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- PDB-8da0: Crystal structure of Mamba alpha-neurotoxin in complex with Centi... -

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Basic information

Entry
Database: PDB / ID: 8da0
TitleCrystal structure of Mamba alpha-neurotoxin in complex with Centi-LNX-D09 antibody
Components
  • (Centi-LNX-D09 Fab ...) x 2
  • Alpha-elapitoxin-Dpp2d
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 / Alpha-elapitoxin-Dpp2d
Similarity search - Component
Biological speciesHomo sapiens (human)
Dendroaspis polylepis polylepis (black mamba)
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_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_peptide_omega / 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 / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _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 3.0Oct 9, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_torsion / struct_conn
Item: _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num ..._pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_label_atom_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
C: Centi-LNX-D09 Fab light chain
D: Centi-LNX-D09 Fab heavy chain
E: Alpha-elapitoxin-Dpp2d
F: Alpha-elapitoxin-Dpp2d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,86935
Polymers112,9766
Non-polymers1,89329
Water9,800544
1
A: Centi-LNX-D09 Fab light chain
B: Centi-LNX-D09 Fab heavy chain
E: Alpha-elapitoxin-Dpp2d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,46418
Polymers56,4883
Non-polymers97615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Centi-LNX-D09 Fab light chain
D: Centi-LNX-D09 Fab heavy chain
F: Alpha-elapitoxin-Dpp2d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,40517
Polymers56,4883
Non-polymers91714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.703, 145.537, 64.207
Angle α, β, γ (deg.)90.00, 104.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules EF

#3: Protein Alpha-elapitoxin-Dpp2d / Alpha-EPTX-Dpp2d


Mass: 8015.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendroaspis polylepis polylepis (black mamba)
Production host: Homo sapiens (human) / References: UniProt: C0HJD7

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Antibody , 2 types, 4 molecules ACBD

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


Mass: 23339.740 Da / Num. of mol.: 2
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.: 2
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 , 4 types, 573 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M Tris pH 8.5, 10% PEG4000, 50mM Proline

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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: 50268 / % possible obs: 94.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.168 / Rrim(I) all: 0.296 / Χ2: 1.397 / Net I/σ(I): 5.6 / Num. measured all: 138319
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.281.70.6342720.5430.5520.8410.99780.8
2.28-2.3720.65848210.5180.5420.8570.96491
2.37-2.482.20.6150740.5670.4810.780.96995.7
2.48-2.612.50.56750280.6010.4270.7141.02295.2
2.61-2.773.10.51352550.7240.3460.6211.10499.6
2.77-2.993.30.41953060.8060.2720.5011.28699.5
2.99-3.293.30.29952120.8890.1960.3591.49198.9
3.29-3.7630.18650760.9460.1280.2271.60995.2
3.76-4.733.20.12750540.9690.0870.1541.82295.5
4.73-303.10.12151700.9640.0830.1471.88795.7

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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: 2.2→29.78 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 8.079 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24848 989 2 %RANDOM
Rwork0.19641 ---
obs0.19746 49249 94.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.638 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å2-0 Å2-0.16 Å2
2---1.59 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.2→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7397 0 66 544 8007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137654
X-RAY DIFFRACTIONr_bond_other_d0.0010.0186931
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.64210394
X-RAY DIFFRACTIONr_angle_other_deg1.2511.57916066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1295979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7623.433335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.168151218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.91527
X-RAY DIFFRACTIONr_chiral_restr0.0620.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021720
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_it1.7642.4073931
X-RAY DIFFRACTIONr_mcbond_other1.7562.4033921
X-RAY DIFFRACTIONr_mcangle_it2.8773.5974899
X-RAY DIFFRACTIONr_mcangle_other2.8763.5984900
X-RAY DIFFRACTIONr_scbond_it2.1322.5613723
X-RAY DIFFRACTIONr_scbond_other2.1322.5613724
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4623.7455496
X-RAY DIFFRACTIONr_long_range_B_refined5.66828.2358189
X-RAY DIFFRACTIONr_long_range_B_other5.5527.978059
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 71 -
Rwork0.277 2820 -
obs--74.01 %

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