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- PDB-8da1: Crystal structure of Krait alpha-neurotoxin in complex with Centi... -

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Basic information

Entry
Database: PDB / ID: 8da1
TitleCrystal structure of Krait alpha-neurotoxin in complex with Centi-LNX-D09 antibody
Components
  • Alpha-bungarotoxin
  • Centi-LNX-D09 Fab heavy chain
  • Centi-LNX-D09 Fab light chain
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 three-finger toxin / : / Snake toxin cobra-type / Snake toxin-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Bungarus multicinctus (many-banded krait)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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_mean / _refine.B_iso_min / _refine.ls_number_reflns_R_work / _refine_hist.cycle_id / _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 / _refine_ls_shell.pdbx_total_number_of_bins_used / _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 3.0Oct 9, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet_range
Item: _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_prop.value ..._entity.pdbx_number_of_molecules / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _software.version / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Sequence discrepancy / Details: The Fab chains were renumbered to Kabat system / Provider: author / Type: Coordinate replacement

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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
I: Alpha-bungarotoxin


Theoretical massNumber of molelcules
Total (without water)56,4783
Polymers56,4783
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-29 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.326, 63.862, 77.437
Angle α, β, γ (deg.)90.00, 101.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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)
#3: Protein Alpha-bungarotoxin / Alpha-Bgtx / Alpha-Btx / Alpha-bungarotoxin / isoform A31 / Alpha-BTX A31 / Alpha-BgTx(A31) / Alpha- ...Alpha-Bgtx / Alpha-Btx / Alpha-bungarotoxin / isoform A31 / Alpha-BTX A31 / Alpha-BgTx(A31) / Alpha-bungarotoxin (A31) / BGTX A31 / Alpha-elapitoxin-Bm2a / Alpha-EPTX-Bm2a / Long neurotoxin 1


Mass: 8005.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bungarus multicinctus (many-banded krait)
Production host: Homo sapiens (human) / References: UniProt: P60615
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 40% PEG 400, 5% PEG 3350, 0.1M sodium acetate pH 5.5

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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: 2.67→30 Å / Num. obs: 19031 / % possible obs: 98.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.103 / Rrim(I) all: 0.27 / Χ2: 1.88 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.84.21.60118460.3060.8391.8171.57797.3
2.8-2.915.11.41818700.4080.6821.5811.59297.7
2.91-3.046.41.09918930.5930.4611.1941.70298.4
3.04-3.27.50.83719080.8170.3260.8991.86699.7
3.2-3.47.90.58718960.90.2230.6291.95599.7
3.4-3.667.80.40119300.9410.1530.432.03999.7
3.66-4.037.50.29119060.9450.1150.3141.97999
4.03-4.616.60.18819010.9560.0820.2071.96998.2
4.61-5.87.40.1619260.9720.0660.1741.92498.6
5.8-306.80.15719550.9690.0690.1721.89898.2

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Processing

Software
NameVersionClassification
PHENIXdev_5245refinement
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: 2.67→29.51 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 1020 5.36 %
Rwork0.1957 --
obs0.1987 19015 93.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.67→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3879 0 0 3 3882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033971
X-RAY DIFFRACTIONf_angle_d0.6515399
X-RAY DIFFRACTIONf_dihedral_angle_d18.9361419
X-RAY DIFFRACTIONf_chiral_restr0.044604
X-RAY DIFFRACTIONf_plane_restr0.006697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.810.37351020.3241631X-RAY DIFFRACTION60
2.81-2.990.37631270.30362681X-RAY DIFFRACTION97
2.99-3.220.34581750.25222719X-RAY DIFFRACTION100
3.22-3.540.29631660.2262709X-RAY DIFFRACTION100
3.54-4.050.24721530.18792743X-RAY DIFFRACTION99
4.05-5.10.21721520.16442712X-RAY DIFFRACTION98
5.1-29.510.21751450.17522800X-RAY DIFFRACTION98

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