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- PDB-8d9y: Crystal structure of Taipan alpha-neurotoxin in complex with Cent... -

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Basic information

Entry
Database: PDB / ID: 8d9y
TitleCrystal structure of Taipan 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 three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake toxin-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-PG6 / Long neurotoxin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Oxyuranus scutellatus scutellatus (Australian taipan)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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_distant_solvent_atoms / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / 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: _entity.pdbx_description / _entity.pdbx_number_of_molecules ..._entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_PDB_ins_code / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.PDB_ins_code_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_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 / _refine_ls_shell.pdbx_total_number_of_bins_used / _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 / _struct_sheet_range.pdbx_end_PDB_ins_code
Description: Sequence discrepancy / Details: 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 / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / cell / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_oper / struct_sheet / struct_sheet_order / struct_sheet_range
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_seq_id / _atom_site.label_asym_id / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][3] / _cell.angle_beta / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _refine.pdbx_overall_phase_error / _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_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet.number_strands
Description: Sequence discrepancy / Details: 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
C: Centi-LNX-D09 Fab light chain
D: Centi-LNX-D09 Fab heavy chain
E: Centi-LNX-D09 Fab light chain
F: Centi-LNX-D09 Fab heavy chain
G: Centi-LNX-D09 Fab light chain
H: Centi-LNX-D09 Fab heavy chain
I: Long neurotoxin 1
J: Long neurotoxin 1
K: Long neurotoxin 1
L: Long neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,30616
Polymers225,51512
Non-polymers7914
Water17,204955
1
A: Centi-LNX-D09 Fab light chain
B: Centi-LNX-D09 Fab heavy chain
I: Long neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6174
Polymers56,3793
Non-polymers2381
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Centi-LNX-D09 Fab light chain
D: Centi-LNX-D09 Fab heavy chain
J: Long neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8395
Polymers56,3793
Non-polymers4612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Centi-LNX-D09 Fab light chain
F: Centi-LNX-D09 Fab heavy chain
K: Long neurotoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4714
Polymers56,3793
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Centi-LNX-D09 Fab light chain
H: Centi-LNX-D09 Fab heavy chain
L: Long neurotoxin 1


Theoretical massNumber of molelcules
Total (without water)56,3793
Polymers56,3793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.808, 87.228, 101.302
Angle α, β, γ (deg.)109.29, 104.25, 106.48
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules IJKL

#3: Protein
Long neurotoxin 1 / LNTX-1


Mass: 7906.118 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oxyuranus scutellatus scutellatus (Australian taipan)
Production host: Homo sapiens (human) / References: UniProt: A8HDK9

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Antibody , 2 types, 8 molecules ACEGBDFH

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


Mass: 23339.740 Da / Num. of mol.: 4
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.: 4
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 , 5 types, 959 molecules

#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 955 / 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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100mM Sodium Acetate pH 5.5, 14% PEG8000, 2.65% PEG 400, 500mM NaCl

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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: 2.2→30 Å / Num. obs: 99175 / % possible obs: 86.8 % / Redundancy: 2 % / Biso Wilson estimate: 35.97 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.065 / Rrim(I) all: 0.099 / Χ2: 0.738 / Net I/σ(I): 6.4 / Num. measured all: 200208
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.2820.486750.7620.3460.5310.44776.1
2.28-2.3720.31595980.8530.2760.420.46483.6
2.37-2.4820.26899510.8920.2370.3590.47987.6
2.48-2.6120.21798450.9210.1930.2910.52786.1
2.61-2.7720.16997930.9450.1520.2280.64285.8
2.77-2.992.10.126107010.9680.1130.170.7493.6
2.99-3.292.10.089105740.9810.0790.1190.88792.4
3.29-3.7620.065100590.9860.0580.0871.02388.3
3.76-4.7320.04599390.9930.0390.061.05287
4.73-3020.042100400.990.0370.0561.03187.7

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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: 2.2→29.54 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 1954 1.99 %RANDOM
Rwork0.2123 ---
obs0.2133 98261 86.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15145 0 52 955 16152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215544
X-RAY DIFFRACTIONf_angle_d0.55521102
X-RAY DIFFRACTIONf_dihedral_angle_d17.25586
X-RAY DIFFRACTIONf_chiral_restr0.0432350
X-RAY DIFFRACTIONf_plane_restr0.0052719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.34981240.32775935X-RAY DIFFRACTION75
2.26-2.320.28681330.29586340X-RAY DIFFRACTION80
2.32-2.380.34431420.28526686X-RAY DIFFRACTION85
2.38-2.460.30391490.28226958X-RAY DIFFRACTION87
2.46-2.550.31541360.27246923X-RAY DIFFRACTION87
2.55-2.650.35521360.25876431X-RAY DIFFRACTION81
2.65-2.770.31191420.24837162X-RAY DIFFRACTION90
2.77-2.920.29281450.23277453X-RAY DIFFRACTION94
2.92-3.10.33171380.23297398X-RAY DIFFRACTION93
3.1-3.340.25831750.22037217X-RAY DIFFRACTION92
3.34-3.670.25911340.19947026X-RAY DIFFRACTION88
3.67-4.20.21481250.18186717X-RAY DIFFRACTION84
4.21-5.290.19011360.15897105X-RAY DIFFRACTION89
5.29-29.540.25721390.18386956X-RAY DIFFRACTION88

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