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- PDB-3r0l: Crystal structure of crotoxin -

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Basic information

Entry
Database: PDB / ID: 3r0l
TitleCrystal structure of crotoxin
Components
  • (Crotoxin chain ...) x 3
  • Phospholipase A2 CB
KeywordsTOXIN/HYDROLASE / crotoxin / presynaptic neurotoxin / snake venom / phospholipase A2 / heterodimer interface / hydrolase / lipid degradation / metal-binding / TOXIN-HYDROLASE complex
Function / homology
Function and homology information


venom-mediated edema / venom-mediated muscle damage in another organism / venom-mediated myocyte killing in another organism / venom-mediated platelet aggregation / ion channel regulator activity / phospholipase A2 / : / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation ...venom-mediated edema / venom-mediated muscle damage in another organism / venom-mediated myocyte killing in another organism / venom-mediated platelet aggregation / ion channel regulator activity / phospholipase A2 / : / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / phospholipid binding / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / : / Phospholipase A2 homolog crotoxin acid subunit CA / Phospholipase A2 crotoxin basic subunit CBb / Phospholipase A2 crotoxin basic subunit CBc
Similarity search - Component
Biological speciesCrotalus durissus terrificus (tropical rattlesnake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSaul, F.A. / Faure, G.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of Crotoxin Reveals Key Residues Involved in the Stability and Toxicity of This Potent Heterodimeric Beta-Neurotoxin
Authors: Faure, G. / Xu, H. / Saul, F.A.
History
DepositionMar 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 2.0Dec 25, 2019Group: Database references / Polymer sequence / Category: entity_poly / struct_ref_seq_dif / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 20, 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: Crotoxin chain A
B: Crotoxin chain B
C: Crotoxin chain C
D: Phospholipase A2 CB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8339
Polymers23,6384
Non-polymers1955
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-87 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.664, 65.309, 37.429
Angle α, β, γ (deg.)90.00, 103.90, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL UNIT IS A HETERODIMER FORMED BY THE NON-COVALENT ASSOCIATION OF THE CROTOXIN ACID SUBUNIT (CHAINS A, B, C) WITH THE BASIC SUBUNIT (CHAIN D).

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Components

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Crotoxin chain ... , 3 types, 3 molecules ABC

#1: Protein/peptide Crotoxin chain A / CA / Crotapotin / Crotoxin chain A


Mass: 4159.536 Da / Num. of mol.: 1 / Fragment: Crotoxin acidic subunit isoform CA2 alpha chain / Source method: isolated from a natural source / Details: from South American rattlesnake venom
Source: (natural) Crotalus durissus terrificus (tropical rattlesnake)
References: UniProt: P08878
#2: Protein/peptide Crotoxin chain B / CA / Crotapotin / Crotoxin chain B


Mass: 3753.091 Da / Num. of mol.: 1 / Fragment: Crotoxin acidic subunit isoform CA2 beta chain / Source method: isolated from a natural source / Details: from South American rattlesnake venom
Source: (natural) Crotalus durissus terrificus (tropical rattlesnake)
References: UniProt: P08878
#3: Protein/peptide Crotoxin chain C / CA / Crotapotin / Crotoxin chain C


Mass: 1536.599 Da / Num. of mol.: 1 / Fragment: Crotoxin acidic subunit isoform CA2 gamma chain / Source method: isolated from a natural source / Details: from South American rattlesnake venom
Source: (natural) Crotalus durissus terrificus (tropical rattlesnake)
References: UniProt: P08878

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Protein , 1 types, 1 molecules D

#4: Protein Phospholipase A2 CB / Crotoxin basic chain / Phosphatidylcholine 2-acylhydrolase


Mass: 14188.321 Da / Num. of mol.: 1 / Fragment: Crotoxin basic subunit CB / Source method: isolated from a natural source / Details: from South American rattlesnake venom
Source: (natural) Crotalus durissus terrificus (tropical rattlesnake)
References: UniProt: P62022, UniProt: P0CG56*PLUS, phospholipase A2

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Non-polymers , 5 types, 270 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsIN CHAINS B AND C, THE N-TERMINI ARE MODIFIED WITH A PCA IN PLACE OF GLN. CHAIN A ISOFORM CA2 ...IN CHAINS B AND C, THE N-TERMINI ARE MODIFIED WITH A PCA IN PLACE OF GLN. CHAIN A ISOFORM CA2 CONTAINS 39 AMINO ACID RESIDUES (FAURE ET AL. (1991) BIOCHEMISTRY 30:8074-8083). CHAIN D REPRESENTS A NEW ISOFORM DIFFERENT FROM CB1 (P62022) AND CB2 (P24027). THIS HAS BEEN IDENTIFIED THROUGH EXAMINATION OF ELECTRON DENSITY MAPS IN THIS STRUCTURE.

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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: 1.73 Å3/Da / Density % sol: 28.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG 4000, 0.1 M sodium acetate, 0.1 M magnesium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.918
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2009
RadiationMonochromator: Si (111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.35→36.33 Å / Num. obs: 35132 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 12.98 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.9
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 1.9 / % possible all: 96.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QOG

2qog


Resolution: 1.35→36.33 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.088 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1762 5 %RANDOM
Rwork0.165 ---
obs0.166 33344 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-1.11 Å2
2--0.39 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.35→36.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 8 265 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211597
X-RAY DIFFRACTIONr_bond_other_d0.0030.021109
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.9442165
X-RAY DIFFRACTIONr_angle_other_deg0.8432677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4635204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53223.275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57315258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0351512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211827
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02353
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_it1.1742987
X-RAY DIFFRACTIONr_mcbond_other0.3062409
X-RAY DIFFRACTIONr_mcangle_it1.97531564
X-RAY DIFFRACTIONr_scbond_it2.1443610
X-RAY DIFFRACTIONr_scangle_it3.3334594
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.37 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.279 56 -
Rwork0.305 1127 -
obs--90.58 %

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