[English] 日本語
Yorodumi
- PDB-6cnu: Crystal Structure of JzTX-V -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cnu
TitleCrystal Structure of JzTX-V
Components
  • JzTx-V
  • JzTx-V(D)
KeywordsTOXIN / inhibitor cysteine knot
Function / homologypotassium channel regulator activity / sodium channel regulator activity / toxin activity / extracellular region / BROMIDE ION / polypeptide(D) / polypeptide(D) (> 10) / Beta/kappa-theraphotoxin-Cg2a
Function and homology information
Biological speciesChilobrachys guangxiensis (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.05 Å
AuthorsMin, X. / Wang, Z.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery of Tarantula Venom-Derived NaV1.7-Inhibitory JzTx-V Peptide 5-Br-Trp24 Analogue AM-6120 with Systemic Block of Histamine-Induced Pruritis.
Authors: Wu, B. / Murray, J.K. / Andrews, K.L. / Sham, K. / Long, J. / Aral, J. / Ligutti, J. / Amagasu, S. / Liu, D. / Zou, A. / Min, X. / Wang, Z. / Ilch, C.P. / Kornecook, T.J. / Lin, M.J. / Be, X. ...Authors: Wu, B. / Murray, J.K. / Andrews, K.L. / Sham, K. / Long, J. / Aral, J. / Ligutti, J. / Amagasu, S. / Liu, D. / Zou, A. / Min, X. / Wang, Z. / Ilch, C.P. / Kornecook, T.J. / Lin, M.J. / Be, X. / Miranda, L.P. / Moyer, B.D. / Biswas, K.
History
DepositionMar 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp / pdbx_entity_src_syn ...chem_comp / pdbx_entity_src_syn / pdbx_struct_mod_residue / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 2.0Mar 4, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn / entity / entity_poly / entity_poly_seq / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_asym / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _diffrn.pdbx_serial_crystal_experiment / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_FOM_work_R_set / _refine.overall_SU_B / _refine.overall_SU_R_Cruickshank_DPI / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Description: Ligand identity / Details: Replace NH4 with NH2 for the C-terminal residue / Provider: author / Type: Coordinate replacement

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: JzTx-V(D)
B: JzTx-V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8538
Polymers7,3172
Non-polymers5366
Water99155
1
A: JzTx-V(D)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9014
Polymers3,6331
Non-polymers2683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: JzTx-V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9514
Polymers3,6831
Non-polymers2683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.160, 37.160, 64.605
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Components on special symmetry positions
IDModelComponents
11A-102-

SO4

21B-102-

SO4

31A-220-

HOH

41A-222-

HOH

51B-230-

HOH

-
Components

-
Polypeptide(D) / Protein/peptide , 2 types, 2 molecules AB

#1: Polypeptide(D) JzTx-V(D)


Mass: 3633.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Chilobrachys guangxiensis (spider)
#2: Protein/peptide JzTx-V


Mass: 3683.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Chilobrachys guangxiensis (spider) / References: UniProt: Q2PAY4

-
Non-polymers , 4 types, 61 molecules

#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate, 1.5-2.0 M Ammonium Acetate / PH range: 3.6-5.6

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9976 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9976 Å / Relative weight: 1
ReflectionResolution: 1.05→32.31 Å / Num. obs: 24183 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Net I/σ(I): 15.4 / Num. measured all: 184278
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.05-1.077.21.671855611820.6170.6611.81.2100
5.75-32.316.10.04210481730.9980.020.04746.297.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimless0.3.6data scaling
PDB_EXTRACT3.24data extraction
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.05→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.2092 / WRfactor Rwork: 0.1899 / FOM work R set: 0.8138 / SU B: 1.045 / SU ML: 0.024 / SU R Cruickshank DPI: 0.0379 / SU Rfree: 0.0364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 1191 4.9 %RANDOM
Rwork0.1899 ---
obs0.1908 22986 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 185.39 Å2 / Biso mean: 14.695 Å2 / Biso min: 7.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å2-0 Å2
3---0.34 Å2
Refinement stepCycle: final / Resolution: 1.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms496 0 26 55 577
Biso mean--26.62 26.72 -
Num. residues----60
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.02573
X-RAY DIFFRACTIONr_bond_other_d0.0260.02507
X-RAY DIFFRACTIONr_angle_refined_deg2.2542.284750
X-RAY DIFFRACTIONr_angle_other_deg3.18831169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.291562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.9821.81811
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9191548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.84153
X-RAY DIFFRACTIONr_chiral_restr0.1290.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02572
X-RAY DIFFRACTIONr_gen_planes_other0.0660.02131
X-RAY DIFFRACTIONr_rigid_bond_restr3.12231074
X-RAY DIFFRACTIONr_sphericity_free24.456525
X-RAY DIFFRACTIONr_sphericity_bonded11.49351089
LS refinement shellResolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 68 -
Rwork0.32 1695 -
all-1763 -
obs--100 %

+
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://pdbjlvh1.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