[English] 日本語
Yorodumi
- PDB-4u5g: Crystal structure of con-ikot-ikot toxin -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more