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- PDB-5epm: Ceratotoxin variant in complex with specific antibody Fab fragment -

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Basic information

Entry
Database: PDB / ID: 5epm
TitleCeratotoxin variant in complex with specific antibody Fab fragment
Components
  • Antibody Fab fragment heavy chain
  • Antibody Fab fragment light chain
  • Beta-theraphotoxin-Cm1a
KeywordsTOXIN/IMMUNE SYSTEM / Ceratotoxin / random mutagenesis / Nav1.7 ion chanel / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of voltage-gated sodium channel activity in another organism / sodium channel inhibitor activity / calcium channel regulator activity / toxin activity / extracellular space
Similarity search - Function
Huwentoxin-1 family signature. / Huwentoxin, conserved site-1 / Huwentoxin-1 family / Ion channel inhibitory toxin / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-theraphotoxin-Cm1a
Similarity search - Component
Biological speciesMus musculus (house mouse)
Ceratogyrus marshalli (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsStrop, P. / Shcherbatko, A. / Rossi, A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Engineering Highly Potent and Selective Microproteins against Nav1.7 Sodium Channel for Treatment of Pain.
Authors: Shcherbatko, A. / Rossi, A. / Foletti, D. / Zhu, G. / Bogin, O. / Galindo Casas, M. / Rickert, M. / Hasa-Moreno, A. / Bartsevich, V. / Crameri, A. / Steiner, A.R. / Henningsen, R. / Gill, A. ...Authors: Shcherbatko, A. / Rossi, A. / Foletti, D. / Zhu, G. / Bogin, O. / Galindo Casas, M. / Rickert, M. / Hasa-Moreno, A. / Bartsevich, V. / Crameri, A. / Steiner, A.R. / Henningsen, R. / Gill, A. / Pons, J. / Shelton, D.L. / Rajpal, A. / Strop, P.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.0Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody Fab fragment heavy chain
B: Antibody Fab fragment light chain
C: Beta-theraphotoxin-Cm1a
D: Beta-theraphotoxin-Cm1a
E: Antibody Fab fragment heavy chain
F: Antibody Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)103,7166
Polymers103,7166
Non-polymers00
Water17,060947
1
A: Antibody Fab fragment heavy chain
B: Antibody Fab fragment light chain
C: Beta-theraphotoxin-Cm1a


Theoretical massNumber of molelcules
Total (without water)51,8583
Polymers51,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Beta-theraphotoxin-Cm1a
E: Antibody Fab fragment heavy chain
F: Antibody Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)51,8583
Polymers51,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.322, 98.438, 107.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Antibody Fab fragment heavy chain


Mass: 23751.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Antibody Fab fragment light chain


Mass: 24120.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide Beta-theraphotoxin-Cm1a / Beta-TRTX-Cm1a / CcoTx1 / Ceratotoxin-1


Mass: 3985.772 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Ceratogyrus marshalli (spider) / References: UniProt: P84507
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 947 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 13% PEG8000; Zink Acetate; Sodium Cacodylate; Glycerol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→47 Å / Num. obs: 103911 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 49.57
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 6 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 6.07 / % possible all: 99.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VL5, 1NIY

2vl5

1niy


Resolution: 1.75→47 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.308 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 5172 5 %RANDOM
Rwork0.1903 ---
obs0.1918 98659 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.08 Å2 / Biso mean: 21.451 Å2 / Biso min: 9.32 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.75→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7274 0 0 947 8221
Biso mean---28.05 -
Num. residues----940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.027841
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.95310752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg651037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23524.211304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.285151289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4421533
X-RAY DIFFRACTIONr_chiral_restr0.0860.21191
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216015
LS refinement shellResolution: 1.751→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 347 -
Rwork0.228 6778 -
all-7125 -
obs--98.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8121-0.94910.35552.6012-0.66581.03890.02910.1457-0.0607-0.011-0.03410.02040.1710.06760.00490.05640.0112-0.01440.0396-0.01420.0178-57.284-9.45-18.903
21.36810.31850.07192.39380.93942.80250.0561-0.1470.13170.1452-0.0128-0.05480.0022-0.0534-0.04340.0292-0.0128-0.00170.0296-0.01190.0165-45.103-12.38212.448
32.52120.44511.52491.29880.0942.19820.0248-0.01240.10340.02690.0036-0.0759-0.06760.0505-0.02840.01680.00760.00910.0145-0.00260.0212-45.2018.776-18.291
40.8814-0.05220.19343.1314-1.07641.28080.0302-0.072-0.06910.0912-0.1104-0.21040.08040.15140.08030.0513-0.0069-0.00780.04530.00270.0464-29.562-11.00811.721
54.4673-0.64541.03332.50960.60854.444-0.04940.31110.0398-0.3247-0.13660.2831-0.0468-0.2820.18610.11670.012-0.04620.1254-0.01790.0657-67.1477.208-36.522
63.04071.27011.30835.08562.02724.7977-0.1295-0.34520.41490.1009-0.10350.1028-0.30250.02260.23310.1190.0296-0.04570.1496-0.04890.0915-76.831-5.27-46.722
71.9131-0.7903-0.62040.9070.51711.202-0.0532-0.01830.00220.11230.0252-0.11060.03350.14780.02810.04420.0056-0.02740.0560.00380.0461-62.213-17.221-63.046
82.23310.72911.48921.03810.48432.60520.00060.0402-0.1127-0.11960.04390.0359-0.02040.0297-0.04460.0259-0.0021-0.00880.04710.00220.0254-61.849-29.367-92.43
91.81790.11210.17942.8241.09921.79710.0714-0.0133-0.16-0.0325-0.06220.11640.1004-0.1948-0.00930.04570.0179-0.0020.05680.02030.0351-80.713-28.71-62.355
104.0280.9603-1.16141.5022-0.01451.8426-0.12990.1212-0.4285-0.13040.0459-0.22570.18320.17450.08390.05870.0119-0.01820.059-0.01540.126-63.097-44.75-93.235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119
2X-RAY DIFFRACTION2A120 - 219
3X-RAY DIFFRACTION3B1 - 112
4X-RAY DIFFRACTION4B113 - 218
5X-RAY DIFFRACTION5C1 - 33
6X-RAY DIFFRACTION6D1 - 33
7X-RAY DIFFRACTION7E1 - 119
8X-RAY DIFFRACTION8E120 - 219
9X-RAY DIFFRACTION9F1 - 112
10X-RAY DIFFRACTION10F113 - 218

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