Fab ...) x 2
  • Long neurotoxin 1
KeywordsIMMUNE SYSTEM / ANTITOXIN/TOXIN / antivenom / 3-finger toxin / alpha-neurotoxin / long neurotoxin 1 / antibody / ANTITOXIN / ANTITOXIN-TOXIN complex
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Long neurotoxin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Naja nivea (cape cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPletnev, S. / Verardi, R. / Tully, E.S. / Glanville, J. / Kwong, P.D.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Venom protection by antibody from a snakebite hyperimmune subject
Authors: Glanville, J. / Andrade, J. / Bellin, M. / Kim, S. / Pletnev, S. / Tsao, D. / Verardi, R. / Bedi, R. / Friede, T. / Tully, E. / Zhang, B. / Bylund, T. / Liu, T. / Kwong, P.D.
History
DepositionJun 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 2.0Sep 4, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / entity / entity_src_gen / pdbx_contact_author / pdbx_database_related / pdbx_initial_refinement_model / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_seq_id / _atom_site.pdbx_PDB_ins_code ..._atom_site.auth_seq_id / _atom_site.pdbx_PDB_ins_code / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _refine.B_iso_max / _refine.B_iso_min / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_R_Cruickshank_DPI / _refine.pdbx_ls_sigma_F / _refine_hist.cycle_id / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.number_reflns_all / _software.classification / _software.name / _software.version / _struct.title / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.pdbx_beg_PDB_ins_code
Description: Sequence discrepancy / Details: The Fab chains were renumbered to Kabat system / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centi-LNX-D09 Fab light chain
B: Centi-LNX-D09 Fab heavy chain
D: Long neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,09814
Polymers57,1183
Non-polymers98011
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-35 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.285, 61.285, 260.046
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
11A-559-

HOH

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Components

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Protein , 1 types, 1 molecules D

#3: Protein Long neurotoxin 1 / Neurotoxin alpha


Mass: 8645.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja nivea (cape cobra) / Production host: Homo sapiens (human) / References: UniProt: P01390

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Antibody , 2 types, 2 molecules AB

#1: Antibody Centi-LNX-D09 Fab light chain


Mass: 23339.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Centi-LNX-D09 Fab heavy chain


Mass: 25132.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 362 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 200mM ammonium sulfate, 100mM sodium acetate pH 4.6, 19% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 53294 / % possible obs: 98.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.042 / Rrim(I) all: 0.125 / Χ2: 0.636 / Net I/σ(I): 4.8 / Num. measured all: 468793
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.867.61.05252300.7080.3981.1260.34799
1.86-1.949.20.80752370.8440.2770.8540.36899.4
1.94-2.039.60.5852990.9220.1940.6120.40799.6
2.03-2.139.30.42352700.950.1440.4470.46299.6
2.13-2.278.90.29853320.9650.1040.3160.52699.7
2.27-2.449.90.23753260.980.0780.250.57699.6
2.44-2.699.40.16753580.990.0570.1770.69999.8
2.69-3.088.40.11253770.9930.0410.120.91599.3
3.08-3.887.90.07653080.9960.0280.0811.08196.9
3.88-307.90.05855570.9970.0220.0621.0795.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model found by BALBES software using input sequence

Resolution: 1.8→29.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.739 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19811 973 1.8 %RANDOM
Rwork0.16464 ---
obs0.16525 52273 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.624 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å2-0 Å2
2---0.1 Å20 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 1.8→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 64 351 4261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134088
X-RAY DIFFRACTIONr_bond_other_d0.0030.0183700
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.6415557
X-RAY DIFFRACTIONr_angle_other_deg1.4351.5798590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3015527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90723.184179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74515639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1151516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02918
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_it2.3642.7682085
X-RAY DIFFRACTIONr_mcbond_other2.3652.7652083
X-RAY DIFFRACTIONr_mcangle_it3.3834.132619
X-RAY DIFFRACTIONr_mcangle_other3.3824.1322620
X-RAY DIFFRACTIONr_scbond_it3.9213.1262003
X-RAY DIFFRACTIONr_scbond_other3.923.1282004
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.584.5172939
X-RAY DIFFRACTIONr_long_range_B_refined7.0833.0044306
X-RAY DIFFRACTIONr_long_range_B_other6.92132.5134236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 86 -
Rwork0.283 3760 -
obs--98.87 %

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