[English] 日本語
Yorodumi
- PDB-1t1d: CRYSTAL STRUCTURE OF THE TETRAMERIZATION DOMAIN OF THE SHAKER POT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t1d
TitleCRYSTAL STRUCTURE OF THE TETRAMERIZATION DOMAIN OF THE SHAKER POTASSIUM CHANNEL
ComponentsPROTEIN (POTASSIUM CHANNEL KV1.1)
KeywordsMEMBRANE PROTEIN / POTASSIUM CHANNELS / TETRAMERIZATION DOMAIN / APLYSIA KV1.1 / PROTON TRANSPORT
Function / homology
Function and homology information


delayed rectifier potassium channel activity / action potential / voltage-gated potassium channel complex / protein homooligomerization
Similarity search - Function
Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily ...Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsKreusch, A. / Pfaffinger, P.J. / Stevens, C.F. / Choe, S.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Zn2+-binding and molecular determinants of tetramerization in voltage-gated K+ channels.
Authors: Bixby, K.A. / Nanao, M.H. / Shen, N.V. / Kreusch, A. / Bellamy, H. / Pfaffinger, P.J. / Choe, S.
History
DepositionSep 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (POTASSIUM CHANNEL KV1.1)


Theoretical massNumber of molelcules
Total (without water)12,0971
Polymers12,0971
Non-polymers00
Water1,946108
1
A: PROTEIN (POTASSIUM CHANNEL KV1.1)

A: PROTEIN (POTASSIUM CHANNEL KV1.1)

A: PROTEIN (POTASSIUM CHANNEL KV1.1)

A: PROTEIN (POTASSIUM CHANNEL KV1.1)


Theoretical massNumber of molelcules
Total (without water)48,3904
Polymers48,3904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)59.710, 59.710, 146.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein PROTEIN (POTASSIUM CHANNEL KV1.1)


Mass: 12097.453 Da / Num. of mol.: 1 / Fragment: TETRAMERIZATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Strain: BL21 (DE3) / Cell line: CENTRAL NERVOUS SYSTEM / Cellular location: CYTOPLASM / Plasmid: PET20B / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q16968
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.5
Details: 24% ISOPROPANOL, .2M MGCL2, .1 M HEPES PH 7.5, 1MM DTT
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12.5 Msodium formate1reservoir
20.1 Mbis-Tris-propane1reservoir
30.2 M1reservoirMgCl2
40.15 M1reservoirNaCl
510 mMbeta-mercaptoethanol1reservoir
624 %isopropanol1drop
70.2 M1dropMgCl2
80.1 MHEPES1droppH7.5
91 mMdithiothreitol1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: PT-COATED-MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.51→25 Å / Num. obs: 26768 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 19.35 Å2 / Rsym value: 0.049 / Net I/σ(I): 10.2
Reflection shellResolution: 1.51→1.54 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.16 / % possible all: 93.7
Reflection
*PLUS
Num. obs: 24631 / % possible obs: 93.7 % / Num. measured all: 135247 / Rmerge(I) obs: 0.066

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
REFMACrefinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A68

1a68


Resolution: 1.51→19.8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 -5 %RANDOM
Rwork0.229 ---
obs-21355 92.1 %-
Refinement stepCycle: LAST / Resolution: 1.51→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 0 108 959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3542
X-RAY DIFFRACTIONp_mcangle_it2.0493
X-RAY DIFFRACTIONp_scbond_it1.7612
X-RAY DIFFRACTIONp_scangle_it2.7553
X-RAY DIFFRACTIONp_plane_restr0.0192
X-RAY DIFFRACTIONp_chiral_restr0.1260.15
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1380.3
X-RAY DIFFRACTIONp_planar_tor3.27
X-RAY DIFFRACTIONp_staggered_tor15.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2120
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19.8 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_scangle_it3

+
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