[English] 日本語
Yorodumi
- PDB-5vk6: Open conformation of KcsA non-inactivating E71A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vk6
TitleOpen conformation of KcsA non-inactivating E71A mutant
Components
  • Antibody Heavy ChainImmunoglobulin heavy chain
  • Antibody Light ChainImmunoglobulin light chain
  • pH-gated potassium channel KcsA
KeywordsIMMUNE SYSTEM/TRANSPORT PROTEIN / KcsA / open / non-inactivating / potassium channel / IMMUNE SYSTEM-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


delayed rectifier potassium channel activity / voltage-gated potassium channel complex / identical protein binding
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
Chem-1EM / NONAN-1-OL / : / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsCuello, L.G. / Perozo, E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1RO1GM097159-01A1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM087519 United States
Welch FoundationBI-1757 United States
CitationJournal: Elife / Year: 2017
Title: The gating cycle of a K+ channel at atomic resolution.
Authors: Cuello, L.G. / Cortes, D.M. / Perozo, E.
History
DepositionApr 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antibody Heavy Chain
B: Antibody Light Chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,81312
Polymers56,9533
Non-polymers8619
Water1,820101
1
A: Antibody Heavy Chain
B: Antibody Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Heavy Chain
B: Antibody Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Heavy Chain
B: Antibody Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Antibody Heavy Chain
B: Antibody Light Chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,25448
Polymers227,81112
Non-polymers3,44236
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area33700 Å2
ΔGint-224 kcal/mol
Surface area85250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.544, 156.544, 74.618
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-2003-

K

21C-2004-

K

31C-2005-

K

41C-2006-

K

51C-2007-

K

61C-2008-

K

71C-2009-

K

-
Components

-
Protein , 1 types, 1 molecules C

#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 10105.825 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334

-
Antibody , 2 types, 2 molecules AB

#1: Antibody Antibody Heavy Chain / Immunoglobulin heavy chain


Mass: 23411.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Antibody Light Chain / Immunoglobulin light chain


Mass: 23435.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

-
Non-polymers , 4 types, 110 molecules

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


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical ChemComp-1EM / (1S)-2-HYDROXY-1-[(NONANOYLOXY)METHYL]ETHYL MYRISTATE


Mass: 442.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H50O5
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 4.01 Å3/Da / Density % sol: 69.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG400, 50 mM magnesium acetate, 50 mM sodium acetate

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→26.091 Å / Num. obs: 42661 / % possible obs: 99.1 % / Redundancy: 5 % / Net I/σ(I): 3.9

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.25→26.091 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.77
RfactorNum. reflection% reflection
Rfree0.2134 1280 3 %
Rwork0.1859 --
obs0.1867 42599 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→26.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 48 101 4088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064078
X-RAY DIFFRACTIONf_angle_d0.7555566
X-RAY DIFFRACTIONf_dihedral_angle_d4.2782393
X-RAY DIFFRACTIONf_chiral_restr0.05640
X-RAY DIFFRACTIONf_plane_restr0.005701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.340.25921420.2284583X-RAY DIFFRACTION100
2.34-2.44650.25461420.21614577X-RAY DIFFRACTION100
2.4465-2.57530.25631410.20994613X-RAY DIFFRACTION100
2.5753-2.73650.22261420.19044588X-RAY DIFFRACTION100
2.7365-2.94760.25191420.20364611X-RAY DIFFRACTION100
2.9476-3.24370.22821440.19944635X-RAY DIFFRACTION100
3.2437-3.71190.21221380.18664598X-RAY DIFFRACTION100
3.7119-4.67220.17121450.1654628X-RAY DIFFRACTION99
4.6722-26.09240.22061440.18084486X-RAY DIFFRACTION95
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)
11.82810.11441.40651.62550.00760.9068-0.2418-0.19090.49780.06990.27970.1186-0.5915-0.3384-0.05940.64470.14710.01920.39630.01580.5801-13.982233.66945.1568
20.1188-0.0760.17030.0887-0.10620.1551-0.11680.12250.5650.38480.0455-0.6376-0.37640.23860.00010.71110.0498-0.0450.4310.01780.671-4.07631.380410.365
31.0367-0.25250.6790.47630.10591.0495-0.2701-0.07960.25490.16310.0902-0.0579-0.5331-0.28710.00040.56630.14430.02480.33520.05590.5426-18.90337.64-2.8248
40.48030.05010.72870.3434-0.14430.3467-0.1756-0.19220.3222-0.2103-0.094-0.0184-0.7057-0.58840.010.77110.3321-0.0980.71440.07330.6667-33.251743.1387-13.6225
50.2497-0.514-0.06320.7989-0.02330.27710.18130.0046-0.1275-0.2914-0.0359-0.06680.31350.11010.00090.4740.009-0.05950.39970.03130.4233-16.385510.6705-5.8608
60.05950.13980.10720.16680.18920.1992-0.1953-0.21790.0305-0.21750.38210.4659-0.5584-0.32730.00070.48960.0908-0.04270.44790.09960.4867-22.425621.1978-0.8946
70.17310.13940.16460.1857-0.13870.2320.0894-0.5182-0.5570.06140.26160.55490.7128-0.53120.00550.4095-0.0708-0.03850.53210.10320.5396-23.612310.51282.303
80.2082-0.65210.28010.6065-0.01910.17580.2216-0.113-0.2209-0.37430.04670.16090.1363-0.23080.00010.42980.0326-0.07780.43260.07680.4412-21.57817.7337-7.0214
91.6665-0.0561-0.00950.31430.04460.251-0.09841.0897-0.18520.2929-0.1653-0.4248-0.5822-0.7692-0.13890.97750.3687-0.09950.68410.31860.4935-31.535540.1667-28.9508
100.26430.11740.32330.0090.00980.16050.3476-0.0914-0.17870.59430.0593-0.229-0.4243-0.3657-0.00050.7670.1633-0.04240.70060.11270.6284-27.522530.9257-21.9127
110.58150.15370.34470.283-0.0550.2074-0.1411.33340.107-0.81820.4246-0.1988-0.4139-0.28320.06581.07880.2077-0.06820.9340.46110.564-32.636842.17-34.0571
120.16310.18660.06710.1685-0.07250.0952-0.0745-0.14510.54730.21970.03140.0853-0.41030.2047-0.08580.46940.0730.06650.4051-0.1320.4191-7.627516.724726.6337
130.5018-0.3463-0.07470.52870.11850.3475-0.1378-0.36930.14390.2720.0120.1271-0.1364-0.1513-0.01790.43670.01710.06320.4885-0.06830.2886-6.10267.593331.5162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 219 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 32 )
6X-RAY DIFFRACTION6chain 'B' and (resid 33 through 48 )
7X-RAY DIFFRACTION7chain 'B' and (resid 49 through 75 )
8X-RAY DIFFRACTION8chain 'B' and (resid 76 through 113 )
9X-RAY DIFFRACTION9chain 'B' and (resid 114 through 155 )
10X-RAY DIFFRACTION10chain 'B' and (resid 156 through 174 )
11X-RAY DIFFRACTION11chain 'B' and (resid 175 through 212 )
12X-RAY DIFFRACTION12chain 'C' and (resid 26 through 61 )
13X-RAY DIFFRACTION13chain 'C' and (resid 62 through 121 )

+
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