[English] 日本語
Yorodumi
- PDB-4uuj: POTASSIUM CHANNEL KCSA-FAB WITH TETRAHEXYLAMMONIUM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uuj
TitlePOTASSIUM CHANNEL KCSA-FAB WITH TETRAHEXYLAMMONIUM
Components
  • (ANTIBODY FAB FRAGMENT ...) x 2
  • VOLTAGE-GATED POTASSIUM CHANNEL KCSA
KeywordsIMMUNE SYSTEM/METAL TRANSPORT / IMMUNE SYSTEM-METAL TRANSPORT COMPLEX / QUATERNARY AMMONIUM / PROTEIN-ANTIBODY FAB COMPLEX / IONIC CHANNEL / ION TRANSPORT / POTASSIUM CHANNEL
Function / homology
Function and homology information


voltage-gated potassium channel activity / identical protein binding / plasma membrane
Similarity search - Function
Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / DIACYL GLYCEROL / NONAN-1-OL / INDOLE / : / PHOSPHATE ION / TETRAHEXYL AMMONNIUM / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
STREPTOMYCES LIVIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLenaeus, M.J. / Burdette, D. / Wagner, T. / Focia, P.J. / Gross, A.
CitationJournal: Biochemistry / Year: 2014
Title: Structures of Kcsa in Complex with Symmetrical Quaternary Ammonium Compounds Reveal a Hydrophobic Binding Site.
Authors: Lenaeus, M.J. / Burdette, D. / Wagner, T. / Focia, P.J. / Gross, A.
History
DepositionJul 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: VOLTAGE-GATED POTASSIUM CHANNEL KCSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,87317
Polymers58,5353
Non-polymers2,33914
Water1,56787
1
A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: VOLTAGE-GATED POTASSIUM CHANNEL KCSA
hetero molecules

A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: VOLTAGE-GATED POTASSIUM CHANNEL KCSA
hetero molecules

A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: VOLTAGE-GATED POTASSIUM CHANNEL KCSA
hetero molecules

A: ANTIBODY FAB FRAGMENT LIGHT CHAIN
B: ANTIBODY FAB FRAGMENT HEAVY CHAIN
C: VOLTAGE-GATED POTASSIUM CHANNEL KCSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,49468
Polymers234,13812
Non-polymers9,35556
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area42890 Å2
ΔGint-239.8 kcal/mol
Surface area87010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.615, 154.615, 75.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-1125-

K

21C-1126-

K

31C-1127-

K

41C-1128-

K

51C-1130-

CO

61C-1131-

XA7

71C-1132-

XA7

-
Components

-
Protein , 1 types, 1 molecules C

#3: Protein VOLTAGE-GATED POTASSIUM CHANNEL KCSA / STREPTOMYCES LIVIDANS K+ CHANNEL / KCSA


Mass: 11687.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A334

-
Antibody , 2 types, 2 molecules AB

#1: Antibody ANTIBODY FAB FRAGMENT LIGHT CHAIN


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: MUS MUSCULUS (house mouse)
#2: Antibody ANTIBODY FAB FRAGMENT HEAVY CHAIN


Mass: 23435.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: MUS MUSCULUS (house mouse)

-
Non-polymers , 8 types, 101 molecules

#4: Chemical
ChemComp-F09 / NONAN-1-OL


Mass: 144.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical ChemComp-IND / INDOLE


Mass: 117.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#8: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#9: Chemical ChemComp-XA7 / TETRAHEXYL AMMONNIUM


Mass: 354.676 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H52N
#10: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.8 % / Description: NONE
Crystal growpH: 5.4
Details: CRYSTALLIZATION CONDITIONS: 18-25% PEG400, 50 MM SODIUM REMARK 280 ACETATE, 50 MM MAGNESIUM ACETATE, pH 5.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 32854 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.31 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 3.31 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K4C

1k4c


Resolution: 2.4→28.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.451 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24823 1732 5 %RANDOM
Rwork0.19148 ---
obs0.19436 32852 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.704 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4091 0 128 87 4306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024398
X-RAY DIFFRACTIONr_bond_other_d0.0010.024201
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.975966
X-RAY DIFFRACTIONr_angle_other_deg0.83339686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0985545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15423.313160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31415639
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.721523
X-RAY DIFFRACTIONr_chiral_restr0.0860.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02983
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.5867.1182183
X-RAY DIFFRACTIONr_mcbond_other5.5857.1182182
X-RAY DIFFRACTIONr_mcangle_it8.2710.6482727
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.9367.4612215
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 118 -
Rwork0.389 2441 -
obs--98.61 %

+
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://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