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- PDB-1umr: Crystal structure of the platelet activator convulxin, a disulfid... -

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Basic information

Entry
Database: PDB / ID: 1umr
TitleCrystal structure of the platelet activator convulxin, a disulfide linked a4b4 cyclic tetramer from the venom of Crotalus durissus terrificus
Components
  • CONVULXIN ALPHA
  • CONVULXIN BETA
KeywordsSUGAR BINDING PROTEIN / LECTIN / C-TYPE LECTIN / PLATELET / SUGAR-BINDING PROTEIN / ACTIVATOR / SNAKE VENOM
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily ...: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Snaclec convulxin subunit alpha / Snaclec convulxin subunit beta
Similarity search - Component
Biological speciesCROTALUS DURISSUS TERRIFICUS (tropical rattlesnake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMurakami, M.T. / Zela, S.P. / Gava, L.M. / Michelan-Duarte, S. / Cintra, A.C.O. / Arni, R.K.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: Crystal Structure of the Platelet Activator Convulxin, a Disulfide Linked A4B4 Cyclic Tetramer from the Venom of Crotalus Durissus Terrificus
Authors: Murakami, M.T. / Zela, S.P. / Gava, L.M. / Michelan-Duarte, S. / Cintra, A.C.O. / Arni, R.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Initial Structural Analysis of an Alpha(4)Beta(4) C-Type Lectin from the Venom of Crotalus Durissus Terrificus
Authors: Murakami, M.T. / Watanabe, L. / Gava, L.M. / Zela, S.P. / Cintra, A.C.O. / Arni, R.K.
History
DepositionAug 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2003Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CONVULXIN ALPHA
B: CONVULXIN ALPHA
C: CONVULXIN BETA
D: CONVULXIN BETA


Theoretical massNumber of molelcules
Total (without water)61,4134
Polymers61,4134
Non-polymers00
Water3,549197
1
A: CONVULXIN ALPHA
C: CONVULXIN BETA

A: CONVULXIN ALPHA
C: CONVULXIN BETA

A: CONVULXIN ALPHA
C: CONVULXIN BETA

A: CONVULXIN ALPHA
C: CONVULXIN BETA


Theoretical massNumber of molelcules
Total (without water)122,8268
Polymers122,8268
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665y+1,-x+1,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation2_755-x+2,-y,z1
MethodPQS
2
B: CONVULXIN ALPHA
D: CONVULXIN BETA

B: CONVULXIN ALPHA
D: CONVULXIN BETA

B: CONVULXIN ALPHA
D: CONVULXIN BETA

B: CONVULXIN ALPHA
D: CONVULXIN BETA


Theoretical massNumber of molelcules
Total (without water)122,8268
Polymers122,8268
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
3
A: CONVULXIN ALPHA
C: CONVULXIN BETA

A: CONVULXIN ALPHA
C: CONVULXIN BETA

A: CONVULXIN ALPHA
C: CONVULXIN BETA

A: CONVULXIN ALPHA
C: CONVULXIN BETA

B: CONVULXIN ALPHA
D: CONVULXIN BETA

B: CONVULXIN ALPHA
D: CONVULXIN BETA

B: CONVULXIN ALPHA
D: CONVULXIN BETA

B: CONVULXIN ALPHA
D: CONVULXIN BETA


Theoretical massNumber of molelcules
Total (without water)245,65216
Polymers245,65216
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation5_544x+1/2,y-1/2,z-1/21
crystal symmetry operation6_654-x+3/2,-y+1/2,z-1/21
crystal symmetry operation7_644-y+3/2,x-1/2,z-1/21
crystal symmetry operation8_554y+1/2,-x+1/2,z-1/21
Buried area43810 Å2
ΔGint-240 kcal/mol
Surface area91700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.906, 131.906, 112.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsTHE QUATERNARY STRUCTURE IS OF THE TYPE A4B4 CYCLICTETRAMER (HETERO-OCTAMERIC)

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Components

#1: Protein CONVULXIN ALPHA / CVX ALPHA


Mass: 15745.936 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) CROTALUS DURISSUS TERRIFICUS (tropical rattlesnake)
Tissue: VENOM GLAND / References: UniProt: O93426
#2: Protein CONVULXIN BETA / CVX BETA


Mass: 14960.623 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) CROTALUS DURISSUS TERRIFICUS (tropical rattlesnake)
Tissue: VENOM GLAND / References: UniProt: O93427
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 4.8 Å3/Da / Density % sol: 73 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMsodium acetate1reservoir
3200 mM1reservoirpH4.6CaCl2
414 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 36900 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.1
Reflection shellResolution: 2.4→2.6 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.9 / % possible all: 98.8
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3A

1c3a


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.669 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1845 5 %RANDOM
Rwork0.187 ---
obs0.19 34998 97.6 %-
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: 47.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å20 Å2
2--1.16 Å20 Å2
3----2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4318 0 0 197 4515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0214478
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6931.8926072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4295516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2070.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023452
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2560.32138
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.5400
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4470.348
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.514
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.97122592
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.52934184
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.10321886
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.45631888
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 123
Rwork0.253 2594
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.032
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.639
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg8.429

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