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- PDB-4u5g: Crystal structure of con-ikot-ikot toxin -

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Basic information

Entry
Database: PDB / ID: 4u5g
TitleCrystal structure of con-ikot-ikot toxin
ComponentsCon-ikot-ikot
KeywordsTOXIN
Function / homology
Function and homology information


host cell postsynaptic membrane / ion channel regulator activity / toxin activity / extracellular region / identical protein binding
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1800 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesConus striatus (striated cone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1997 Å
AuthorsChen, L. / Gouaux, E.
CitationJournal: Science / Year: 2014
Title: X-ray structures of AMPA receptor-cone snail toxin complexes illuminate activation mechanism.
Authors: Chen, L. / Durr, K.L. / Gouaux, E.
History
DepositionJul 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification
Revision 1.4Dec 27, 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 / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Con-ikot-ikot
B: Con-ikot-ikot
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6374
Polymers19,5062
Non-polymers1312
Water45025
1
A: Con-ikot-ikot
hetero molecules

B: Con-ikot-ikot


Theoretical massNumber of molelcules
Total (without water)19,6374
Polymers19,5062
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_564x-y,-y+1,-z-1/31
Buried area990 Å2
ΔGint-71 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.499, 56.499, 86.782
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 4 - 86 / Label seq-ID: 8 - 90

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Con-ikot-ikot


Mass: 9753.155 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Conus striatus (striated cone) / Production host: Escherichia coli (E. coli) / References: UniProt: P0CB20
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M MES pH 6.0, 0.2 M ZnAc2, 15% ethanol, 35% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.75 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 2.1997→50 Å / Num. obs: 8570 / % possible obs: 99.8 % / Redundancy: 35 % / Biso Wilson estimate: 38.06 Å2 / Net I/σ(I): 30.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementResolution: 2.1997→19.833 Å / FOM work R set: 0.7642 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 403 4.73 %
Rwork0.202 8115 -
obs0.2037 8518 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.41 Å2 / Biso mean: 44.58 Å2 / Biso min: 23.87 Å2
Refinement stepCycle: final / Resolution: 2.1997→19.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 2 25 1287
Biso mean--35.84 43.72 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091294
X-RAY DIFFRACTIONf_angle_d1.3251716
X-RAY DIFFRACTIONf_chiral_restr0.069184
X-RAY DIFFRACTIONf_plane_restr0.007228
X-RAY DIFFRACTIONf_dihedral_angle_d15.444476
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A721X-RAY DIFFRACTION10.812TORSIONAL
12B721X-RAY DIFFRACTION10.812TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1997-2.51740.34051540.234626252779
2.5174-3.16960.2661210.22326862807
3.1696-19.83410.20721280.187128042932
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)
12.0123.46972.00811.99856.36752.0155-0.53290.3950.88520.3174-0.47910.33760.4148-0.05971.07650.37620.01980.00980.4375-0.01880.369616.278737.95061.7297
23.90940.7488-0.70033.10750.97394.14750.032-0.16780.01610.4420.61391.13650.4816-0.902-0.54670.3765-0.1960.00380.58540.20680.42559.144636.8401-8.9024
35.37750.54891.39923.91761.57174.4845-0.1334-0.1017-0.3769-0.30410.72680.69540.4045-1.1756-0.76890.3466-0.1121-0.0270.62970.15970.48356.345641.4718-20.32
41.8114-1.493-1.27942.46672.10476.18060.18530.30450.3172-0.1850.0785-0.047-0.2924-0.2174-0.27710.2526-0.02220.01730.30390.08530.298716.486342.2445-11.0146
53.5568-0.88981.28771.6285-0.56684.373-0.24680.48840.1899-0.65440.18560.27570.0944-0.40170.1460.3501-0.126-0.01750.48060.07810.348216.080933.7829-13.8539
62.0112.05473.45772.02226.21684.66330.28570.0731-0.57260.510.1648-0.51250.020.2767-0.30840.47920.0138-0.01030.43640.04480.46738.406431.7218-24.2743
76.38172.6806-1.97855.9844-1.60455.60470.1964-0.7468-0.75620.7078-0.2782-0.22360.5028-0.25140.13590.49410.06410.05110.53690.11990.42225.550920.6714-16.157
82.88740.0101-0.22881.4520.67962.6315-0.0156-0.08890.03210.15770.00080.19770.1041-0.15350.01840.2609-0.02460.030.3990.02220.32825.912227.0476-23.5594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:9)A4 - 9
2X-RAY DIFFRACTION2(chain A and resid 10:21)A10 - 21
3X-RAY DIFFRACTION3(chain A and resid 22:35)A22 - 35
4X-RAY DIFFRACTION4(chain A and resid 36:64)A36 - 64
5X-RAY DIFFRACTION5(chain A and resid 65:86)A65 - 86
6X-RAY DIFFRACTION6(chain B and resid 4:11)B4 - 11
7X-RAY DIFFRACTION7(chain B and resid 12:30)B12 - 30
8X-RAY DIFFRACTION8(chain B and resid 31:86)B31 - 86

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